Commit 135206c2 authