diff --git a/src/resources/html_doc/lpdp.html b/src/resources/html_doc/lpdp.html
new file mode 100644
index 0000000000000000000000000000000000000000..a5d319b9215b740be88a87f9b288a8bab4cbb0ce
--- /dev/null
+++ b/src/resources/html_doc/lpdp.html
@@ -0,0 +1,128 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>list path, default parameters</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>list path, default parameters</h1>
+<p>Value is an ASCII text string describing a configuration file.</p>
+<h2>Notes</h2>
+<ol>
+<li>Relative or absolute path names can be used.</li>
+<li>If the configuration file are resident on a remote disk, a full UNC path name is usually required.</li>
+<li>Any allowed file name can be used, but only one taxonomy configuration file can be specified per input.</li>
+</ol>
+<h2>Description</h2>
+<p>X! TANDEM uses a two pass system for reading input parameters. In the first pass, the input XML file
+is opened and the string corresponding to <span class="e">list path, default parameters</span> is read. The
+input file is then closed and the file corresponding to this string is opened. If the file exists, TANDEM then
+reads all of the API parameters available in the file into memory. The file is then closed and the original
+input file is opened. Any API parameters in the input file are then read and stored, over-riding any values
+that have were set by the default file.</p>
+<p>This type of system means that it is possible to write very small input files, containing the few parameters
+that are to be varied from experiment to experiment, storing the majority of the API parameters in default
+method files that can be reused.</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="eg.xml">input file format</a> </span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/lpti.html b/src/resources/html_doc/lpti.html
new file mode 100644
index 0000000000000000000000000000000000000000..e6b1de156fd7b910646c7047d1985f14ac213627
--- /dev/null
+++ b/src/resources/html_doc/lpti.html
@@ -0,0 +1,164 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>list path, taxonomy information</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>list path, taxonomy information</h1>
+<h2>Syntax</h2>
+<p>Value is an ASCII text string describing a configuration file.</p>
+<h2>Notes</h2>
+<ol>
+<li>Relative or absolute path names can be used.</li>
+<li>If the configuration file are resident on a remote disk, a full UNC path name is usually required.</li>
+<li>Any allowed file name can be used, but only one taxonomy configuration file can be specified per input.</li>
+</ol>
+<h2>Description</h2>
+<p>The parameter is used to pass the location of the file that translates the "taxonomy" information
+in the value <span class="e">protein, taxon</span> into a list of FASTA file names. A simple taxonomy file is illustrated below.</p>
+<pre>
+<?xml version="1.0"?>
+<bioml label="x! taxon-to-file matching list">
+ <taxon label="human">
+ <file format="peptide" URL="../fasta/human.fasta.pro" />
+ <file format="peptide" URL="../fasta/human_extra.fasta" />
+ <file format="spectrum" URL="../lib/human_fasta.hlf" />
+ <file format="saps" URL="../fasta/human_saps.xml; />
+ <file format="mods" URL="../mods/human_mod.xml" />
+ </taxon>
+ <taxon label="yeast">
+ <file format="peptide" URL="../fasta/scd.fasta.pro" />
+ <file format="peptide" URL="../fasta/scd_1.fasta.pro" />
+ <file format="peptide" URL="../fasta/extras.fasta.pro" />
+ </taxon>
+</bioml>
+</pre>
+<p>If the <span class="e">protein, taxon</span> value is set to <span class="v">human</span>, then the files examined by TANDEM to find
+a matching peptide sequence would be as follows, in the order listed:</p>
+<ol>
+<li>../fasta/human.fasta.pro</li>
+<li>../fasta/human_extra.fasta</li>
+</ol>
+<p>The additional files listed for <span class="v">human</span> would be used as follows:
+<ul>
+<li>The file "../fasta/saps/human_saps.xml" would be loaded in to provide information about known single amino acid polymorphisms.</li>
+<li>The file "../fasta/mods/human_mod.xml" would be loaded in to provide information about known potential modifications.</li>
+<li>If X! Hunter was being used, the file "../lib/human_fasta.hlf" would be used to provide annotation spectrum library information.</li>
+</ul>
+
+<p><b>Notes:</b></p>
+<ol>
+<li>If a file is listed more than once, it is only used one time.</li>
+<li>Do not use commas in the labels for taxon entries: all other normal characters are allowed. X! Tandem interprets a comma as separating multiple
+taxon entries. For example, <span class="v">human,yeast</span> would be interpreted as the union of all of the
+sequence files in both the <span class="v">human</span> and <span class="v">yeast</span> taxon entries.</li>
+<li>If a sequence file does not exist, processing continues if at least one sequence file for the taxon
+does exist. The output file records all of the sequence files actually used: non-existent files are not
+listed.</li>
+<li>Avoid using the same taxon label twice in a taxonomy file. If more than one instance of a taxon label is found, the
+union of all of the sequence files for the multiple instances of that taxon label are used for the calculation.</li>
+</ol>
+<hr align="left" width="200">
+<span class="also">see also: <a href="pt.html">protein, taxon</a> | <a href="fastapro.html">FASTA-pro format</a></span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/mzid.html b/src/resources/html_doc/mzid.html
new file mode 100644
index 0000000000000000000000000000000000000000..c557aa295d3ba2f92ce2ef6fba274b515364b0f6
--- /dev/null
+++ b/src/resources/html_doc/mzid.html
@@ -0,0 +1,119 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, xsl path</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, mzid</h1>
+<h2>Syntax</h2>
+<p>Value is "yes" or "no".</p>
+
+<h2>Description</h2>
+<p>Since the X!Tandem version PILEDRIVER (2015.04.01), it is possible to use the mzIdentML file format as output result files.
+If it is set to "yes", this will produce output files with the .mzid extension.
+Beware that mzIdentML files are not yet supported as input in X!TandemPipeline.
+</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="opath.html">output, path</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/ohcw.html b/src/resources/html_doc/ohcw.html
new file mode 100644
index 0000000000000000000000000000000000000000..620cfc00c3155ef8f2d170d4a75782d7d2831920
--- /dev/null
+++ b/src/resources/html_doc/ohcw.html
@@ -0,0 +1,126 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, histogram column width</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, histogram column width</h1>
+<h2>Syntax</h2>
+<p>The value is an integer H<sub>width</sub> > <span class="v">0</span></p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated by an inappropriate value.</li>
+<li>The normally recommended value for this parameter is <span class="v">50</span>.</li>
+<li>This parameter is only used when <span class="e">output, histograms</span> is set to <span class="v">yes</span>.</li>
+
+</ol>
+<h2>Description</h2>
+<p>This parameter sets the number of values in a GAML-type histogram that are listed on
+a single line of output. It can be used to limit the length of lines in the output file,
+although it has no effect on true XML parsers.
+</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="ohist.html">output, histograms</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/ohist.html b/src/resources/html_doc/ohist.html
new file mode 100644
index 0000000000000000000000000000000000000000..353798d066d719d62be027a01fad460cd44a5980
--- /dev/null
+++ b/src/resources/html_doc/ohist.html
@@ -0,0 +1,124 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, histograms</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, histograms</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated for an inappropriate value.</li>
+<li>The default value is <span class="v">yes</span>.</li>
+
+</ol>
+<h2>Description</h2>
+<p>When this value is set to <span class="v">yes</span>, the histograms containing the statistical
+information about an spectrum-to-sequence assignment are written to the output file. If it is set
+to <span class="v">no</span>, then these histograms are not recorded.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="ohcw.html">output, histogram column width</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/olp.html b/src/resources/html_doc/olp.html
new file mode 100644
index 0000000000000000000000000000000000000000..948825e947eb156020137e2973a1d08bf24b5031
--- /dev/null
+++ b/src/resources/html_doc/olp.html
@@ -0,0 +1,128 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, log path</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, log path</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is a string corresponding to a valid file path.</p>
+<h2>Notes</h2>
+<ol>
+<li>This parameter was introduced in version 2006.04.01</li>
+<li>If this parameter is absent or does not correspond to a valid path, no log file is created.</li>
+<li>No error is indicated if the path is not valid.</li>
+
+</ol>
+<h2>Description</h2>
+<p>It is convenient in some circumstances to generate a disk file that records the progress of a
+search. By using this parameter, such a log is created. Each line in the log file starts with
+a date and time stamp and then a message that is similar to the messages produced by the console
+output of X! Tandem. The exact contents of this log file will change from time-to-time, as users
+request more (or less) information to be displayed.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="spsbs.html">spectrum, sequence batch size</a> |
+<a href="rtp.html">refine, tic percent</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/om.html b/src/resources/html_doc/om.html
new file mode 100644
index 0000000000000000000000000000000000000000..25dca3ef50c7a84bbe68d116f334dcc01618a563
--- /dev/null
+++ b/src/resources/html_doc/om.html
@@ -0,0 +1,130 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, message</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, message</h1>
+<h2>Syntax</h2>
+<p>A character string that does not contain HTML control characters, such as &, < or >.</p>
+<h2>Notes</h2>
+<ol>
+<li>This parameter was introduced in version 2006.04.01</li>
+<li>If this parameter is zero-length or absent, a default string will be substituted.</li>
+
+
+</ol>
+<h2>Description</h2>
+<p>While X! Tandem is performing the first stage of searching, characters are sent to the
+console (and if desired the log file) to show that the process is continuing normally. The value
+of this parameter sets the string of characters used to create that display. For example, if
+this string contains the single character "*", then this character will be repeated
+across the screen. If the string "happy" is used, then "happy" will be
+spelled out repeatedly, one character at a time. The rate at which these characters
+appear is governed by the value of the <span class="e">spectrum, sequence batch size</span> parameter.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="spsbs.html">spectrum, sequence batch size</a>
+</span>
+
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/omvev.html b/src/resources/html_doc/omvev.html
new file mode 100644
index 0000000000000000000000000000000000000000..41bc446b668bbcffa46c89cca2907f92282a9623
--- /dev/null
+++ b/src/resources/html_doc/omvev.html
@@ -0,0 +1,127 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, maximum valid expectation value</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, maximum valid expectation value</h1>
+<h2>Syntax</h2>
+<p>This value is a positive floating point number represented as a character string.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error is generated when an uninterpretable value is used.</li>
+<li>If this parameter is missing, a default value of <span class="v">0.01</span> is used.</li>
+
+</ol>
+<h2>Description</h2>
+<p> When the <span class="e">output, results</span> value is set to <span class="v">valid</span>, the
+value of this parameter sets the maximum expectation value recorded in the output file for a modelling
+session. All results with expectation values less than this value are considered to be statisitically
+significant and are recorded. In the case that <span class="e">output, results</span> value is set to <span class="v">stochastic</span>,
+results with expectation values greater than this value are recorded.
+</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="oresu.html">output, results</a> |
+<a href="refmvev.html">refine, maximum valid expectation value</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/oosc.html b/src/resources/html_doc/oosc.html
new file mode 100644
index 0000000000000000000000000000000000000000..064c9038ea4f267efedc484f6a8dce5093751e66
--- /dev/null
+++ b/src/resources/html_doc/oosc.html
@@ -0,0 +1,126 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, one sequence copy</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, one sequence copy</h1>
+<h2>Syntax</h2>
+<p>The value for this parameter can be <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>If this parameter is invalid or absent, the default value <span class="v">no</span> will be used.</li>
+</ol>
+<h2>Description</h2>
+<p>Protein sequences are normally stored in the X! Tandem output file format, represented in BIOML.
+If multiple peptides from a single protein sequence are found, then that protein sequence is by default reported
+for each peptide. If this parameter is set to <span class="v">yes</span>, then the full protein
+sequence is only recorded for the first peptide in a file corresponding to that protein. Subsequent
+peptides only have the protein's unique identifier (UID) recorded. This UID is assigned by X! Tandem,
+based on the ordinal position of the protein in a sequence file. For example, if a protein was the
+123rd protein read from a file during a search, then that protein's UID would be "123".</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="osequ.html">output, sequences</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/opara.html b/src/resources/html_doc/opara.html
new file mode 100644
index 0000000000000000000000000000000000000000..c4894bad4d0ce71f3367f7ff259e8fc6d80dc318
--- /dev/null
+++ b/src/resources/html_doc/opara.html
@@ -0,0 +1,125 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, parameters</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, parameters</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated for an inappropriate value.</li>
+<li>The default value is <span class="v">yes</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>When this value is set to <span class="v">yes</span>, all of the modelling session parameters supplied to
+X! TANDEM are written into the XML output file. These input parameters are recorded
+in the same format as the input XML file, allowing the output of a modelling session
+to be used as either as an input file for another modelling session.</p>
+<p>If it is set to <span class="v">no</span>, then these parameters are not recorded.</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="operf.html">output, performance</a> |
+<a href="oresu.html">output, results</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/opath.html b/src/resources/html_doc/opath.html
new file mode 100644
index 0000000000000000000000000000000000000000..2b66fdf21fbf264e3b905ebf3e6706c8999d20d5
--- /dev/null
+++ b/src/resources/html_doc/opath.html
@@ -0,0 +1,130 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, path</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, path</h1>
+<h2>Syntax</h2>
+<p>Value is an ASCII text string describing an output filename.</p>
+<h2>Notes</h2>
+<ol>
+<li>Relative or absolute path names can be used</li>
+<li>If the output file will be resident on a remote disk, a full UNC path name is usually required.</li>
+<li>Any file name allowed by an operating system can be used, although the extension "xml" is recommended.</li>
+
+</ol>
+<h2>Description</h2>
+<p>X! TANDEM uses the XML language BIOML to record the output of a modelling session. Each of the
+peptides discovered are recorded, along with additional information, as specified by the other
+<span class="e">output</span> parameters. The pathname given in this parameter sets the disk
+location where this output file may be found. The pathname can be altered automatically, when
+the <span class="e">output, path hashing</span> parameter is set to <span class="v">yes</span>.
+</p>
+<p>X! TANDEM supports a number of different computer operating systems. Please consult your operating
+specific documentation for allowed names and illegal symbols before setting a file name yourself.
+</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="oph.html">output, path hashing</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/operf.html b/src/resources/html_doc/operf.html
new file mode 100644
index 0000000000000000000000000000000000000000..21e02aa349fa22e390a587102e17c0601cb187b6
--- /dev/null
+++ b/src/resources/html_doc/operf.html
@@ -0,0 +1,148 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, performance</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, performance</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated for an inappropriate value.</li>
+<li>The default value is <span class="v">yes</span>.</li>
+
+
+</ol>
+<h2>Description</h2>
+<p>When this value is set to <span class="v">yes</span>, all of the modelling session performance parameters
+supplied by X! TANDEM are written into the XML output file. These performance statistics recorded include the following
+information:
+<ol>
+<li>list path, sequence sources</li>
+<li>modelling, estimated false positives</li>
+<li>modelling, total proteins used</li>
+<li>modelling, total spectra assigned</li>
+<li>modelling, total spectra used</li>
+<li>modelling, total unique assigned</li>
+<li>process, start time</li>
+<li>process, version</li>
+<li>refining, # input models</li>
+<li>refining, # input spectra</li>
+<li>refining, # partial cleavage</li>
+<li>refining, # point mutations</li>
+<li>refining, # potential C-terminii</li>
+<li>refining, # potential N-terminii</li>
+<li>refining, # unanticipated cleavage</li>
+<li>timing, initial modelling total (sec)</li>
+<li>timing, initial modelling/spectrum (sec)</li>
+<li>timing, load sequence models (sec)</li>
+<li>timing, refinement/spectrum (sec)</li>
+</ol>
+<p>If it is set to <span class="v">no</span>, then these parameters are not recorded.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="opara.html">output, parameters</a> |
+<a href="oresu.html">output, results</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/oph.html b/src/resources/html_doc/oph.html
new file mode 100644
index 0000000000000000000000000000000000000000..d4d0dfefd9dbc46868af5e85e50721337407e490
--- /dev/null
+++ b/src/resources/html_doc/oph.html
@@ -0,0 +1,128 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, path hashing</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, path hashing</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span value="v">yes</span> or <span value="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
+<li>f no value is set, the default value is <span value="v">no</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>When the value for this parameter is set to <span value="v">no</span>, the value for the
+<span value="e">output, path</span> parameter is used as the XML file output pathname, without
+modification. When the value for this parameter is set to <span value="v">yes</span>,
+an additional date and time stamp string is inserted into the filename portion of the pathname, ensuring that
+a unique pathname is generated for every use of X! TANDEM. This date and time stamping can
+be useful for running X! TANDEM in a fully automated mode, where new filenames must be
+generated automatically by the system.
+</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="opath.html">output, path</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/oprot.html b/src/resources/html_doc/oprot.html
new file mode 100644
index 0000000000000000000000000000000000000000..742aa08905bb1a2767f48b40ff3afd19ac46fbf0
--- /dev/null
+++ b/src/resources/html_doc/oprot.html
@@ -0,0 +1,134 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, proteins</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, proteins</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated for an inappropriate value.</li>
+<li>The default value is <span class="v">yes</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>When this value is set to <span class="v">yes</span>, the BIOML <protein> information
+associated
+with a peptide-to-spectrum match are recorded in the XML output file. This is the
+recommended mode of operation for X! TANDEM, as it records the version of the protein
+sequence actually used for the identification. Sequence lists generated from
+database systems can change from time-to-time, with the deletion of accession numbers and
+the alteration of protein sequences associated with a particular accession number. If the
+<span class="e">output, sequences</span> value is <span class="v">no</span>, then all of the
+information in the <protein> node is written, except for the full sequence of the protein.</p>
+<p>If it is set to <span class="v">no</span>, then the <protein> nodes are not recorded. The recording
+of the input parameters,performance statistics or other types of results are not affected by the value of
+this parameter.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="ohist.html">output, histograms</a> |
+<a href="ospec.html">output, spectra</a> |
+<a href="osequ.html">output, sequences</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/oresu.html b/src/resources/html_doc/oresu.html
new file mode 100644
index 0000000000000000000000000000000000000000..d71dbaacd12325f235296bf0d2aaae3a3a37de2c
--- /dev/null
+++ b/src/resources/html_doc/oresu.html
@@ -0,0 +1,141 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, results</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, results</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is an ASCII string, with three possible values: <span class="v">all</span>, <span class="v">valid</span>, and <span class="v">stochastic</span></p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated by an invalid value for this parameter.</li>
+<li>The default value for this parameter is <span value="v">valid</span></li>
+
+</ol>
+<h2>Description</h2>
+<p>The value for this parameter determines which results are written to the output file at the
+end of a modelling session. The three possible values cover the most interesting use cases for
+X! TANDEM, from a bioinformatics perspective. The exact form of the reported results will depend
+on the values chosen for other <span class="e">output</span> parameters.
+</p>
+<ol>
+<li><span class="v">all</span> - When this value is set, results are reported for all of the
+spectra that were used in the modelling session. This value is not recommended for normal use, as
+most spectra in a large data set will not return useful results. Storing the large volume of purely
+stochastic matches that can results is a waste of resources, for most users.</li>
+<li><span class="v">valid</span> - When this value is set, results that have an expectation value less
+than <span class="e">output, maximum valid expectation value</span> are reported. This setting
+is of the most general use.</li>
+<li><span class="v">stochastic</span> - When this value is set, results that have an expectation value greater than
+<span class="e">output, maximum valid expectation value</span> are all reported. This is the compliment to
+the <span class="v">valid</span> set, and it can be useful for debugging and bioinformatics purposes.</li>
+</ol>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="osequ.html">output, sequences</a> |
+<a href="ospec.html">output, spectra</a> |
+<a href="oprot.html">output, protein</a> |
+<a href="omvev.html">output, maximum valid expectation value</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/osequ.html b/src/resources/html_doc/osequ.html
new file mode 100644
index 0000000000000000000000000000000000000000..3d88a75d500107574cacacf3c1917eeabe0310a1
--- /dev/null
+++ b/src/resources/html_doc/osequ.html
@@ -0,0 +1,133 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, sequences</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, sequences</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated for an inappropriate value.</li>
+<li>The default value is <span class="v">yes</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>When this value is set to <span class="v">yes</span>, the protein sequences associated
+with a peptide-to-spectrum match are recorded in the XML output file. This is the
+recommended mode of operation for X! TANDEM, as it records the version of the protein
+sequence actually used for the identification. Sequence lists generated from
+database systems can change from time-to-time, with the deletion of accession numbers and
+the alteration of protein sequences associated with a particular accession number. If the
+<span class="e">output, proteins</span> value is <span class="v">no</span>, then this
+parameter is ignored.</p>
+<p>If it is set to <span class="v">no</span>, then these sequences are not recorded. The recording
+of the input parameters,performance statistics or other types of results are not affected by the value of
+this parameter.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="ohist.html">output, histograms</a> |
+<a href="ospec.html">output, spectra</a> |
+<a href="oprot.html">output, proteins</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/osp.html b/src/resources/html_doc/osp.html
new file mode 100644
index 0000000000000000000000000000000000000000..1ecc4c6f20d05223a4b8e7b9a017ed571432902c
--- /dev/null
+++ b/src/resources/html_doc/osp.html
@@ -0,0 +1,129 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, sequence path</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, sequence path</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is a string containing the full or relative path to a valid output file.</p>
+<h2>Notes</h2>
+<ol>
+<li>This parameter was introduced in version 2006.04.01</li>
+<li>If this parameter is absent or does not represent a valid file path, no file is generated.</li>
+<li>No error condition is displayed if a file cannot be created.</li>
+
+</ol>
+<h2>Description</h2>
+<p>Just prior to executing the refinement steps of a search, a list of protein sequences to use
+for the refinement is created. When this parameter is a valid file path, that list of
+proteins is written to that file, using the same format at X! Tandem's normal results output.
+This output file can be generated, even if refinement is not used for a search. The sequences
+output in this file can be imported into a subsequent search run using the
+<span class="e">refine, sequence path</span> parameter.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="rsp.html">refine, sequence path</a> |
+<a href="refine.html">refine</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/ospec.html b/src/resources/html_doc/ospec.html
new file mode 100644
index 0000000000000000000000000000000000000000..b2a370cfc1334e6e53f77098b286e3a016bcb3a8
--- /dev/null
+++ b/src/resources/html_doc/ospec.html
@@ -0,0 +1,130 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, spectra</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, spectra</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated for an inappropriate value.</li>
+<li>The default value is <span class="v">yes</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>When this value is set to <span class="v">yes</span>, the spectra used in the modelling
+session, are recorded in GAML format in the output XML file. When these spectra have been
+recorded in an output file, the output file can be used as an input spectrum source file
+for further analysis with X! TANDEM.</p>
+<p>If it is set to <span class="v">no</span>, then these spectra are not recorded. The recording
+of the input parameters,performance statistics or other types of results are not affected by the value of
+this parameter.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="opara.html">output, parameters</a> |
+<a href="operf.html">output, performance</a> |
+<a href="oresu.html">output, results</a> |
+
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/osrb.html b/src/resources/html_doc/osrb.html
new file mode 100644
index 0000000000000000000000000000000000000000..c1b0fb32e014e643de95fe6ada26ed66826d09dd
--- /dev/null
+++ b/src/resources/html_doc/osrb.html
@@ -0,0 +1,133 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, sort results by</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, sort results by</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is an ASCII string, with two possible values: <span class="v">protein</span> or <span class="v">spectrum</span>.
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated by an invalid value for this parameter.</li>
+<li>The default value for this parameter is <span value="v">protein</span></li>
+
+</ol>
+<h2>Description</h2>
+<p>When this value is set to <span class="v">spectrum</span>, the output file contains the results of a modelling session
+in the same order as the spectra were recorded in the original spectra file. Each result group is numbered with
+the ordinal position of the spectrum, or the spectrum number obtained from the original file (if available).
+</p>
+<p>When this value is set to <span class="v">protein</span>, the output file contains the results of a modelling session
+listed according to a particular spectrum's corresponding peptide's position in the most likely protein sequence, starting
+at the N-terminus of the protein. All of the peptides associated with a particular protein are list sequentially. The most
+likely protein in the data set is listed first, with others listed in order of descending confidence of assignment.
+</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="osequ.html">output, sequences</a> |
+<a href="ospec.html">output, spectra</a> |
+<a href="oprot.html">output, protein</a> |
+<a href="omvev.html">output, maximum valid expectation value</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/oxp.html b/src/resources/html_doc/oxp.html
new file mode 100644
index 0000000000000000000000000000000000000000..8edb8aced666c98becc9da137213f2c3d9be378f
--- /dev/null
+++ b/src/resources/html_doc/oxp.html
@@ -0,0 +1,130 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>output, xsl path</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>output, xsl path</h1>
+<h2>Syntax</h2>
+<p>Value is an ASCII text string describing an XML transforming stylesheet filename.</p>
+
+<h2>Notes</h2>
+<ol>
+<li>Relative or absolute path names can be used.</li>
+<li>If the output file will be resident on a remote disk, a full URL declaration is required</li>
+
+</ol>
+<h2>Description</h2>
+<p>X! TANDEM uses the XML language BIOML to record the output of a modelling session. Each of the
+peptides discovered are recorded, along with additional information, as specified by the other
+
+<span class="e">output</span> parameters. The pathname given in this parameter is used to set the
+XSLT file that is used to create useful displays of the XML data.
+</p>
+<p>X! TANDEM supports a number of different computer operating systems. Please consult your operating
+specific documentation for allowed names and illegal symbols before setting a file name yourself.
+</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="opath.html">output, path</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/pcctmc.html b/src/resources/html_doc/pcctmc.html
new file mode 100644
index 0000000000000000000000000000000000000000..13e813bde5e76ccc2ab4272e3d41f6277aad77a6
--- /dev/null
+++ b/src/resources/html_doc/pcctmc.html
@@ -0,0 +1,126 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>protein, cleavage C-terminal mass change</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>protein, cleavage C-terminal mass change</h1>
+<h2>Syntax</h2>
+<p>This value is a floating point number represented by a character string</p>
+<h2>Notes</h2>
+<ol>
+<li>Positive and negative values are allowed.</li>
+<li>If this value is not present, the default value is <span class="v">17.00305</span>.</li>
+
+</ol>
+<h2>Description</h2>
+<p>This value represents the mass added to the C-terminus of a peptide after undergoing
+peptide bond cleavage by a chemical or enzymatic reagent, in Daltons. The default value is
+the mass change associated with hydrolytic cleavage in normal water.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="pcntmc.html">protein, cleavage N-terminal mass change</a> |
+<a href="pntrmm.html">protein, N-terminal residue modification mass</a> |
+<a href="pctrmm.html">protein, C-terminal residue modification mass</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/pcntmc.html b/src/resources/html_doc/pcntmc.html
new file mode 100644
index 0000000000000000000000000000000000000000..d2086ccbf7411115043f7e127488f6db9fdc731e
--- /dev/null
+++ b/src/resources/html_doc/pcntmc.html
@@ -0,0 +1,126 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>protein, cleavage N-terminal mass change</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>protein, cleavage N-terminal mass change</h1>
+<h2>Syntax</h2>
+<p>This value is a floating point number represented by a character string</p>
+<h2>Notes</h2>
+<ol>
+<li>Positive and negative values are allowed.</li>
+<li>If this value is not present, the default value is <span class="v">1.00794</span>.</li>
+
+</ol>
+<h2>Description</h2>
+<p>This value represents the mass added to the N-terminus of a peptide after undergoing
+peptide bond cleavage by a chemical or enzymatic reagent, in Daltons. The default value is
+the mass change associated with hydrolytic cleavage in normal water.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="pcctmc.html">protein, cleavage C-terminal mass change</a> |
+<a href="pntrmm.html">protein, N-terminal residue modification mass</a> |
+<a href="pctrmm.html">protein, C-terminal residue modification mass</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/pcs.html b/src/resources/html_doc/pcs.html
new file mode 100644
index 0000000000000000000000000000000000000000..447408c1aabbd3cc263a045a9c3bb81c50efe9c5
--- /dev/null
+++ b/src/resources/html_doc/pcs.html
@@ -0,0 +1,141 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>protein, cleavage site</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>protein, cleavage site</h1>
+<h2>Syntax</h2>
+<p>This parameter is a formatted text string with three fields. The first and third fields
+are square - [] - or french - {} - brace pairs, containing single amino acid residue symbols. These two
+fields are separated by a vertical line, <i>e.g.</i>, <span class="v">[KR]|{P}</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>Braces are required in the first and third fields.</li>
+<li>Only one set of braces is allowed per field.</li>
+<li>The character representing any residue is "<span class="v">X</span>"</li>
+<li>Multiple cleavage site rules may be specified by separating them with a comma, <i>e.g.</i> <span class="v">[KR]|{P},[X]|[D]</span>.
+</li>
+<li>Multiple rules are applied individually in the order written, from left-to-right. If the conditions of any of the rules are met, then a cleavage occurs.</li>
+
+</ol>
+<h2>Description</h2>
+<p>Short peptides are generated from longer protein sequences by the use of either chemical or
+enzymatic cleavage. Both types of cleavage tend to have preferred sites of cleavage, based on the
+residues on either side of the peptide bond to be cleaved. Proteomics experiments frequently
+use enzymes with very strong sequence specificity, to limit the number of peptides generated and
+the assure that there are a reasonable number of peptides in the length range most useful for
+protein identification.</p>
+<p>The value of this parameter allows the description of this sequence specificity. A list of residues
+in square braces means that those residues are required in that position, while a list of
+residues in french braces means that those residues will block cleavage. For example,</p>
+<ol>
+<li><span class="v">[KR]|{P}</span> means cleavage C-terminal to every lysine or arginine, except
+when followed by a proline;</li>
+<li><span class="v">[X]|[D]</span> means cleavage N-terminal to every aspartic acid residue; and</li>
+<li><span class="v">[X]|[X]</span> means cleavage at every peptide bond.
+</ol>
+<hr align="left" width="200">
+<span class="also">see also: <a href="smmcs.html">scoring, maximum missed cleavage sites</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/pcsemi.html b/src/resources/html_doc/pcsemi.html
new file mode 100644
index 0000000000000000000000000000000000000000..bf956013006bdd3e739d65ea050ef66ac4abf1ec
--- /dev/null
+++ b/src/resources/html_doc/pcsemi.html
@@ -0,0 +1,145 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>protein, cleavage semi</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>protein, cleavage semi</h1>
+<h2>Syntax</h2>
+<p>This parameter is a text string that may be <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>Introduced in version 2005.12.01.</li>
+<li>Default value is <span class="v">no</span></li>
+<li>The value of this parameter is only used in the first round of identification: to apply this semi cleavage
+to refinement rounds, use the <span class="e">refine, cleavage semi</span> parameter.
+</ol>
+<h2>Description</h2>
+<p>In real experiments, there are often contaminating proteolytic enzymes which will act on proteins
+in a difficult to predict manner. Therefore, the idea of a "semi-tryptic" digest was
+developed to attempt to compensate for this additional cleavage activity. This cleavage type assumes that one
+of the cleavage sites is tryptic ([KR]|{P}), but the other site may be at any residue. For example, if an expected tryptic
+peptide has a sequence of TFGQVVAR, then the semi-tryptic peptides associated with this sequence would be:</p>
+<pre>
+TFGQVVAR
+ FGQVVAR
+ GQVVAR
+ QVVAR
+ VVAR
+ VAR
+ AR
+TFGQVVA
+TFGQVV
+TFGQV
+TFGQ
+TFG
+TF
+</pre>
+<p>Tandem has broadened this concept to include any cleavage site specification, except for cleavage
+at any site ([X]|[X]), which doesn't require any additional type of cleavage.</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="pcs.html">protein, cleavage site</a> |
+<a href="rcsemi.html">refine, cleavage semi</a>
+
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/pctrmm.html b/src/resources/html_doc/pctrmm.html
new file mode 100644
index 0000000000000000000000000000000000000000..2171cb19acbba502874cf15aaa93c6f0e88e5e9d
--- /dev/null
+++ b/src/resources/html_doc/pctrmm.html
@@ -0,0 +1,126 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>protein, C-terminal residue modification mass</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>protein, C-terminal residue modification mass</h1>
+<h2>Syntax</h2>
+<p>This value is a floating point number represented by a character string.</p>
+<h2>Notes</h2>
+<ol>
+<li>Positive and negative values are allowed.</li>
+<li>If this value is not present, the default value is <span class="v">0.0</span>.</li>
+
+</ol>
+<h2>Description</h2>
+<p>This value represents any additional fixed modification mass added only to the C-terminal residue
+in an intact protein, in Daltons.</p>
+
+<hr align="left" width="200">
+<span class="also">see also:
+<a href="pcctmc.html">protein, cleavage C-terminal mass change</a> |
+<a href="pcntmc.html">protein, cleavage N-terminal mass change</a> |
+<a href="pntrmm.html">protein, N-terminal residue modification mass</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/pmrmf.html b/src/resources/html_doc/pmrmf.html
new file mode 100644
index 0000000000000000000000000000000000000000..3fa41570c9a6ba39d39621c87a744757d944ffe7
--- /dev/null
+++ b/src/resources/html_doc/pmrmf.html
@@ -0,0 +1,161 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>protein, modified residue mass file</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>protein, modified residue mass file</h1>
+<h2>Syntax</h2>
+<p>This parameter is a text string corresponding to the path to a file containing specifications for the residues
+to be modified.</p>
+<h2>Notes</h2>
+<ol>
+<li>The file path name may be full or relative.</li>
+</ol>
+<h2>Description</h2>
+<p>X! Tandem uses default values for the mass of each peptide residue. These masses correspond to the
+monoisotopic mass of the corresponding amino acid, less the mass of water (m<sub>aa</sub> - 18.01056470).
+In some cases, samples may be created inwhich one or more of the amino acids has been deliberately
+substituted with an amino acid with an isotopic label. If only a small number of residues have been
+substituted, the <span class="e">residue, modification mass</span> command may be used to inform X! Tandem. However,
+if most (or all) of the residues have been modified, it is simpler to create a file containing this
+information and use the <span class="e">protein, modified residue mass file</span> command.
+</p>
+<p>The format of the file pointed to be this command is illustrated below, which is the file needed to
+deal with the case of an all-<sup>15</sup>N labelled organism:
+<pre>
+<?xml version="1.0"?>
+<bioml title="peptide residue molecular mass values for an all 15N organism">
+<aa type="A" mass="72.034144" />
+<aa type="B" mass="116.036998" />
+<aa type="C" mass="104.006224" />
+<aa type="D" mass="116.023974" />
+<aa type="E" mass="130.039624" />
+<aa type="F" mass="148.065444" />
+<aa type="G" mass="58.018494" />
+<aa type="H" mass="140.050012" />
+<aa type="I" mass="114.081094" />
+<aa type="J" mass="0.0" />
+<aa type="K" mass="130.089028" />
+<aa type="L" mass="114.081094" />
+<aa type="M" mass="132.037524" />
+<aa type="N" mass="116.036998" />
+<aa type="O" mass="0.0" />
+<aa type="P" mass="98.049794" />
+<aa type="Q" mass="130.052648" />
+<aa type="R" mass="159.092212" />
+<aa type="S" mass="88.029064" />
+<aa type="T" mass="102.044714" />
+<aa type="V" mass="100.065444" />
+<aa type="W" mass="187.076344" />
+<aa type="X" mass="112.057034" />
+<aa type="Y" mass="164.060364" />
+<aa type="Z" mass="130.052648" />
+<molecule type="NH3" mass="18.02358311" />
+<molecule type="H2O" mass="18.01056470" />
+</bioml>
+</pre>
+<hr align="left" width="200">
+<span class="also">see also: <a href="rmm.html">residue, modification mass</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/pntrmm.html b/src/resources/html_doc/pntrmm.html
new file mode 100644
index 0000000000000000000000000000000000000000..2820ee0588dda88cdbb7b4f4741529f8971f62b8
--- /dev/null
+++ b/src/resources/html_doc/pntrmm.html
@@ -0,0 +1,126 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>protein, N-terminal residue modification mass</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>protein, N-terminal residue modification mass</h1>
+<h2>Syntax</h2>
+<p>This value is a floating point number represented by a character string.</p>
+<h2>Notes</h2>
+<ol>
+<li>Positive and negative values are allowed.</li>
+<li>If this value is not present, the default value is <span class="v">0.0</span>.</li>
+
+</ol>
+<h2>Description</h2>
+<p>This value represents any additional fixed modification mass added only to the N-terminal residue
+in an intact protein, in Daltons.</p>
+
+<hr align="left" width="200">
+<span class="also">see also:
+<a href="pcctmc.html">protein, cleavage C-terminal mass change</a> |
+<a href="pcntmc.html">protein, cleavage N-terminal mass change</a> |
+<a href="pctrmm.html">protein, C-terminal residue modification mass</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/pqa.html b/src/resources/html_doc/pqa.html
new file mode 100644
index 0000000000000000000000000000000000000000..51a73061b850112317daf2dca0499e62322c4fdb
--- /dev/null
+++ b/src/resources/html_doc/pqa.html
@@ -0,0 +1,126 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>protein, quick acetyl</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>protein, quick acetyl</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>Default value = <span class="v">yes</span>.</li>
+<li>Introduced in version 2010.01.01.1.</li>
+</ol>
+<h2>Description</h2>
+<p>Most intracellular proteins in eukaryotes (and all prokaryote proteins) have the N-terminal methionine
+residue removed immediately following translation. In prokaryotes, the new N-terminal residue is left unmodified. In eukaryotes,
+the new N-terminal residue is often acetylated (H<sub>2</sub>C<sub>2</sub>O, +42 Da). If the N-terminal methionine is not removed in eukaryotes, the
+methionine itself can be acetylated.
+</p>
+<p>When this parameter is <span class="v">yes</span>, these common modifications are checked for the peptides
+generated from the protein's N-terminus, at all stages of analysis.</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="pqp.html">protein, quick pyrolidone</a>, <a href="refpntm.html">refine, potential N-terminus modifications</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/pqp.html b/src/resources/html_doc/pqp.html
new file mode 100644
index 0000000000000000000000000000000000000000..77a0681d235d986e4a5821d61586c1d72d3798cf
--- /dev/null
+++ b/src/resources/html_doc/pqp.html
@@ -0,0 +1,130 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>protein, quick pyrolidone</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>protein, quick pyrolidone</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>Default value = <span class="v">yes</span>.</li>
+<li>Introduced in version 2010.01.01.1.</li>
+</ol>
+<h2>Description</h2>
+<p>Peptides that have N-terminal glutamine (Q) residues in solution will spontaneous form the cyclic pyrolidone
+derivative by the loss of NH<sub>3</sub> (-17 Da). A similar solution phase reaction can occur with peptides with
+N-terminal glutamic acid residues through the loss of H<sub>2</sub>O (-18 Da) or for N-terminal cysteine residues that
+have been chemically blocked using iodoacetimide, through the loss of NH<sub>3</sub> (-17 Da). When this parameter
+is <span class="v">yes</span>, these derivatives are checked, as well as the underivatized forms of the residues.
+Using this parameter is a much more efficient calculation than using the potential modifications "-17@["
+or "-18@[".
+</p>
+<p>This behavior has always been the default for X! Tandem: this parameter allows users to control this behavior.
+It is HIGHLY recommended that this parameter be set to <span class="v">yes</span> unless there is a good reason
+not to check for this very common modification.
+<hr align="left" width="200">
+<span class="also">see also: <a href="pqa.html">protein, quick acetyl</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/pstpb.html b/src/resources/html_doc/pstpb.html
new file mode 100644
index 0000000000000000000000000000000000000000..72a52266ba76d81c4b70dd6a311a425d8f9beb5f
--- /dev/null
+++ b/src/resources/html_doc/pstpb.html
@@ -0,0 +1,140 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>protein, stP bias</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>protein, stP bias</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>Default value = <span class="v">yes</span>.</li>
+<li>Introduced in version 2010.01.01.1.</li>
+</ol>
+<h2>Description</h2>
+<p>Assigning phosphorylation sites to sequences identified from tandem mass spectra can be challenging. Often there
+is little evidence for assigning one phosphorylation site versus another. For example, the following two interpretations
+may be equivalent in terms of the underlying MS/MS data:
+</p>
+<ol>
+<li>AGGPTtPLSPTR</li>
+<li>AGGPtTPLSPTR</li>
+</ol>
+<p>where the phosphorylated residue is indicated by the lower case "t". However, it is known that the motif
+[ST]P corresponds to a very common type of kinase specificity. When this parameter is set to <span class="v">yes</span>,
+phosphorylations that correspond to the motif [ST]P are given a very small (0.1%) scoring advantage over all other
+phosphorylated models. This advantage is small enough that any signal in a spectrum that could be used to choose one model
+over another will produce a much larger increase in score than this bias.</p>
+<p>Another common case in phosphorylation analysis is attempting to distingish between model solutions such as:
+<ol>
+<li>AySFCGTVEYMAPEVVNR</li>
+<li>AYsFCGTVEYMAPEVVNR</li>
+</ol>
+<p>in which there is the potential for the phosphorylation to occur on a tyrosine or a nearby serine (or threonine). When
+ this parameter is set to <span class="v">yes</span>, models containing phosphorylated serine or threonine that have a pronounced peak (relative intensity > 20)
+corresponding to the neutral loss of phosphoric acid (H<sub>3</sub>PO<sub>4</sub>, -98 Da) are given additional scoring weight. The
+additional weight is significantly less than would be added for a sequence-specific ion, but it may be sufficient to
+distinguish between two solutions of the type shown above.</p>
+<hr align="left" width="200">
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/pt.html b/src/resources/html_doc/pt.html
new file mode 100644
index 0000000000000000000000000000000000000000..b2827ee25b0d9a83ee94cdd66c819cae213c777f
--- /dev/null
+++ b/src/resources/html_doc/pt.html
@@ -0,0 +1,125 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>protein, taxon</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>protein, taxon</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is a character string.</p>
+<h2>Notes</h2>
+<ol>
+<li>An error message is generated if an invalid value is entered and TANDEM terminates.</li>
+<li>Allowed values are determined by the configuration file pointed to by <span class="v">list path, taxonomy information</span></li>
+
+</ol>
+<h2>Description</h2>
+<p>The file pointed to by <span class="v">list path, taxonomy information</span> contains a list of
+FASTA or FASTA.pro formatted sequence listing files associated with a key word (or words). The
+value entered for this parameter must be at least one of the key words documented in that file. The
+key words are case sensitive. Multiple keywords can be used, separated by commas.</p>
+<hr align="left" width="200">
+<span class="also">see also:
+<a href="lpti.html">list path, taxonomy information</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/pua.html b/src/resources/html_doc/pua.html
new file mode 100644
index 0000000000000000000000000000000000000000..629d5c71bff85c8cf1227ab16f86f91761fba0ed
--- /dev/null
+++ b/src/resources/html_doc/pua.html
@@ -0,0 +1,129 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>protein, use annotations</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>protein, use annotations</h1>
+<h2>Syntax</h2>
+<p>This parameter is a text string that may be <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>Introduced in version 2008.02.01.</li>
+<li>Default value is <span class="v">no</span></li>
+<li>The value of this parameter is only used in the first round of identification: to apply the annotations
+to refinement rounds, use the <span class="e">refine, use annotations</span> parameter.
+</ol>
+<h2>Description</h2>
+<p>It is known that different proteins have different post-translational modifications. In some cases, proteins
+may be highly modified by unusual modifications, such as the highly variable modification of histones or collagens.
+When the parameter is set to <span class="v">yes</span>, an annotation file that contains the modifications
+known to be present in each protein will be added to the search, on a protein by protein basis. Any other
+modifications that you have specified will over-ride these annotations, if there is a conflict between
+the annotation and your specified modification.
+</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="rua.html">refine, use annotations</a> |
+
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/rcsemi.html b/src/resources/html_doc/rcsemi.html
new file mode 100644
index 0000000000000000000000000000000000000000..84e85fe4e8c88641415c54c6d84dab99f7575474
--- /dev/null
+++ b/src/resources/html_doc/rcsemi.html
@@ -0,0 +1,145 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, cleavage semi</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, cleavage semi</h1>
+<h2>Syntax</h2>
+<p>This parameter is a text string that may be <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>Introduced in version 2005.12.01.</li>
+<li>Default value is <span class="v">no</span></li>
+<li>The value of this parameter is only used in the refinement rounds of identification: to apply this semi cleavage
+to first round, use the <span class="e">protein, cleavage semi</span> parameter.
+</ol>
+<h2>Description</h2>
+<p>In real experiments, there are often contaminating proteolytic enzymes which will act on proteins
+in a difficult to predict manner. Therefore, the idea of a "semi-tryptic" digest was
+developed to attempt to compensate for this additional cleavage activity. This cleavage type assumes that one
+of the cleavage sites is tryptic ([KR]|{P}), but the other site may be at any residue. For example, if an expected tryptic
+peptide has a sequence of TFGQVVAR, then the semi-tryptic peptides associated with this sequence would be:</p>
+<pre>
+TFGQVVAR
+ FGQVVAR
+ GQVVAR
+ QVVAR
+ VVAR
+ VAR
+ AR
+TFGQVVA
+TFGQVV
+TFGQV
+TFGQ
+TFG
+TF
+</pre>
+<p>Tandem has broadened this concept to include any cleavage site specification, except for cleavage
+at any site ([X]|[X]), which doesn't require any additional type of cleavage.</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="pcs.html">protein, cleavage site</a> |
+<a href="pcsemi.html">protein, cleavage semi</a>
+
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/refine.html b/src/resources/html_doc/refine.html
new file mode 100644
index 0000000000000000000000000000000000000000..2f674efe731abaa86f0d95d560d19e32922c36e1
--- /dev/null
+++ b/src/resources/html_doc/refine.html
@@ -0,0 +1,134 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
+<li>If no value is set, the default value is <span class="v">no</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>X! TANDEM uses a process called "refinement" to improve the speed and accuracy of
+peptide modelling. When the parameter value is <span class="v">yes</span>, then the refinement
+process is used, otherwise X! TANDEM functions like other sequence modelling engines.</p>
+ <p>The algorithm used by Tandem is an example of possible algorithms that belong
+ to this class of methods for obtaining similar results. Variations
+ of the scheme may be necessary to adequately capture all of the
+ details of specific experimental protocols. The steps in a simple
+ refinement-based identification/modeling process are as follows:</p>
+ <ol>
+<LI>Match a set of tandem mass spectra containing a large set of spectra against a list of proteins, with a small value for the number of missed cleavages (e.g., 0 or 1) and a limited selection of potential modifications and create a set of protein sequences that are most likely to contain valid matches to the spectra (e.g., all proteins containing peptides with an expectation value < 0.1);</LI>
+<LI>Match the tandem spectra against the new, smaller list of protein sequences, using a large value for the number of missed cleavages and a large selection of potential modifications; and</LI>
+ <LI>If desired, perform the same matching procedure as step 2, using nonspecific
+ hydrolysis.</LI>
+
+</OL>
+<hr align="left" width="200">
+<span class="also">see also: <a href="/GPM/refine.html">GPM refinement</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/refmm.html b/src/resources/html_doc/refmm.html
new file mode 100644
index 0000000000000000000000000000000000000000..b937a0c38975634413d9c5dbc5b02806a7f5839c
--- /dev/null
+++ b/src/resources/html_doc/refmm.html
@@ -0,0 +1,171 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, modification mass</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, modification mass</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is an ASCII string, of the format <span class="v">M<sub>1</sub>@X<sub>1</sub>,M<sub>2</sub>@X<sub>2</sub>,..., M<sub>n</sub>@X<sub>n</sub></span></p>
+<p>where <span class="v">M<sub>i</sub></span> is a floating point number (modification mass in Daltons) and <span class="v">
+X<sub>i</sub></span> is a single letter abbreviation for a type of amino acid residue.
+<h2>Notes</h2>
+<ol>
+<li>No error is produced if a non-standard amino acid abbreviation is used.</li>
+<li>If a residue type is listed more than once, the last instance of the residue is used to set the modification.</li>
+<li>Both positive and negative modification masses may be used.</li>
+
+</ol>
+<h2>Description</h2>
+<p>In the course of isolating a protein and generating peptides for use in protein identification
+experiments, it is often necessary to treat the protein sample with reagents that will modify all of
+the residues of a particular type. Commonly, cysteine residues are modified to disrupt and prevent
+the reformation of disulphide bonds. Additionally, other residues may be modified as a predictable
+side product of the protein-to-peptide cleavage process. The modifications encoded in this value
+are applied to every residue of a particular type of amino acid, without exception.</p>
+<p>In the first round of searching, this eventuality is covered by the <span class="e">residue, modification
+mass</span> parameter. If the <span class="e">refine, modification mass</span> parameter is absent or
+zero length, then the value of the <span class="e">residue, modification mass</span> parameter is
+used throughout the refinement steps. If it is not absent, then it over-rides the <span class="p">residue, modification
+mass</span> value. If there are no valid modifications in this string, then no complete residue modifications
+are used.</p>
+<p>If there is some possibility that a residue modification process has not been 100% efficient, it
+may be more practical to include the modification in the <span class="e">refine, potential modification mass</span>
+parameter list.</p>
+<p>If a residue labelling strategy is being used where there are two types of reagents for modifying
+a residue (<i>e.g.</i>, <b>C</b>), one with mass <b>L<sub>1</sub></b> and the other with mass <b>L<sub>2</sub></b>, the following method can be used to
+find both types of labelled peptide in the same analysis.</p>
+<ol>
+<li>Add the value <span class="v">L<sub>1</sub>@C</span> to the <span class="e">refine, modification mass</span> parameter</li>
+<li>Add the value <span class="v">(L<sub>2</sub>-L<sub>1</sub>)@C</span> to the <span class="e">refine, potential modification mass</span> parameter</li>
+</ol>
+<p>Because potential and complete modifications are treated separately internally by TANDEM, this will
+result in finding peptides modified with both types of parameters.
+<h2>New feature, version 2009.04.01</h2>
+<p>In order to facilitate the analysis of SILAC data, the capability of having multiple sets of modifications analyzed simultaneously
+has been added. To specify additional sets of modifications, use the same parameter name with the addition of an incrementing count (starting at 1):
+</p>
+<br> <span class="e">refine, modification mass 1</span>
+<br> <span class="e">refine, modification mass 2</span>
+<br> ...
+<br> <span class="e">refine, modification mass N</span>
+<p>The values for these parameters uses the same syntax as the normal command. Each of these modification sets is applied
+one at a time to the peptides in a sequence file. Processing of these commands stops when a count value is missed (<i>e.g.</i>, if there is a "1"
+ but no "2" then processing stops at "1" even if there is a "3" in the command file).
+Processing is also stoped with a parameter has a zero length string value associated with it. Non-zero length strings that cannot be interpretted as modifications are interpretted as
+no modifications, <i>i.e.</i>, the peptides with be tested for the case where no complete modifications are set.
+<h2>Notes:</h2>
+<ol>
+<li>There is no internal consistency checking to determine if the same set of complete modifications has been
+applied twice, so care should be taken to be sure that a particular modification value occurs once in an
+input file.</li>
+<li>To use the multiple modification set feature, a value for <span class="e">refine, modification mass</span> must be
+set, as this will be used as the first set of complete modifications in an analysis.</li>
+</ol>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="rpmm.html">residue, potential modification mass</a> |
+<a href="refpmm.html">refine, potential modification mass</a> |
+<a href="rmm.html">residue, modification mass</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/refmvev.html b/src/resources/html_doc/refmvev.html
new file mode 100644
index 0000000000000000000000000000000000000000..4c9cf0e260e8ac2db5ff9f2d802a3daace0a6706
--- /dev/null
+++ b/src/resources/html_doc/refmvev.html
@@ -0,0 +1,124 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, maximum valid expectation value</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, maximum valid expectation value</h1>
+<h2>Syntax</h2>
+<p>This value is a positive floating point number represented as a character string.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error is generated when an uninterpretable value is used.</li>
+<li>If this parameter is missing, a default value of <span class="v">0.01</span> is used.</li>
+
+</ol>
+<h2>Description</h2>
+<p>When the refinement process begins, the expectation values for all of the peptides found
+in the first pass search are calculated. Any protein that contains at least one peptide with
+an expectation value lower than the value for this parameter is then included in the list of
+proteins that will be used during the refinement process.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="refine.html">refine</a></span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/refpctm.html b/src/resources/html_doc/refpctm.html
new file mode 100644
index 0000000000000000000000000000000000000000..a5907954304e0dbcbc0b3a867233f4c46bf8da7d
--- /dev/null
+++ b/src/resources/html_doc/refpctm.html
@@ -0,0 +1,131 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, potential C-terminus modifications</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, potential C-terminus modifications</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is an ASCII string, of the format
+<span class="v">M<sub>1</sub>@],M<sub>2</sub>@],..., M<sub>n</sub>@]</span><p></p>
+<p>where <span class="v">M<sub>i</sub></span> is a floating point number (potential modification mass in Daltons).
+<h2>Notes</h2>
+<ol>
+<li>No error is produced if ] is not used.</li>
+<li>If a residue type is listed more than once, the last instance of the residue is used to set the modification.</li>
+<li>Both positive and negative potential modification masses may be used.</li>
+</ol>
+<h2>Description</h2>
+<p>The format of this parameter is the same as the <span class="e">residue, potential modification mass</span>
+parameter. When a valid string is present for this parameter, a search with cleavage at every residue is performed,
+and the listed potential C-terminal modifications are tested. This test is done on only the first
+50 residues for each protein in the refinement list. If a more general C-terminal modification is desirable, then
+add a modification string with "]" as the residue to modify into the potential modification list.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="rpmm.html">residue, potential modification mass</a> |
+<a href="refine.html">refine</a> |
+<a href="refpntm.html">refine, potential N-terminus modifications</a> |
+<a href="rupmffr.html">refine, use potential modifications for full refinement</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/refpmm.html b/src/resources/html_doc/refpmm.html
new file mode 100644
index 0000000000000000000000000000000000000000..d3572af9e89554e91409b0762928c28715da6de9
--- /dev/null
+++ b/src/resources/html_doc/refpmm.html
@@ -0,0 +1,130 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, potential modification mass</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, potential modification mass</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is an ASCII string, of the format <span class="v">M<sub>1</sub>@X<sub>1</sub>,M<sub>2</sub>@X<sub>2</sub>,..., M<sub>n</sub>@X<sub>n</sub></span></p>
+<p>where <span class="v">M<sub>i</sub></span> is a floating point number (potential modification mass in Daltons) and <span class="v">
+X<sub>i</sub></span> is a single letter abbreviation for a type of amino acid residue.
+<h2>Notes</h2>
+<ol>
+<li>No error is produced if a non-standard amino acid abbreviation is used.</li>
+<li>If a residue type is listed more than once, the last instance of the residue is used to set the modification.</li>
+<li>Both positive and negative potential modification masses may be used.</li>
+</ol>
+<h2>Description</h2>
+<p>The format of this parameter is the same as the <span class="e">residue, potential modification mass</span>
+parameter. See this discussion of this parameter for a general explanation of its meaning and use. The value
+for the refine version of this parameter is used to create a longer, more comprehensive list of relatively
+rare potential modifications. The value of the <span class="e">use potential modifications for full refinement</span>
+parameter controls which steps in the refinement use this parameter.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="rpmm.html">residue, potential modification mass</a> |
+<a href="refine.html">refine</a> |
+<a href="rupmffr.html">refine, use potential modifications for full refinement</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/refpmmotif.html b/src/resources/html_doc/refpmmotif.html
new file mode 100644
index 0000000000000000000000000000000000000000..a5b2a7cf5ab3fe5bcdab08b8ea3963d445e15884
--- /dev/null
+++ b/src/resources/html_doc/refpmmotif.html
@@ -0,0 +1,143 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, potential modification motif</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, potential modification motif</h1>
+<h2>Syntax</h2>
+<p>The value is a comma-separated list of sequence motifs, composed using a modified PROSITE notation format specified
+below.</p>
+<h2>Notes</h2>
+
+ <ol>
+ <li>The first object is a number, corresponding to the mass change associated
+ with the motif, followed by an "@" symbol. If a colon followed by
+ a number is placed between the number and the @, that number is used as
+ a prompt neutral loss from the modified site and it should be a negative value,
+ e.g.,<BR> <span class="v">80:-98@[ST!]</span>.
+ <li>Square brackets "[]" indicate any of the residues contained
+ are possible;</li>
+ <li>French brackets "{}" indicate that any of the residues contained
+ are forbidden;</li>
+ <li>A bare letter is interpreted as if it was in square brackets and can
+ be modified with an exclamation point, e.g.,<BR> <span class="v">16@[M!]</span>
+ is the same as <span class="v">16M!;</span></li>
+ <li>An exclamation point indicates the position of modification;</li>
+ <li>The letter "X" indicates any residue;</li>
+ <li>Round brackets "()" indicate a count, e.g.,<BR>
+ <span class="v">80@KX(10)T!</span>
+ means a K, followed by ten residues followed by a T;</li>
+ <li>All other characters are ignored, e.g.,<BR> <span class="v">80@[ST!]PX[KR]</span>
+ is the same as <span class="v">80@[ST!]-P-X-[KR]</span>.</li>
+ </ol>
+<h2>Description</h2>
+<p>This parameter is used to modify residues selected by the residues surrounding the site of
+modification. Many biologically relavent modifications are performed by enzymes, which
+are normally affected by the sequence surrounding a residue being modified. Finding sequence
+motifs is fairly time consuming, so it is best done in the refinement process.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="rpmmotif.html">residue, potential modification motif</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/refpntm.html b/src/resources/html_doc/refpntm.html
new file mode 100644
index 0000000000000000000000000000000000000000..d1afdc15f0e9e2bf68703a0b2b2607e32257728d
--- /dev/null
+++ b/src/resources/html_doc/refpntm.html
@@ -0,0 +1,131 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, potential N-terminus modifications</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, potential N-terminus modifications</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is an ASCII string, of the format
+<span class="v">M<sub>1</sub>@[,M<sub>2</sub>@[,..., M<sub>n</sub>@[</span><p></p>
+<p>where <span class="v">M<sub>i</sub></span> is a floating point number (potential modification mass in Daltons).
+<h2>Notes</h2>
+<ol>
+<li>No error is produced if [ is not used.</li>
+<li>If a residue type is listed more than once, the last instance of the residue is used to set the modification.</li>
+<li>Both positive and negative potential modification masses may be used.</li>
+</ol>
+<h2>Description</h2>
+<p>The format of this parameter is the same as the <span class="e">residue, potential modification mass</span>
+parameter. When a valid string is present for this parameter, a search with cleavage at every residue is performed,
+and the listed potential N-terminal modifications are tested. This test is done on only the first
+50 residues for each protein in the refinement list. If a more general N-terminal modification is desirable, then
+add a modification string with "[" as the residue to modify into the potential modification list.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="rpmm.html">residue, potential modification mass</a> |
+<a href="refine.html">refine</a> |
+<a href="refpctm.html">refine, potential C-terminus modifications</a> |
+<a href="rupmffr.html">refine, use potential modifications for full refinement</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/rmm.html b/src/resources/html_doc/rmm.html
new file mode 100644
index 0000000000000000000000000000000000000000..b94545a6c67d2152bd2826f6570f9b5bf35fa202
--- /dev/null
+++ b/src/resources/html_doc/rmm.html
@@ -0,0 +1,162 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>residue, modification mass</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>residue, modification mass</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is an ASCII string, of the format <span class="v">M<sub>1</sub>@X<sub>1</sub>,M<sub>2</sub>@X<sub>2</sub>,..., M<sub>n</sub>@X<sub>n</sub></span></p>
+<p>where <span class="v">M<sub>i</sub></span> is a floating point number (modification mass in Daltons) and <span class="v">
+X<sub>i</sub></span> is a single letter abbreviation for a type of amino acid residue.
+<h2>Notes</h2>
+<ol>
+<li>No error is produced if a non-standard amino acid abbreviation is used.</li>
+<li>If a residue type is listed more than once, the last instance of the residue is used to set the modification.</li>
+<li>Both positive and negative modification masses may be used.</li>
+
+</ol>
+<h2>Description</h2>
+<p>In the course of isolating a protein and generating peptides for use in protein identification
+experiments, it is often necessary to treat the protein sample with reagents that will modify all of
+the residues of a particular type. Commonly, cysteine residues are modified to disrupt and prevent
+the reformation of disulphide bonds. Additionally, other residues may be modified as a predictable
+side product of the protein-to-peptide cleavage process. The modifications encoded in this value
+are applied to every residue of a particular type of amino acid, without exception.</p>
+<p>If there is some possibility that a residue modification process has not been 100% efficient, it
+may be more practical to include the modification in the <span class="e">residue, potential modification mass</span>
+parameter list.</p>
+<p>If a residue labelling strategy is being used where there are two types of reagents for modifying
+a residue (<i>e.g.</i>, <b>C</b>), one with mass <b>L<sub>1</sub></b> and the other with mass <b>L<sub>2</sub></b>, the following method can be used to
+find both types of labelled peptide in the same analysis.</p>
+<ol>
+<li>Add the value <span class="v">L<sub>1</sub>@C</span> to the <span class="e">residue, modification mass</span> parameter</li>
+<li>Add the value <span class="v">(L<sub>2</sub>-L<sub>1</sub>)@C</span> to the <span class="e">residue, potential modification mass</span> parameter</li>
+</ol>
+<p>Because potential and complete modifications are treated separately internally by TANDEM, this will
+result in finding peptides modified with both types of parameters.
+<h2>New feature, version 2009.04.01</h2>
+<p>In order to facilitate the analysis of SILAC data, the capability of having multiple sets of modifications analyzed simultaneously
+has been added. To specify additional sets of modifications, use the same parameter name with the addition of an incrementing count (starting at 1):
+</p>
+<br> <span class="e">residue, modification mass 1</span>
+<br> <span class="e">residue, modification mass 2</span>
+<br> ...
+<br> <span class="e">residue, modification mass N</span>
+<p>The values for these parameters uses the same syntax as the normal command. Each of these modification sets is applied
+one at a time to the peptides in a sequence file. Processing of these commands stops when a count value is missed (<i>e.g.</i>, if there is a "1"
+ but no "2" then processing stops at "1" even if there is a "3" in the command file).
+Processing is also stoped with a parameter has a zero length string value associated with it. Non-zero length strings that cannot be interpretted as modifications are interpretted as
+no modifications, <i>i.e.</i>, the peptides with be tested for the case where no complete modifications are set.
+<h2>Notes:</h2>
+<ol>
+<li>There is no internal consistency checking to determine if the same set of complete modifications has been
+applied twice, so care should be taken to be sure that a particular modification value occurs once in an
+input file.</li>
+<li>To use the multiple modification set feature, a value for <span class="e">residue, modification mass</span> must be
+set, as this will be used as the first set of complete modifications in an analysis.</li>
+</ol>
+<hr align="left" width="200">
+<span class="also">see also: <a href="rpmm.html">residue, potential modification mass</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/rpm.html b/src/resources/html_doc/rpm.html
new file mode 100644
index 0000000000000000000000000000000000000000..3ccdad52d9bb80270ffa6fde2d70f155477dde8c
--- /dev/null
+++ b/src/resources/html_doc/rpm.html
@@ -0,0 +1,126 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, point mutations</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, point mutations</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
+<li>If no value is set, the default value is <span class="v">no</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>The last step in the refinement process is to test the selected sequences for the possibility
+of a point mutation in each one of the peptides generated with the initial cleavage chemistry. When
+this parameter is set to <span class="v">yes</span>, point mutations are checked. Otherwise, this
+step is skipped.</p>
+<p>See the explanation of point mutation analysis supplied with the main X! TANDEM documentation,
+using the link given below.</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="refine.html">refine</a> |
+<a href="/TANDEM/pam.html">X! TANDEM point mutations</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/rpmm.html b/src/resources/html_doc/rpmm.html
new file mode 100644
index 0000000000000000000000000000000000000000..833be5c39baef931179be20b58ee739ffc68c004
--- /dev/null
+++ b/src/resources/html_doc/rpmm.html
@@ -0,0 +1,156 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>residue, potential modification mass</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>residue, potential modification mass</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is an ASCII string, of the format <span class="v">M<sub>1</sub>@X<sub>1</sub>,M<sub>2</sub>@X<sub>2</sub>,..., M<sub>n</sub>@X<sub>n</sub></span></p>
+<p>where <span class="v">M<sub>i</sub></span> is a floating point number (potential modification mass in Daltons) and <span class="v">
+X<sub>i</sub></span> is a single letter abbreviation for a type of amino acid residue.
+<h2>Notes</h2>
+<ol>
+<li>No error is produced if a non-standard amino acid abbreviation is used.</li>
+<li>If a residue type is listed more than once, the last instance of the residue is used to set the modification.</li>
+<li>Both positive and negative potential modification masses may be used.</li>
+
+</ol>
+<h2>Description</h2>
+<p>In the course of isolating a protein and generating peptides for use in protein identification
+experiments,some fraction of the residues of a particular type may be modified (<i>e.g.</i>, methionine
+residues are often oxidized). Additionally, other residues may be have been modified in the orginal
+protein through a process commonly referred to as post-translational modification. These modifications
+may be quite rare in a protein sample, but knowing which residues are modified in this way
+may be very important biologically. These post-translational modifications are normally the
+result of enzyme reactions and are therefore very specific to the type of residue modified.</p>
+<p>The modifications encoded in this value are applied sequentially to every possible combination
+of modified and unmodified residues in a particular peptide. The number of possibilities for
+a particular peptide (N) depends on the number of residues with potential modifications in a peptide (n):</p>
+<p>N = 2<sup>n</sup>
+<p>The exponential nature of this expression makes calculating all possible potentially modified
+pepides increasingly difficult as the number of modifications increases. If long lists of relatively rare potential
+modifications are to be applied, it is better to use the <span class="e">refine, potential modification mass</span> parameter
+when looking at large numbers of mass spectra.</p>
+<p>If a residue labelling strategy is being used where there are two types of reagents for modifying
+a residue (<i>e.g.</i>, <b>C</b>), one with mass <b>L<sub>1</sub></b> and the other with mass <b>L<sub>2</sub></b>, the following method can be used to
+find both types of labelled peptide in the same analysis.</p>
+<ol>
+<li>Add the value <span class="v">L<sub>1</sub>@C</span> to the <span class="e">residue, modification mass</span> parameter</li>
+<li>Add the value <span class="v">(L<sub>2</sub>-L<sub>1</sub>)@C</span> to the <span class="e">residue, potential modification mass</span> parameter</li>
+</ol>
+<p>Because potential and complete modifications are treated separately internally by TANDEM, this will
+result in finding peptides modified with both types of parameters.</p>
+<p><b>NOTE</b>: When a peptide starts with E or Q, TANDEM automatically checks for the formation
+of pyroglutamic acid, i.e., the loss of water or ammonia, respectively. This modification
+happens spontaneously in solution and failure to test for it can result in missing significant peptide hits. The
+analogous reaction for iodoacetimide blocked cysteine (loss of ammonia) is also considered. This
+modification is considered to be an N-terminal modification only, so it does not affect any potential
+modifications specified for Q, E or C.</p>
+
+<hr align="left" width="200">
+<span class="also">see also:
+<a href="rmm.html">residue, modification mass</a> |
+<a href="refpmm.html">refine, potential modification mass</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/rpmmotif.html b/src/resources/html_doc/rpmmotif.html
new file mode 100644
index 0000000000000000000000000000000000000000..0c063db5add4fb74233d0d15aaaaee1fe35ff6f1
--- /dev/null
+++ b/src/resources/html_doc/rpmmotif.html
@@ -0,0 +1,142 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>residue, potential modification motif</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>residue, potential modification motif</h1>
+<h2>Syntax</h2>
+<p>The value is a comma-separated list of sequence motifs, composed using a modified PROSITE notation format specified
+below.</p>
+<h2>Notes</h2>
+
+ <ol>
+ <li>The first object is a number, corresponding to the mass change associated
+ with the motif, followed by an "@" symbol. If a colon followed by
+ a number is placed between the number and the @, that number is used as
+ a prompt neutral loss from the modified site and it should be a negative value,
+ e.g.,<BR> <span class="v">80:-98@[ST!]</span>.
+ <li>Square brackets "[]" indicate any of the residues contained
+ are possible;</li>
+ <li>French brackets "{}" indicate that any of the residues contained
+ are forbidden;</li>
+ <li>A bare letter is interpreted as if it was in square brackets and can
+ be modified with an exclamation point, e.g.,<BR> <span class="v">16@[M!]</span>
+ is the same as <span class="v">16M!;</span></li>
+ <li>An exclamation point indicates the position of modification;</li>
+ <li>The letter "X" indicates any residue;</li>
+ <li>Round brackets "()" indicate a count, e.g.,<BR> <span class="v">80@KX(10)T!</span>
+ means a K, followed by ten residues followed by a T;</li>
+ <li>All other characters are ignored, e.g.,<BR> <span class="v">80@[ST!]PX[KR]</span>
+ is the same as <span class="v">80@[ST!]-P-X-[KR]</span>.</li>
+ </ol>
+<h2>Description</h2>
+<p>This parameter is used to modify residues selected by the residues surrounding the site of
+modification. Many biologically relavent modifications are performed by enzymes, which
+are normally affected by the sequence surrounding a residue being modified. Finding sequence
+motifs is fairly time consuming, so it is best done in the refinement process.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="refpmmotif.html">refine, potential modification motif</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/rsaps.html b/src/resources/html_doc/rsaps.html
new file mode 100644
index 0000000000000000000000000000000000000000..dac8566fbf55ce1c8d2c375540f1f576768d5fc0
--- /dev/null
+++ b/src/resources/html_doc/rsaps.html
@@ -0,0 +1,174 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, saps</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, saps</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
+<li>If no value is set, the default value is <span class="v">yes</span>.</li>
+<li>This option was introduced in X! Tandem and P3 in version 2007.04.01.</li>
+</ol>
+<h2>Description</h2>
+<p>When this parameter is set to <span class="v">yes</span>, a list of known potential single amino
+acid polymorphisms is checked for each peptide residue considered in the first round of modelling. The default
+lists are based on known coding non-synonymous single nucleotide polymorphisms derived from the SNP annotations
+in ENSEMBL: the amino acid consequence of a nsSNP is commonly referred to as a snAPs.
+The annotation file format is the same as the file format used to annotate mutations in GPM
+BIOML files, for example:</p>
+<pre>
+<?xml version="1.0"?>
+<bioml label="human sap listing, 2007.04.01, for ENSEMBL human, version 43">
+<protein id="ENSP00000286809">
+ <aa id="rs686364" at="151" type="S" mut="P" />
+ <aa id="rs685967" at="129" type="T" mut="A" />
+ <aa id="rs1557294" at="25" type="T" mut="A" />
+</protein>
+<protein id="ENSP00000372288">
+ <aa id="rs8127420" at="40" type="S" mut="P" />
+</protein>
+...
+<protein id="ENSP00000373050">
+ <aa id="rs17002888" at="1325" type="S" mut="N" />
+ <aa id="rs17002890" at="1165" type="M" mut="I" />
+ <aa id="rs5758651" at="722" type="S" mut="G" />
+ <aa id="rs1064961" at="681" type="G" mut="V" />
+ <aa id="rs6002656" at="485" type="T" mut="N" />
+ <aa id="rs34030679" at="405" type="M" mut="V" />
+ <aa id="rs4484130" at="10" type="Y" mut="F" />
+</protein>
+<note>Total SAPS: 138704</note>
+<note>Created from: human_saps.txt</note>
+<note>Original name: human_saps.xml</note>
+</bioml>
+</pre>
+<p>You can check <a href="ftp://ftp.thegpm.org/fasta/ENSEMBL/saps">GPM SAP repository</a> for latest
+versions of these annoation files for ENSEMBL species. Please be aware that these files can be quite large and they may
+cause problems when they are opened by HTML WWW browsers. If you wish to look at the details of these files,
+a text editor is usually the best choice.</p>
+<p>The search engine requires that the protein id string matches the FASTA description line string, in order
+to make a one-to-one correspondence between a protein sequence and an SAP annoation. This may cause some
+problems when FASTA description lines that contain more than simply the protein accession number are used.</p>
+<p>The association of an SAP annotation file with a <a href="lpti.html">taxonomy key word</a> is made
+using a special entry in any taxonomy file. An example for a "human" entry is as follows:
+<pre>
+ <taxon label="human">
+ <file format="peptide" URL="../fasta/human.fasta.pro" />
+ <file format="peptide" URL="../fasta/human_extra.fasta" />
+ <file format="spectrum" URL="../fasta/human_fasta.hlf" />
+ <file format="saps" URL="../fasta/human_saps.xml; />
+ </taxon>
+</pre>
+<p>Any number of SAP annotation files may be associated with any taxon entry. If no SAP annotation file is
+specified or a specified file does not exist, the search will continue without failure. The X! series output
+file will contain a listing of the SAP files that were actually used.
+</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="refine.html">refine</a> | <a href="rpm.html">point mutations</a> |
+<a href="lpti.html">taxonomy</a> | <a href="/TANDEM/pam.html">X! TANDEM point mutations</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/rsp.html b/src/resources/html_doc/rsp.html
new file mode 100644
index 0000000000000000000000000000000000000000..c0e3f3cd546623779b9ccb67acab76e1bdd3e375
--- /dev/null
+++ b/src/resources/html_doc/rsp.html
@@ -0,0 +1,133 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, sequence path</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, sequence path</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is a string containing the full or relative path to an existing
+sequence file, in valid BIOML format.</p>
+<h2>Notes</h2>
+<ol>
+<li>This parameter was introduced in version 2006.04.01</li>
+<li>If this parameter is absent or does not represent a valid file path, nothing is done.</li>
+<li>No error condition is displayed if a file cannot be read.</li>
+
+</ol>
+<h2>Description</h2>
+<p>Just prior to executing the refinement steps of a search, a list of protein sequences to use
+for the refinement steps is created. When this parameter is a valid input file path, that list of
+proteins is altered by adding the sequences present in the input file. Repeated sequences are
+not included. The input file can either be an X! Tandem BIOML ouput file or a file generated by
+the use of the <span class="e">output, sequence path</span> parameter. This sequence import step occurs
+prior to the generation of a file by the use of the <span class="e">output, sequence path</span> parameter,
+so using both parameters will generate an output file that is a composite of the sequences found
+during the first step of the search and the sequences imported. Sequences are imported even if there
+will be no refinement steps executed.
+</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="osp.html">output, sequence path</a> |
+<a href="refine.html">refine</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/rss.html b/src/resources/html_doc/rss.html
new file mode 100644
index 0000000000000000000000000000000000000000..412e0f20e0fd91121c8429295f972810e3a76584
--- /dev/null
+++ b/src/resources/html_doc/rss.html
@@ -0,0 +1,129 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, spectrum synthesis</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, spectrum synthesis</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
+<li>If no value is set, the default value is <span class="v">no</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>When X! TANDEM scores a model peptide sequence with a spectrum, it can take into account
+the probablity that a particular bond will break preferentially, relative to other bonds.</p>
+<ol>
+<li><span class="v">yes</span> - When this value is found, bonds N-terminal to proline residues and
+bonds C-terminal to aspartic acid, glutamic acid, valine, leucine, isoleucine, glutamine and asparagine
+are favoured. This process effectively predicts a "synthetic" spectrum and rewards
+ions that agree with the predicted spectrum.</li>
+<li><span class="v">no</span> - When this value is found, all bonds are considered to be equivalent.</li>
+</ol>
+<hr align="left" width="200">
+<span class="also">see also: <a href="refine.html">refine</a>
+
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/rtp.html b/src/resources/html_doc/rtp.html
new file mode 100644
index 0000000000000000000000000000000000000000..4885fd40dcf80615f4a36975748a4a3dae251146
--- /dev/null
+++ b/src/resources/html_doc/rtp.html
@@ -0,0 +1,131 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, tic percent</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, tic percent</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is a percentage, a floating point number ><span class="v">0.0</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>This parameter was introduced in version 2006.04.01</li>
+<li>If the value of this parameter is zero or absent, the default value <span class="v">20.0</span> is used.</li>
+
+
+</ol>
+<h2>Description</h2>
+<p>When X! Tandem is executing a refinement job, the number of protein sequences to be tested is
+known. During the job, X! Tandem sends a dot "." character to the console (and log file, if desired)
+when the fraction of the job corresponding to the value of this parameter has
+been finished. For exmaple, if this parameter is set to <span class="v">10</span>,
+and 1000 protein sequences are being tested, then a character is sent to the
+console every time <i>1000 x 10/100 = 100</i> sequences have been processed. The
+total number of characters (tics) would be <i>10</i>.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="spsbs.html">spectrum, sequence batch size</a> |
+<a href="olp.html">output, log path</a> |
+<a href="refine.html">refine</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/rua.html b/src/resources/html_doc/rua.html
new file mode 100644
index 0000000000000000000000000000000000000000..139ab35eb7cfc4437bd16517f8d37363640c3837
--- /dev/null
+++ b/src/resources/html_doc/rua.html
@@ -0,0 +1,129 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, use annotations</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, use annotations</h1>
+<h2>Syntax</h2>
+<p>This parameter is a text string that may be <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>Introduced in version 2008.02.01.</li>
+<li>Default value is <span class="v">yes</span></li>
+<li>The value of this parameter is only used in the refinement rounds of identification: to apply the annotations
+to initial round, use the <span class="e">protein, use annotations</span> parameter.
+</ol>
+<h2>Description</h2>
+<p>It is known that different proteins have different post-translational modifications. In some cases, proteins
+may be highly modified by unusual modifications, such as the highly variable modification of histones or collagens.
+When the parameter is set to <span class="v">yes</span>, an annotation file that contains the modifications
+known to be present in each protein will be added to the search, on a protein by protein basis. Any other
+modifications that you have specified will over-ride these annotations, if there is a conflict between
+the annotation and your specified modification.
+</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="pua.html">protein, use annotations</a> |
+
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/ruc.html b/src/resources/html_doc/ruc.html
new file mode 100644
index 0000000000000000000000000000000000000000..40d4da6433d1b4f797b56d59b5c23047becb5920
--- /dev/null
+++ b/src/resources/html_doc/ruc.html
@@ -0,0 +1,127 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, unanticipated cleavage</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, unanticipated cleavage</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
+<li>If no value is set, the default value is <span class="v">no</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>As the second step in the refinement process, the sequences selected for refinement are
+modelled using the cleavage conditions <span class="v">[X]|[X]</span>, with the number of missed cleavages set
+to <span class="v">50</span>. When the value of the parameter is <span class="v">yes</span>, then this step is
+performed. Otherwise, this step is not carried out.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="refine.html">refine</a> |
+<a href="rupmffr.html">refine, use potential modifications for full refinement</a> |
+<a href="pcs.html">protein, cleavage site</a> |
+<a href="smmcs.html">scoring, maximum missed cleavage sites</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/rupmffr.html b/src/resources/html_doc/rupmffr.html
new file mode 100644
index 0000000000000000000000000000000000000000..e61226db1400f1522a26dffdfe50f1253bf837d3
--- /dev/null
+++ b/src/resources/html_doc/rupmffr.html
@@ -0,0 +1,128 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>refine, use potential modifications for full refinement</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>refine, use potential modifications for full refinement</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
+<li>If no value is set, the default value is <span class="v">no</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>The first step in the refinement process is to model the selected sequences with the <span class="e">scoring, maximum
+missed cleavage</span> parameter set to <span class="v">5</span>, the a list of list of potential modficiations
+defined by the <span class="e">refine, potential modification mass</span> value. If this parameter
+is set to <span class="v">yes</span>, then the new list of potential modifications are used in the
+subsequent steps of the refinement. If it is set to <span class="v">no</span>, then the <span class="e">residue,
+potential modification mass</span> value is used for the subsequent steps.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="rpmm.html">residue, potential modification mass</a> |
+<a href="refpmm.html">refine, potential modification mass</a> |
+<a href="smmcs.html">scoring, maximum missed cleavage sites</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sai.html b/src/resources/html_doc/sai.html
new file mode 100644
index 0000000000000000000000000000000000000000..816628024af5e7275ec86d3ffa625e8b0501d6a1
--- /dev/null
+++ b/src/resources/html_doc/sai.html
@@ -0,0 +1,124 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>scoring, a ions</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>scoring, a ions</h1>
+<h2>Syntax</h2>
+<p>The value can have only two value: <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated if an uninterpretable value is entered.</li>
+<li>If no value is present, the default value is <span class="v">no</span>.</li>
+
+</ol>
+<h2>Description</h2>
+<p>If the value is <span class="v">yes</span>, then peptide sequence a ions are used in the
+spectrum scoring algorithm.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="syi.html">scoring, y ions</a> |
+<a href="smic.html">scoring, minimum ion count</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sbi.html b/src/resources/html_doc/sbi.html
new file mode 100644
index 0000000000000000000000000000000000000000..ff12debd2403294f8ec2cdc28e7607957c631fcc
--- /dev/null
+++ b/src/resources/html_doc/sbi.html
@@ -0,0 +1,124 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>scoring, b ions</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>scoring, b ions</h1>
+<h2>Syntax</h2>
+<p>The value can have only two value: <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated if an uninterpretable value is entered.</li>
+<li>If no value is present, the default value is <span class="v">yes</span>.</li>
+
+</ol>
+<h2>Description</h2>
+<p>If the value is <span class="v">yes</span>, then peptide sequence b ions are used in the
+spectrum scoring algorithm.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="syi.html">scoring, y ions</a> |
+<a href="smic.html">scoring, minimum ion count</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sca.html b/src/resources/html_doc/sca.html
new file mode 100644
index 0000000000000000000000000000000000000000..0718400c469099b3660dc946c749c23edbaa2fad
--- /dev/null
+++ b/src/resources/html_doc/sca.html
@@ -0,0 +1,136 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, contrast angle</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, contrast angle</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is an floating point number, in the range <span class="v">0 - 90</span>.
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated by an invalid value for this parameter.</li>
+<li>The default value for this parameter is <span value="v">0</span></li>
+
+</ol>
+<h2>Description</h2>
+<p>When <span class="e">spectrum, use contrast angle</span> is set to <span class="v">yes</span>, this
+parameter is used to set the stringency of filtering used to remove redundant peptide spectra from
+a list of spectra. The value is applied to the spectrum data set according to the following algorithm.
+</p>
+<ol>
+<li>The opening angles between all pairs of spectra in the data set are calculated, by
+computing the inner product of each pair and then dividing it by the lengths of both
+vectors:<BR>
+v = cos<sup>-1</sup>(inner(<b>a</b>,<b>b</b>)/(|<b>a</b>||<b>b</b>|))
+</li>
+<li>All spectrum pairs that have parent ion masses within 1000 ppm are tested to see if their
+opening angle v is less than <span class="e">spectrum ,contrast angle</span>.</li>
+<li>If this test is true, then the most intense spectrum of the pair is kept and the
+less intensity spectrum is deleted from the list to be searched.</li>
+</ol>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="suca.html">spectrum, use contrast angle</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sci.html b/src/resources/html_doc/sci.html
new file mode 100644
index 0000000000000000000000000000000000000000..8689acaf6b4b19cd34f8cc0a6933462381c00181
--- /dev/null
+++ b/src/resources/html_doc/sci.html
@@ -0,0 +1,124 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>scoring, c ions</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>scoring, c ions</h1>
+<h2>Syntax</h2>
+<p>The value can have only two value: <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated if an uninterpretable value is entered.</li>
+<li>If no value is present, the default value is <span class="v">no</span>.</li>
+
+</ol>
+<h2>Description</h2>
+<p>If the value is <span class="v">yes</span>, then peptide sequence c ions are used in the
+spectrum scoring algorithm.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="syi.html">scoring, y ions</a> |
+<a href="smic.html">scoring, minimum ion count</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/scp.html b/src/resources/html_doc/scp.html
new file mode 100644
index 0000000000000000000000000000000000000000..eb8cea45affb5a354c32745c0580858a3c289a31
--- /dev/null
+++ b/src/resources/html_doc/scp.html
@@ -0,0 +1,151 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>scoring, cyclic permutation</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>scoring, cyclic permutation</h1>
+<h2>Syntax</h2>
+<p>This parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>This parameter was introduced in version 2006.04.01</li>
+<li>The default value for this parameter is <span class="v">no</span>.</li>
+
+
+</ol>
+<h2>Description</h2>
+<p>X! Tandem performs a detailed statistical analysis on the peptides found during
+a search to determine which results are statistically valid. This analysis depends
+on comparing the best result of a search to the distribution of all other peptide sequences
+that matched the parent ion mass tolerance test. While it only takes approximately
+300 peptides to generate a reliable distribution, if a very small sequence
+collection is used, there may be too few matching peptides to generate a reliable
+distribution. If the distribution is too small, default values are used to
+calculate the expectation value for a result.</p>
+<p>While the default values are reasonable, they may lead to over or under estimation
+of the true expectation value. To try to generate a distribution for very small sequence
+collections, setting this parameter to <span class="v">yes</span> generates a set of
+cyclic permutations of each peptide that falls within the parent ion tolerance. This
+set of peptides, given the sequence "YGGFLR" would be:</p>
+<ol>
+<li>YGGFLR - the initial sequence</li>
+<li>RYGGFL</li>
+<li>LRYGGF</li>
+<li>FLRYGG</li>
+<li>GFLRYG</li>
+<li>GGFLRY</li>
+<li>RLFGGY</li>
+<li>YRLFGG</li>
+<li>GYRLFG</li>
+<li>GGYRLF</li>
+<li>FGGYRL</li>
+<li>LFGGYR</li>
+</ol>
+<p>Each of these alternative sequences is scored and used to construct the scoring distribution,
+but they are not stored in the output, even if they have better scores than the initial
+peptide sequence.</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="sir.html">scoring, include reverse</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sdr.html b/src/resources/html_doc/sdr.html
new file mode 100644
index 0000000000000000000000000000000000000000..54a80ec24568258eb6fbe08c007f950930a37df7
--- /dev/null
+++ b/src/resources/html_doc/sdr.html
@@ -0,0 +1,130 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, dynamic range</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, dynamic range</h1>
+<h2>Syntax</h2>
+<p>The value is a floating point number D<sub>range</sub> > 1.0</p>
+<h2>Notes</h2>
+<ol>
+<li>The value <span class="v">100.0</span> is used as a default if the parameter is absent or has a value < 1.0.</li>
+<li>No error message is generated by an inappropriate value for this parameter.</li>
+<li>The recommended value for general use is <span class="v">100.0</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>This parameter is used to normalize the intensity values of fragment ions, from spectrum to spectrum.
+For example, if D<sub>range</sub> = 100.0, then the intensity of the most intense peak in a spectrum is set to 100,
+and all of the other intensities are linearly scaled to that intensity. Any peak with a scaled intensity of
+less than 1 is rejected as being outside of the dynamic range. Therefore, in addition to normalizing the
+spectra, it sets an effective relative threshold for peaks. </p>
+
+<hr align="left" width="200">
+<span class="also">
+see also: <a href="smpmh.html">spectrum, minimum parent m+h</a> |
+<a href="smfmz.html">spectrum, minimum fragment mz</a> <br>
+<a href="smp.html">spectrum, minimum peaks</a> |
+<a href="suns.html">spectrum, use noise suppression</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sfme.html b/src/resources/html_doc/sfme.html
new file mode 100644
index 0000000000000000000000000000000000000000..b92bd450e7eb8749107643021d7a4cd9a39033ee
--- /dev/null
+++ b/src/resources/html_doc/sfme.html
@@ -0,0 +1,138 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, fragment mass error</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>spectrum, fragment mass error</h1>
+<h2>Syntax</h2>
+<p>The value is a floating point number (T<sub>f</sub> > 0.0), represented as a character string.</p>
+<h2>Notes</h2>
+<ol>
+<li>Interpretation of this value depends on the value set for <span class="e">spectrum, fragment mass error units</span>.</li>
+<li>Interpretation of this value depends on the value set for <span class="e">spectrum, fragment mass type</span>.</li>
+<li>TANDEM inserts a default value for this parameter if it doesn't exist or is set to <span class="v">0.0.</span></li>
+</ol>
+<h2>Description</h2>
+<p>The measurement of fragment ion mass values may result in either monoisotopic masses, or chemical average
+masses. When <span class="e">spectrum, fragment mass type</span> is set to <span class="v">average</span>, this value is used, otherwise the value supplied
+for <span class="e">spectrum, fragment monoisotopic mass error</span> is used.</p>
+<p>
+<p>The fragment ion mass error is the most important single parameter in finding a good
+peptide model for a tandem mass spectrum. For example, if a fragment ion has a measured mass of m<sub>1</sub>
+and a mass p<sub>1</sub> is predicted from a peptide sequence, then the difference between the
+two masses (d<sub>1</sub>) is given by the following:</p>
+<p>
+d<sub>1</sub> = | m<sub>1</sub> - p<sub>1</sub> |<br></p>
+<p>If d<sub>1</sub> < T<sub>f</sub>, then the fragment is considered as found. Otherwise, the
+fragment is ignored, without penalty. Peptide modeling for identification depends strongly on
+counting the number of predicted fragments that are found in a spectrum, so setting this value
+correctly will determine the success or failure of an identficiation. It is worthwhile to experiment
+with this value when using a new instrument, to determine the best settings for identifying a
+known set of peptides.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="sfmeu.html">spectrum, fragment mass error units</a> |
+<a href="sfmt.html">spectrum, fragment mass type</a> |</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sfmeu.html b/src/resources/html_doc/sfmeu.html
new file mode 100644
index 0000000000000000000000000000000000000000..b66d34092bf340d28e4dc9993c013249c84345a3
--- /dev/null
+++ b/src/resources/html_doc/sfmeu.html
@@ -0,0 +1,139 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, fragment mass error units</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>spectrum, fragment mass error units</h1>
+<h2>Syntax</h2>
+<p>The value for this parameter is an ASCII string, with two possible values:
+<span class="v">Daltons</span> or <span class="v">ppm</span></p>
+<h2>Notes</h2>
+<ol>
+<li>If this parameter is not present or set to a unexpected value, a default value is substituted.</li>
+<li>No error message is generated when a bad value is used for this parameter.</li>
+<li>Interpretation of this value depends on the value set for <span class="e">spectrum, fragment mass type</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>The value for this parameter alters the interpretation of the value for the parameter named
+<span class="e">spectrum, fragment mass error</span>. The interpretation of the two values
+are described below.</p>
+<ol>
+<li><span class="v">Daltons</span>: If this value is set, then the value of
+<span class="e">spectrum, fragment mass error</span> (T<sub>f</sub>) is
+simply interpreted as a mass and the condition for a fragment ion to be considered found is
+given by:<br>
+| m - p | < T<sub>f</sub><br>
+where m is a mass in a spectrum and p is the calculated mass of a peptide fragment.
+</li>
+<li><span class="v">ppm</span>: If this value is set, then the value of T<sub>f</sub> is
+interpreted as representing parts-per-million (commonly used in mass spectrometry to
+express precision), altering the condition for a fragment ion to be as follows:<br>
+| m - p | < m(T<sub>f</sub> x 10<sup>-6</sup>)<br>
+</li>
+</ol>
+<hr align="left" width="200">
+<span class="also">see also: <a href="sfme.html">spectrum, fragment mass error</a> |
+<a href="sfmt.html">spectrum, fragment mass type</a> |</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sfmme.html b/src/resources/html_doc/sfmme.html
new file mode 100644
index 0000000000000000000000000000000000000000..9f91af79cdd84118749c2b6377b158829c4bed22
--- /dev/null
+++ b/src/resources/html_doc/sfmme.html
@@ -0,0 +1,133 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, fragment monoisotopic mass error</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>spectrum, fragment monoisotopic mass error</h1>
+<h2>Syntax</h2>
+<p>The value is a floating point number (T<sub>f</sub> > 0.0), represented as a character string.</p>
+<h2>Notes</h2>
+<ol>
+<li>Interpretation of this value depends on the value set for <span class="e">spectrum, fragment monoisotopic mass error units</span>.</li>
+<li>TANDEM inserts a default value for this parameter if it doesn't exist or is set to <span class="v">0.0.</span></li>
+</ol>
+<h2>Description</h2>
+<p>The fragment ion monoisotopic mass error is the most important single parameter in finding a good
+peptide model for a tandem mass spectrum. For example, if a fragment ion has a measured mass of m<sub>1</sub>
+and a mass p<sub>1</sub> is predicted from a peptide sequence, then the difference between the
+two masses (d<sub>1</sub>) is given by the following:</p>
+<p>
+d<sub>1</sub> = | m<sub>1</sub> - p<sub>1</sub> |<br></p>
+<p>If d<sub>1</sub> < T<sub>f</sub>, then the fragment is considered as found. Otherwise, the
+fragment is ignored, without penalty. Peptide modeling for identification depends strongly on
+counting the number of predicted fragments that are found in a spectrum, so setting this value
+correctly will determine the success or failure of an identficiation. It is worthwhile to experiment
+with this value when using a new instrument, to determine the best settings for identifying a
+known set of peptides.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="sfmmeu.html">spectrum, fragment monoisotopic mass error units</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sfmmeu.html b/src/resources/html_doc/sfmmeu.html
new file mode 100644
index 0000000000000000000000000000000000000000..c86bcc1d84c6020d62d86611b4f27ccb700dee45
--- /dev/null
+++ b/src/resources/html_doc/sfmmeu.html
@@ -0,0 +1,137 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, fragment monoisotopic mass error units</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>spectrum, fragment monoisotopic mass error units</h1>
+<h2>Syntax</h2>
+<p>The value for this parameter is an ASCII string, with two possible values:
+<span class="v">Daltons</span> or <span class="v">ppm</span></p>
+<h2>Notes</h2>
+<ol>
+<li>If this parameter is not present or set to a unexpected value, a default value is substituted.</li>
+<li>No error message is generated when a bad value is used for this parameter.</li>
+</ol>
+<h2>Description</h2>
+<p>The value for this parameter alters the interpretation of the value for the parameter named
+<span class="e">spectrum, fragment monoisotopic mass error</span>. The interpretation of the two values
+are described below.</p>
+<ol>
+<li><span class="v">Daltons</span>: If this value is set, then the value of
+<span class="e">spectrum, fragment monoisotopic mass error</span> (T<sub>f</sub>) is
+simply interpreted as a mass and the condition for a fragment ion to be considered found is
+given by:<br>
+| m - p | < T<sub>f</sub><br>
+where m is a mass in a spectrum and p is the calculated mass of a peptide fragment.
+</li>
+<li><span class="v">ppm</span>: If this value is set, then the value of T<sub>f</sub> is
+interpreted as representing parts-per-million (commonly used in mass spectrometry to
+express precision), altering the condition for a fragment ion to be as follows:<br>
+| m - p | < m(T<sub>f</sub> x 10<sup>-6</sup>)<br>
+</li>
+</ol>
+<hr align="left" width="200">
+<span class="also">see also: <a href="sfmme.html">spectrum, fragment monoisotopic mass error</a> </span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sfmt.html b/src/resources/html_doc/sfmt.html
new file mode 100644
index 0000000000000000000000000000000000000000..2ef1f097ee0300995ba5b3932a087e754620c2dc
--- /dev/null
+++ b/src/resources/html_doc/sfmt.html
@@ -0,0 +1,132 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, fragment mass type</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>spectrum, fragment mass type</h1>
+<h2>Syntax</h2>
+<p>The value for this parameter is an ASCII string, with two possible values:
+<span class="v">average</span> or <span class="v">monoisotopic</span></p>
+<h2>Notes</h2>
+<ol>
+<li>If this parameter is not present or set to a unexpected value, the default value <span class="v">monoisotopic</span> will be used.</li>
+<li>No error message is generated when a bad value is used for this parameter.</li>
+</ol>
+<h2>Description</h2>
+<p>Naturally occuring organic molecules do not have a single value corresponding to the "mass" of the molecule.
+Because organic molecules contain carbon, any collection of molecules will have some probability of containing one
+or more <sup>13</sup>C atoms. In mass spectrometry, it is common to refer to the weighted average of all possible
+<sup>13</sup>C-containing molecular masses as the "chemical" or "average" mass of the
+molecule. When this parameter is set to <span class="v">average</span>, this weighted average is used to
+calculate the masses of the fragment ions in a tandem mass spectrum.</p>
+<p>Most modern mass spectrometers have sufficient mass resolution so that the mass of each of the individual
+<sup>13</sup>C-containing species can be measured separately. The lowest mass of these peaks will contain
+only <sup>12</sup>C atoms. This lowest mass peak in the isotopic distribution measured is commonly refered to
+as the "monoisotopic" mass for the molecule (also refered to as the A0 peak). When this parameter is
+set to <span class="v">monoisotopic</span>, this peak is used to define the mass of the fragment ions.</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="sfme.html">spectrum, fragment mass error</a> |
+<a href="sfmeu.html">spectrum, fragment mass error type</a> |</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sir.html b/src/resources/html_doc/sir.html
new file mode 100644
index 0000000000000000000000000000000000000000..15ebdd67ec4cf70119573a74fabbc0a8dbaaa197
--- /dev/null
+++ b/src/resources/html_doc/sir.html
@@ -0,0 +1,136 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>scoring, include reverse</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>scoring, include reverse</h1>
+<h2>Syntax</h2>
+<p>The value for this parameter can be <span class="v">yes</span>, <span class="v">no</span> or <span class="v">only</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>The default value for this parameter is <span class="v">no</span>.</li>
+</ol>
+<h2>Description</h2>
+<p>Due to the structure of some older search engines, no statistical information
+is compiled about the validity of the results. As an after-the-fact kluge to correct
+this problem, it has become common practice to repeat a search using the same
+set of protein sequences, with the protein sequences altered to be written in reverse
+order (a so-called "decoy search"). By comparing the scores
+produced by this "decoy" search and the normal search, it is possible
+to very crudely estimate whether a result is potentially a false positive.</p>
+<p>The statistical analysis done by X! Tandem makes this type of crude estimate
+unnecessary. However, to make comparisons possible, X! Tandem has a protein sequence
+reverse method built in. When the value of this parameter is <span class="v">yes</span>,
+the protein sequences are first searched normally and then reversed in memory and
+searched again. The tag ":reversed" is added to the protein description, so
+that peptides corresponding to reversed sequences can be distinguished in the output.
+Using this feature regularly is not recommended, as it doubles the time required to
+perform a search and the use of reversed searches for validation has no
+general statistical value.</p>
+<p>When the value is <span class="v">only</span>, then results for
+the normal sequences will not be tested: only the reversed sequences will be used.</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="scp.html">scoring, cyclic permutation</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/smfmz.html b/src/resources/html_doc/smfmz.html
new file mode 100644
index 0000000000000000000000000000000000000000..c013b4d73b75cecd43a293517d325df8cd2bf4d6
--- /dev/null
+++ b/src/resources/html_doc/smfmz.html
@@ -0,0 +1,135 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, minimum fragment mz</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, minimum fragment mz</h1>
+<h2>Syntax</h2>
+<p>This value is a positive floating point number, M<sub>fmin</sub>.</p>
+<h2>Notes</h2>
+<ol>
+<li>If no value is specified or it is uninterpretable, the default value is
+<span class="e">M<sub>fmin</sub></span> = <span class="v">200</span></li>
+<li>No error message is generated by inappropriate values.</li>
+</ol>
+<h2>Description</h2>
+<p>The fragment ion mass spectra produced by peptides contain peaks that are sequence-specific and those that
+are caused by individual amino acid residues. The peaks caused by these individual amino acid residues
+tend to be relatively small (m/z < 200) and they do not affect the outcome of a search. However,
+these peaks can be very intense, sometimes dwarfing the sequence-specific peaks used by TANDEM to
+discover appropriate model peptide sequences. The value of <span class="e">M<sub>fmin</sub></span> is used
+to remove these intense (but not very useful) peaks, prior to <a href="sdr.html">normalization</a>. Any peak that <u>does not</u>
+meet the condition:</p>
+<p>m/z > M<sub>fmin</sub><p>
+<p>is rejected.
+
+<hr align="left" width="200">
+<span class="also">see also:
+<a href="sdr.html">spectrum, dynamic range</a> |
+<a href="smpmh.html">spectrum, minimum parent m+h</a> <br>
+<a href="smp.html">spectrum, minimum peaks</a> |
+<a href="suns.html">spectrum, use noise suppression</a>
+
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/smic.html b/src/resources/html_doc/smic.html
new file mode 100644
index 0000000000000000000000000000000000000000..36aa15210952147af055718a9febc4c52c96cba3
--- /dev/null
+++ b/src/resources/html_doc/smic.html
@@ -0,0 +1,127 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>scoring, minimum ion count</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>scoring, minimum ion count</h1>
+<h2>Syntax</h2>
+<p>The value is a positive integer.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated if an uninterpretable value is entered.</li>
+<li>If no value is present, the default value is 4.</li>
+
+</ol>
+<h2>Description</h2>
+<p>Practically, there is some minimum number of assignable sequence-specific ions in a spectrum
+that is necessary to consider the spectrum as a match to a peptide sequence. The value of this
+parameter sets the minumum number of total ions that must be assigned for a score to be calculated and stored
+in the scoring histogram structure used by TANDEM to track the statistical nature of the stochastic
+distribution.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="syi.html">scoring, y ions</a> |
+<a href="sbi.html">scoring, b ions</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/smmcs.html b/src/resources/html_doc/smmcs.html
new file mode 100644
index 0000000000000000000000000000000000000000..ac5c2f711ae1310e79ff897dde32842b4107b888
--- /dev/null
+++ b/src/resources/html_doc/smmcs.html
@@ -0,0 +1,131 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>scoring, maximum missed cleavage sites</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>scoring, maximum missed cleavage sites</h1>
+<h2>Syntax</h2>
+<p>This value is a positive integer represented as a character string.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated when an uninterpretable value is used.</li>
+<li>If this parameter is missing, a default value of <span class="v">1</span> is used.</li>
+</ol>
+<h2>Description</h2>
+<p>When a cleavage reagent (either chemical or enzymatic) is used to cleave the peptide
+backbone of a protein to produce peptides, different sites along the backbone will have
+different reaction rates and kinetics. Therefore, there may be some sites that should be
+cleaved by the reagent that are not completely cleaved during the course of the experiment. The value
+of this parameter represents the maximum number of missed cleavage sites allowed within a peptide.
+For a specific, aggressive enzyme such as trypsin, the number of missed sites will be low: a
+value of <span class="v">1</span> or <span class="v">2</span> is appropriate. For a non-specific
+enzyme, such as pepsin, then a value of <span class="v">50</span> is more appropriate.</p>
+<p>The value chosen for this parameter affects the overall speed of the calculation. The number
+of peptides considered for a particular protein sequence is linearly proportional to the parameter
+value, so the amount of time necessary for the calculation will vary roughly linearly with the
+value chosen. In practice, TANDEM performs somewhat better than linear when doing this type of calculation.
+<hr align="left" width="200">
+<span class="also">see also: <a href="pcs.html">protein, cleavage site</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/smp.html b/src/resources/html_doc/smp.html
new file mode 100644
index 0000000000000000000000000000000000000000..d866dcbcab77d52d8e3d23ef9e78df979fb89f7c
--- /dev/null
+++ b/src/resources/html_doc/smp.html
@@ -0,0 +1,134 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, minimum peaks</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, minimum peaks</h1>
+<h2>Syntax</h2>
+<p>The value is a non-zero, positive integer, <span class="e">N<sub>min</sub></span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>If this value is absent or uninterpretable, a default value of <span class="v">5</span> is used.</li>
+<li>If a floating point number is used, rather than an integer, normal C truncation is used for conversion to an integer value.</li>
+<li>No error messages are generated for out-of-range values.</li>
+
+</ol>
+<h2>Description</h2>
+<p>The MS/MS spectra used in peptide sequence searches are composed of a limited number of
+mass-to-charge ratio:intensity pairs. Many common types of mass spectrometer data systems
+will generate a mass spectrum during a chromatographic run, even if the parent ion does not
+fragment. The value of this parameter is used to screen out spectra that contain too few fragment ions
+to be usefully interpreted.</p>
+<p>If the total number of mass-to-charge ratio:intensity pairs is a particular spectrum is N, then
+the condition that a spectrum is considered to have <u>too few ions</u> to be considered would be:</p>
+<p>N < N<sub>min</sub></p>
+<hr align="left" width="200">
+<span class="also">see also:
+<a href="sdr.html">spectrum, dynamic range</a> |
+<a href="smpmh.html">spectrum, minimum parent m+h</a> <br>
+<a href="smfmz.html">spectrum, minimum fragment mz</a> |
+<a href="suns.html">spectrum, use noise suppression</a>
+
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/smpc.html b/src/resources/html_doc/smpc.html
new file mode 100644
index 0000000000000000000000000000000000000000..d68d27cce3146f8e405f25fe76dd2d13bf610633
--- /dev/null
+++ b/src/resources/html_doc/smpc.html
@@ -0,0 +1,122 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, minimum peaks</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, maximum parent charge</h1>
+<h2>Syntax</h2>
+<p>The value is a non-zero, positive integer.</p>
+<h2>Notes</h2>
+<ol>
+<li>If this value is absent or uninterpretable, a default value of <span class="v">4</span> is used.</li>
+<li>If a floating point number is used, rather than an integer, normal C truncation is used for conversion to an integer value.</li>
+<li>No error messages are generated for out-of-range values.</li>
+
+</ol>
+<h2>Description</h2>
+<p>Each MS/MS spectrum whith a precursor charge higher than this thresold were not select for futher score calculation.</p>
+<hr align="left" width="200">
+<span class="also">see also:
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/smpmh.html b/src/resources/html_doc/smpmh.html
new file mode 100644
index 0000000000000000000000000000000000000000..52d50675e35980fdea23226637ccf0ce9a5e9b21
--- /dev/null
+++ b/src/resources/html_doc/smpmh.html
@@ -0,0 +1,132 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, minimum parent m+h</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, minimum parent m+h</h1>
+<h2>Syntax</h2>
+<p>The value for this parameter is a positive floating point number M<sub>min</sub> > 0.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error is generated for inappropriate values entered in this parameter.</li>
+<li>If this parameter is absent, a default value of <span class="v">850</span> is used.</li>
+<li>In most experimental situations, a value of <span class="v">500</span> is recommended.</li>
+<li>This parameter is not used if the value of <span class="e">spectrum, use noise suppression</span> = <span class="v">no</span>.
+</ol>
+<h2>Description</h2>
+<p>This parameter is used to supress the analysis of spectra that were generated by low
+mass parent ions. Depending on the instrumentation and excitation energy used to generate
+fragment ions, there will be some low mass cutoff value, below which there is very little
+chance of generating an interpretable MS/MS spectrum. In many experimental conditions, there
+will also be noise peaks in the parent ion spectrum, generated by the ion source and chemical
+noise. The value selected for M<sub>min</sub> is used to reject these spectra.</p>
+
+<hr align="left" width="200">
+<span class="also">see also:
+<a href="sdr.html">spectrum, dynamic range</a> |
+<a href="smfmz.html">spectrum, minimum fragment mz</a> <br>
+<a href="smp.html">spectrum, minimum peaks</a> |
+<a href="suns.html">spectrum, use noise suppression</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/snlm.html b/src/resources/html_doc/snlm.html
new file mode 100644
index 0000000000000000000000000000000000000000..a20c455f30749333b439567dd531b0eb6c6eea84
--- /dev/null
+++ b/src/resources/html_doc/snlm.html
@@ -0,0 +1,133 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, neutral loss mass</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, neutral loss mass</h1>
+<h2>Syntax</h2>
+<p>This value is a positive floating point number, <span class="e">M<sub>nl</sub></span> > 0.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
+<li>The value of this parameter is ignored if <span class="e">spectrum, use neutral loss window</span> = <span class="v">yes</span>
+</li>
+
+</ol>
+<h2>Description</h2>
+<p>Some types of post-translational or chemical modifications can produce intense peaks in a spectrum
+because of a favoured fragmentation mechanism produced by the loss of a stable neutral molecule. These
+"neutral loss" peaks can be removed from a spectrum by setting appropriate values for the
+<span class="e">spectrum, neutral loss window, W<sub>nl</sub></span> and <span class="e">M<sub>nl</sub></span>
+parameters.</p>
+<p>If the <span class="e">spectrum, use neutral loss window</span> value is <span class="v">yes</span>, then
+any peaks with an m/z value that meets the following condition is rejected:</p>
+<p> | m/z - M<sub>nl</sub> | < W<sub>nl</sub></p>
+<p>Any peak that has been removed using this mechanism is reinserted into the spectrum before the spectrum
+is written to the output XML data file, even though it was not considered during the peptide modelling process.
+<hr align="left" width="200">
+<span class="also">see also:
+<a href="snlw.html">spectrum, neutral loss window</a> |
+<a href="sunlw.html">spectrum, use neutral loss window</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/snlw.html b/src/resources/html_doc/snlw.html
new file mode 100644
index 0000000000000000000000000000000000000000..a0c04f84ba160e90debd00590cbafe23b5a8378b
--- /dev/null
+++ b/src/resources/html_doc/snlw.html
@@ -0,0 +1,133 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, neutral loss window</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, neutral loss window</h1>
+<h2>Syntax</h2>
+<p>This value is a positive floating point number, <span class="e">W<sub>nl</sub></span> > 0.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
+<li>The value of this parameter is ignored if <span class="e">spectrum, use neutral loss window</span> = <span class="v">yes</span>
+</li>
+
+</ol>
+<h2>Description</h2>
+<p>Some types of post-translational or chemical modifications can produce intense peaks in a spectrum
+because of a favoured fragmentation mechanism produced by the loss of a stable neutral molecule. These
+"neutral loss" peaks can be removed from a spectrum by setting appropriate values for the
+<span class="e">W<sub>nl</sub></span> and <span class="e">spectrum, neutral loss mass, M<sub>nl</sub></span>
+parameters.</p>
+<p>If the <span class="e">spectrum, use neutral loss window</span> value is <span class="v">yes</span>, then
+any peaks with an m/z value that meets the following condition is rejected:</p>
+<p> | m/z - M<sub>nl</sub> | < W<sub>nl</sub></p>
+<p>Any peak that has been removed using this mechanism is reinserted into the spectrum before the spectrum
+is written to the output XML data file, even though it was not considered during the peptide modelling process.
+<hr align="left" width="200">
+<span class="also">see also:
+<a href="snlm.html">spectrum, neutral loss mass</a> |
+<a href="sunlw.html">spectrum, use neutral loss window</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sp.html b/src/resources/html_doc/sp.html
new file mode 100644
index 0000000000000000000000000000000000000000..7e81619841d3cd046f960fca8ecfd294d2f26940
--- /dev/null
+++ b/src/resources/html_doc/sp.html
@@ -0,0 +1,144 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, path</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>spectrum, path</h1>
+<p>Value is an ASCII text string describing a spectrum listing file.</p>
+<h2>Notes</h2>
+<ol>
+<li>Relative or absolute path names can be used.</li>
+<li>If the configuration file are resident on a remote disk, a full UNC path name is usually required.</li>
+</ol>
+<h2>Description</h2>
+<p>X! TANDEM reads the MS/MS spectra that it uses to generate a list of model peptides from the
+file named by this parameter. These data files can contain one or more spectra, with the
+peaks in the spectra represented in an ASCII format. The four file formats that X! TANDEM
+currently understands are as follows:</p>
+<ol>
+<li><b>GAML</b>: General Analytical Markup Language representations of mass spectra. GAML is used
+by TANDEM to record spectra in the output XML data file. Because of this feature, TANDEM output
+files can be used as input spectrum files.</li>
+<li><b>DTA</b>: This format is the default representation of data from some types of mass spectrometer
+data systems. Multiple spectra can be stored in a single file by concatenating single spectrum
+DTA files together, leaving a blank line between spectra. The DTA format was originally designed
+to list single spectra only: the extension to multiple spectra described here may make the file
+unreadable to some other applications.</li>
+<li><b>PKL</b>: This format is the default representation of data from some types of mass spectrometer
+data systems. Multiple spectra can be stored in a single file by concatenating single spectrum
+DTA files together, leaving a blank line between spectra. Unlike DTA, the PKL format was originally
+designed to be used to list multiple files.</li>
+<li><b>MGF</b>: Mascot Generic Format is a multiple spectrum ASCII representation that was designed by
+Matrix Science as a replacment for platform-specific ASCII formats. It is well defined (
+see the <a href="http://www.matrixscience.com">Matrix Science</a> web site) and it has a straightforward
+syntax.</li>
+<li><b>mzData</b>: mzData is an evolving XML standard for representing mass spectra. It is specified
+by the PSI group of HUPO, based at EBI.</li>
+<li><b>mzXML</b>: mzXML is an evolving XML standard for representing mass spectra. It is specified
+by the group at the Institute for Systems Biology.</li>
+</ol>
+<hr align="left" width="200">
+<span class="also">see also: <a href="spt.html">spectrum, path type</a> </span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/spmmem.html b/src/resources/html_doc/spmmem.html
new file mode 100644
index 0000000000000000000000000000000000000000..8505141ed45fcc3a8687f1ed48adf0a6340f1b28
--- /dev/null
+++ b/src/resources/html_doc/spmmem.html
@@ -0,0 +1,137 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, parent monoisotopic mass error minus</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>spectrum, parent monoisotopic mass error minus</h1>
+<h2>Syntax</h2>
+<p>The value is a positive floating point number (T<sub>-p</sub>), represented as a character string.</p>
+<h2>Notes</h2>
+<ol>
+<li>Interpretation of this value depends on the value set for <span class="e">spectrum, parent monoisotopic mass error units</span>.</li>
+<li>TANDEM inserts a default value for this parameter if it doesn't exist or is set to <span class="v">0.0.</span></li>
+</ol>
+<h2>Description</h2>
+<p>TANDEM uses this value as part of the calculation to determine if a particular peptide
+sequence is to be considered as a possible model for a spectrum. The calculated mass of
+the peptide is compared with the value using the following expression, where m<sub>p</sub> and
+ p<sub>p</sub> are the measured mass from the spectrum and the calculated mass from the
+ candidate peptide, respectively:</p>
+<p>d = m<sub>p</sub> - p<sub>p</sub></p>
+<p>If the conditions d < 0 and T<sub>-p</sub> > -d are met, then the peptide is a candidate sequence.
+</p>
+<p>This condition (as well as the "plus" condition) are used to limit the extent of
+the more elaborate fragment by fragment calculations that are performed to truly match a
+peptide with a spectrum. From a mathematical point of view, if these conditions are not met, the peptide sequence
+is assigned a score of -∞ and discarded. </p>
+<p>Most protein identification tools use a single parameter for this type of matching, requiring
+a symmetric condition T<sub>p</sub> < |d|. TANDEM allows the user to set assymetric values
+for the parent ion mass error, to compensate for the assymetric systematic mass errors generated
+by some types of mass spectrometers, particularly the currently popular ion trap instruments.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="spmmep.html">spectrum, parent monoisotopic mass error plus</a> |
+<a href="spmmeu.html">spectrum, parent monoisotopic mass error units</a> </span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/spmmep.html b/src/resources/html_doc/spmmep.html
new file mode 100644
index 0000000000000000000000000000000000000000..c3bd6ba053faf14c5af910fb4f397700d4992858
--- /dev/null
+++ b/src/resources/html_doc/spmmep.html
@@ -0,0 +1,136 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, parent monoisotopic mass error plus</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>spectrum, parent monoisotopic mass error plus</h1>
+<h2>Syntax</h2>
+<p>The value is a positive floating point number (T<sub>+p</sub>), represented as a character string.</p>
+<h2>Notes</h2>
+<ol>
+<li>Interpretation of this value depends on the value set for <span class="e">spectrum, parent monoisotopic mass error units</span>.</li>
+<li>TANDEM inserts a default value for this parameter if it doesn't exist or is set to <span class="v">0.0.</span></li>
+</ol>
+<h2>Description</h2>
+<p>TANDEM uses this value as part of the calculation to determine if a particular peptide
+sequence is to be considered as a possible model for a spectrum. The calculated mass of
+the peptide is compared with the value using the following expression, where m<sub>p</sub> and
+ p<sub>p</sub> are the measured mass from the spectrum and the calculated mass from the
+ candidate peptide, respectively:
+<p>d = m<sub>p</sub> - p<sub>p</sub></p>
+<p>If the conditions d > 0 and T<sub>+p</sub> > d are met, then the peptide is a candidate sequence.
+</p>
+<p>This condition (as well as the "minus" condition) are used to limit the extent of
+the more elaborate fragment by fragment calculations that are performed to truly match a
+peptide with a spectrum. From a mathematical point of view, if these conditions are not met, the peptide sequence
+is assigned a score of -∞ and discarded. </p>
+<p>Most protein identification tools use a single parameter for this type of matching, requiring
+a symmetric condition T<sub>p</sub> < |d|. TANDEM allows the user to set assymetric values
+for the parent ion mass error, to compensate for the assymetric systematic mass errors generated
+by some types of mass spectrometers, particularly the currently popular ion trap instruments.</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="spmmem.html">spectrum, parent monoisotopic mass error minus</a> |
+<a href="spmmeu.html">spectrum, parent monoisotopic mass error units</a> </span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/spmmeu.html b/src/resources/html_doc/spmmeu.html
new file mode 100644
index 0000000000000000000000000000000000000000..8bd48a669496ae589761a30010366f4d7ab84786
--- /dev/null
+++ b/src/resources/html_doc/spmmeu.html
@@ -0,0 +1,146 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, parent monoisotopic mass error units</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>spectrum, parent monoisotopic mass error units</h1>
+
+<h2>Syntax</h2>
+<p>The value for this parameter is an ASCII string, with two possible values:
+<span class="v">Daltons</span> or <span class="v">ppm</span></p>
+<h2>Notes</h2>
+<ol>
+<li>If this parameter is not present or set to a unexpected value, a default value is substituted.</li>
+<li>No error message is generated when a bad value is used for this parameter.</li>
+</ol>
+<h2>Description</h2>
+<p>The value for this parameter alters the interpretation of the value for the parameters named
+<span class="e">spectrum, parent monoisotopic mass error plus</span> and <span class="e">spectrum, parent monoisotopic mass error minus</span>. The interpretation of the two values
+are described below.</p>
+<ol>
+<li><span class="v">Da</span>: If this value is set, then the value of
+<span class="e">spectrum, parent monoisotopic mass error plus</span> (T<sub>+p</sub>) is
+simply interpreted as a mass and the condition for a parent ion to be considered found is
+given by:<br>
+ 0 < m - p < T<sub>+p</sub><br>
+where m is a parent ion in a spectrum and p is the calculated mass of a peptide. The interpretation
+for <span class="e">spectrum, parent monoisotopic mass error minus</span> (T<sub>-p</sub>) is given by:
+ 0 > m - p > T<sub>-p</sub><br>
+
+</li>
+<li><span class="v">ppm</span>: If this value is set, then the value of T<sub>+p</sub> is
+interpreted as representing parts-per-million (commonly used in mass spectrometry to
+express precision), altering the condition for a fragment ion to be as follows:<br>
+ 0 < m - p < m(T<sub>+p</sub> x 10<sup>-6</sup>)<br>
+ The interpretation for <span class="e">spectrum, parent monoisotopic mass error minus</span> (T<sub>-p</sub>) is given by:
+ 0 > m - p > m(T<sub>-p</sub> x 10<sup>-6</sup>)<br>
+</li>
+</ol>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="spmmep.html">spectrum, parent monoisotopic mass error plus</a> |
+<a href="spmmem.html">spectrum, parent monoisotopic mass error minus</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/spmmie.html b/src/resources/html_doc/spmmie.html
new file mode 100644
index 0000000000000000000000000000000000000000..8c01568a928ec58e9fc90125d3ebb21b14a74490
--- /dev/null
+++ b/src/resources/html_doc/spmmie.html
@@ -0,0 +1,129 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, parent monoisotopic mass isotope error</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>spectrum, parent monoisotopic mass isotope error</h1>
+<h2>Syntax</h2>
+<p>The only two possible values for this parameter are <span class="v">yes</span>
+or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>If no value, or an unexpected value is supplied, no error message is generated and the default value <span class="v">no</span> is used.</li>
+
+</ol>
+<h2>Description</h2>
+<p>When the value for this parameter is <span class="v">yes</span>, the parent ion mass tolerance is
+expanded by opening up multiple tolerance windows centered on the first and second
+<sup>13</sup>C isotope peaks for a peptide. This behavior is necessary to compensate for the tendency
+of automated peak finding software to return the most intense peak from a cluster of isotopes, rather
+than the all-<sup>12</sup>C peak. It should only be used if the parent ion mass error parameters
+are set so that the error will be < 0.5 Da.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="spmmep.html">spectrum, parent monoisotopic mass error plus</a> |
+<a href="spmmem.html">spectrum, parent monoisotopic mass error minus</a> |
+<a href="spmmeu.html">spectrum, parent monoisotopic mass error units</a></span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/spsbs.html b/src/resources/html_doc/spsbs.html
new file mode 100644
index 0000000000000000000000000000000000000000..9900b62abdf78e6933dfa7d6c22b407cb2158a5e
--- /dev/null
+++ b/src/resources/html_doc/spsbs.html
@@ -0,0 +1,131 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, sequence batch size</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, sequence batch size</h1>
+<h2>Syntax</h2>
+<p>The value is a non-zero integer.</p>
+<h2>Notes</h2>
+<ol>
+<li>This parameter was introduced in version 2006.04.01</li>
+<li>If this parameter is absent or < 0, the default value of 1000 is used.</li>
+
+
+</ol>
+<h2>Description</h2>
+<p>When X! Tandem reads sequences from a source file, such as a FASTA file, it
+reads in a "batch" of sequences at once. The value of this parameter
+sets the number of sequences loaded in as a "batch". Typically, a
+value near 1000 is about the best trade off between efficiency of loading
+sequences in from a file and using too much computer memory to store the
+sequences.</p>
+<p>As batches of sequences are processed, the console display (and log file,
+if desired) display a character as each batch is finished. Setting the value
+of this parameter to 1 will display a character for every sequence.</p>
+<hr align="left" width="200">
+<span class="also">see also: <a href="olp.html">output, log path</a> |
+<a href="om.html">output, message</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/spt.html b/src/resources/html_doc/spt.html
new file mode 100644
index 0000000000000000000000000000000000000000..962877ca6277b3495a486157c0a022bf93d07ef6
--- /dev/null
+++ b/src/resources/html_doc/spt.html
@@ -0,0 +1,135 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, path type</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top">
+<h1>spectrum, path type</h1>
+<p>Value is an ASCII text string describing the format of a spectrum listing file.</p>
+<h2>Notes</h2>
+<ol>
+<li>If absent or a zero length string, the spectrum format detection scheme is used.</li>
+</ol>
+<h2>Description</h2>
+<p>When a spectrum listing file is imported into X! TANDEM, it is necessary to determine
+the format of the file. The automatic routines in X! TANDEM should be able to discover if the
+format is acceptible, however it is possible that some files may be incorrectly typed. This
+type of error can happen if the file is only near to the appropriate file format.
+</p>
+<p>The <span class="e">spectrum, path type</span> parameter can be used to override the format detection routines
+to force X! TANDEM to use a particular file format. The allowed values for this parameter
+are as follows:
+</p>
+<ol>
+<li><span class="v">dta</span>;</li>
+<li><span class="v">pkl</span>;</li>
+<li><span class="v">mgf</span>;</li>
+<li><span class="v">gaml</span>;</li>
+<li><span class="v">mzdata</span>; and</li>
+<li><span class="v">mzxml</span>.</li>
+
+</ol>
+<hr align="left" width="200">
+<span class="also">see also: <a href="sp.html">spectrum, path</a> </span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/st.html b/src/resources/html_doc/st.html
new file mode 100644
index 0000000000000000000000000000000000000000..0f5d2ed7d70858998382d49f3a15f03f428635ac
--- /dev/null
+++ b/src/resources/html_doc/st.html
@@ -0,0 +1,132 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, threads</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, threads</h1>
+<h2>Syntax</h2>
+<p>The value of this paramter is a non-zero, positive integer in the range of
+<span class="v">1</span> to <span class="v">16</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>If the value is set < 1, the value <span class="v">1</span> is substituted.</li>
+<li>If the value is set > 16, the value <span class="v">16</span> is substituted.</li>
+<li>For best performance, this value should be set equal to the number of processors on
+the computer being used to run X! TANDEM.</li>
+
+</ol>
+<h2>Description</h2>
+<p>If a computer has more than one processor, many programs are designed to use only one
+processor at a time. This type of program is referred to as being "single threaded". TANDEM
+is designed to use multiple processors simultaneously to increase the speed of the calculation: this
+type of program is referred to as "multithreaded".</p>
+<p>TANDEM is written to be quite efficient at utilizing any processor as much as possible. Therefore,
+using multiple threads is only helpful if there are spare processors available: using more than
+one thread per processor may actually decrease performance. Also, each thread requires the same amount of
+memory, so running an unnecessarily large number of threads can produce problems resulting using more
+memory than a processor has available to it.
+
+<hr align="left" width="200">
+
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/stp.html b/src/resources/html_doc/stp.html
new file mode 100644
index 0000000000000000000000000000000000000000..7b2a82a61032e179001098618a0ae732f4aeac93
--- /dev/null
+++ b/src/resources/html_doc/stp.html
@@ -0,0 +1,135 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, total peaks</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, total peaks</h1>
+<h2>Syntax</h2>
+<p>The value is a non-zero, positive integer, <span class="e">N<sub>max</sub></span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>If this value is absent or uninterpretable, a default value of <span class="v">50</span> is used.</li>
+<li>If a floating point number is used, rather than an integer, normal C truncation is used for conversion to an integer value.</li>
+<li>No error messages are generated for out-of-range values.</li>
+
+</ol>
+<h2>Description</h2>
+<p>The MS/MS spectra used in peptide sequence searches are composed of a limited number of
+mass-to-charge ratio:intensity pairs. Many common mass spectrometer data systems will record
+large numbers of peaks in a particular spectrum, even though most of these peaks are simply
+noise.</p>
+<p>If the total number of mass-to-charge ratio:intensity pairs is a particular spectrum is N, then
+the condition that a spectrum is considered to have <u>too many ions</u> if the following statement is true:</p>
+<p>N > N<sub>max</sub></p>
+<p>If this condition is met, then the N<sub>max</sub> most intense peaks are used by TANDEM to
+find the best protein model for the spectrum.</p>
+<hr align="left" width="200">
+<span class="also">see also:
+<a href="sdr.html">spectrum, dynamic range</a> |
+<a href="smpmh.html">spectrum, minimum parent m+h</a> <br>
+<a href="smfmz.html">spectrum, minimum fragment mz</a> |
+<a href="suns.html">spectrum, use noise suppression</a>
+
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/suca.html b/src/resources/html_doc/suca.html
new file mode 100644
index 0000000000000000000000000000000000000000..64cd0af675a38c45350b0e45687808b25e7e5f17
--- /dev/null
+++ b/src/resources/html_doc/suca.html
@@ -0,0 +1,125 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, use contrast angle</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, use contrast angle</h1>
+<h2>Syntax</h2>
+<p>The value of this parameter is an ASCII string, with two possible values: <span class="v">yes</span> or <span class="v">no</span>.
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated by an invalid value for this parameter.</li>
+<li>The default value for this parameter is <span value="v">no</span></li>
+
+</ol>
+<h2>Description</h2>
+<p>When this value is set to <span class="v">yes</span>, contrast angle filtering is used to remove similar
+mass spectra from a spectrum list.
+</p>
+
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="sca.html">spectrum, contrast angle</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sunlw.html b/src/resources/html_doc/sunlw.html
new file mode 100644
index 0000000000000000000000000000000000000000..187eb9ce68c77661baa615d13968c050e34e9c02
--- /dev/null
+++ b/src/resources/html_doc/sunlw.html
@@ -0,0 +1,128 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, use neutral loss window</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, use neutral loss window</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
+<li>A default value of <span class="v">no</span> is substituted if the parameter cannot be interpreted or is absent.</li>
+
+</ol>
+<h2>Description</h2>
+<p>Some types of post-translational or chemical modifications can produce intense peaks in a spectrum
+because of a favoured fragmentation mechanism produced by the loss of a stable neutral molecule. These
+"neutral loss" peaks can be removed from a spectrum by setting appropriate values for the
+<span class="e">spectrum, neutral loss window</span> and <span class="e">spectrum, neutral loss mass</span>
+parameters (see the links below).</p>
+
+<hr align="left" width="200">
+<span class="also">see also:
+<a href="snlm.html">spectrum, neutral loss mass</a> |
+<a href="snlw.html">spectrum, neutral loss window</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/suns.html b/src/resources/html_doc/suns.html
new file mode 100644
index 0000000000000000000000000000000000000000..96d2a0fbbe18c4498d826c8169d8b9a2a61911a8
--- /dev/null
+++ b/src/resources/html_doc/suns.html
@@ -0,0 +1,129 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>spectrum, use noise suppression</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>spectrum, use noise suppression</h1>
+<h2>Syntax</h2>
+<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
+<li>A default value of <span class="v">no</span> is substituted if the parameter cannot be interpreted or is absent.</li>
+
+</ol>
+<h2>Description</h2>
+<p>X! TANDEM uses several mechanisms to attempt to reduce the number of spectra considered in a list
+of spectra. When this parameter is set to <span class="v">yes</span>, spectra that fit the pattern
+of "noise" - spectra caused by the fragmentation of chemical noise peaks - are rejected without
+further analysis. This feature can be very useful when dealling with large amounts of data from
+automated LC/MS experiments. Some experimentation may be required to determine what settings
+are appropriate for the noise detection filters (see the links below). Setting the parameter to
+<span class="v">no</span> skips the noise filters and allows all spectra to be modelled.</p>
+
+<hr align="left" width="200">
+<span class="also">see also:<a href="smpmh.html">spectrum, minimum parent m+h</a> |
+<a href="smp.html">spectrum, minimum peaks</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/sxi.html b/src/resources/html_doc/sxi.html
new file mode 100644
index 0000000000000000000000000000000000000000..4e5232a6b98f4c0711abe56ab79a0451e1c12213
--- /dev/null
+++ b/src/resources/html_doc/sxi.html
@@ -0,0 +1,124 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>scoring, x ions</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>scoring, x ions</h1>
+<h2>Syntax</h2>
+<p>The value can have only two value: <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated if an uninterpretable value is entered.</li>
+<li>If no value is present, the default value is <span class="v">no</span>.</li>
+
+</ol>
+<h2>Description</h2>
+<p>If the value is <span class="v">yes</span>, then peptide sequence x ions are used in the
+spectrum scoring algorithm.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="syi.html">scoring, y ions</a> |
+<a href="smic.html">scoring, minimum ion count</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/syi.html b/src/resources/html_doc/syi.html
new file mode 100644
index 0000000000000000000000000000000000000000..263e933ce4293d75b1e3e8c019919ab1828c2ef3
--- /dev/null
+++ b/src/resources/html_doc/syi.html
@@ -0,0 +1,124 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>scoring, y ions</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>scoring, y ions</h1>
+<h2>Syntax</h2>
+<p>The value can have only two value: <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated if an uninterpretable value is entered.</li>
+<li>If no value is present, the default value is <span class="v">yes</span>.</li>
+
+</ol>
+<h2>Description</h2>
+<p>If the value is <span class="v">yes</span>, then peptide sequence y ions are used in the
+spectrum scoring algorithm.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="sbi.html">scoring, b ions</a> |
+<a href="smic.html">scoring, minimum ion count</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/szi.html b/src/resources/html_doc/szi.html
new file mode 100644
index 0000000000000000000000000000000000000000..a6fc586f8ee326db365a6e3908d5154cb1edbb9b
--- /dev/null
+++ b/src/resources/html_doc/szi.html
@@ -0,0 +1,124 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>scoring, z ions</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000000">
+<table>
+<tr>
+<td align="left" valign="top"><h1>scoring, z ions</h1>
+<h2>Syntax</h2>
+<p>The value can have only two value: <span class="v">yes</span> or <span class="v">no</span>.</p>
+<h2>Notes</h2>
+<ol>
+<li>No error message is generated if an uninterpretable value is entered.</li>
+<li>If no value is present, the default value is <span class="v">no</span>.</li>
+
+</ol>
+<h2>Description</h2>
+<p>If the value is <span class="v">yes</span>, then peptide sequence z ions are used in the
+spectrum scoring algorithm.</p>
+
+<hr align="left" width="200">
+<span class="also">see also: <a href="syi.html">scoring, y ions</a> |
+<a href="smic.html">scoring, minimum ion count</a>
+</span>
+<br><br><a href="index.html">X! TANDEM API description project</a>
+</td></tr></table>
+</body>
+</html>
diff --git a/src/resources/html_doc/uml_index.html b/src/resources/html_doc/uml_index.html
new file mode 100644
index 0000000000000000000000000000000000000000..6ddc155416c6a8af8fd1de048b07f8763193dd1b
--- /dev/null
+++ b/src/resources/html_doc/uml_index.html
@@ -0,0 +1,142 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+<head>
+<title>X! TANDEM API Documentation Project - UML diagrams</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<style type="text/css">
+a {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ text-decoration: none;
+ font-size: 10pt;
+}
+
+a:visited {
+ color: blue;
+ cursor: pointer;
+ font-weight: normal;
+ font-style: italic;
+ text-decoration: underline;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+
+
+h1 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+h2 {
+ color: black;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+p {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.also {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+li {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.e {
+ color: red;
+ font-style: italic;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+.v {
+ color: red;
+ font-style: normal;
+ font-weight: bold;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+ margin-bottom:10px;
+}
+
+
+PRE {
+ margin:0px;
+ display:inline
+}
+
+td {
+ color: black;
+ font-weight: normal;
+ font-family: Verdana, Arial, Helvetica,sans-serif;
+ font-size: 10pt;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF">
+<table>
+<tr>
+<td align="left" valign="top">
+ <p>The current documentation for X! TANDEM is in the form of a set of UML diagrams
+ illustrating how the various algorithms in X! TANDEM work in detail. For all other
+ details, please see the documentation in the source code.</p>
+ <ol>
+<li><a href="tandem-process-state.htm"> A state diagram showing how X! TANDEM works</a>.
+</li>
+<li><a href="tandem-load.htm"> An activity diagram of the how information is loaded</a>.
+</li>
+<li><a href="tandem-score.htm"> An activity diagram of how scoring is done</a>.
+</li>
+<li><a href="scoring-state-final.htm"> A state diagram of the scoring mechanism</a>.
+</li>
+<li><a href="peptide-model-state.htm"> A state diagram of how peptide sequences are created from protein sequences</a>.
+</li>
+<li><a href="sequence-server-state.htm"> A state diagram of how protein sequences are loaded from a file</a>.
+</li>
+<li><a href="score-peptide-state.htm"> A state diagram of how spectra are evaluated by peptide mass</a>.
+</li>
+<li><a href="loadmspectrum-class.htm"> A class diagram of the <i>loadmspectrum</i> class</a>.
+</li>
+<li><a href="mprocess-class.htm"> A class diagram of the <i>mprocess</i> class</a>.
+</li>
+<li><a href="mreport-class.htm"> A class diagram of the <i>mreport</i> class</a>.
+</li>
+<li><a href="mscore-class.htm"> A class diagram of the <i>mscore</i> class</a>.
+</li>
+<li><a href="msequence-class.htm"> A class diagram of the <i>msequence</i> class</a>.
+</li>
+<li><a href="mspectrum-class.htm"> A class diagram of the <i>mspectrum</i> class</a>.
+</li>
+ </ol>
+<p>Is there something you would like to see included, or documentation that you would like
+to contribute? Please let use know - <a href="mailto:api@thegpm.org">api@thegpm.org</a>.</p>
+<hr width="200" align="left">
+<span class="also"><br>X! TANDEM API description project</span>
+</td></tr></table>
+</body>
+</html>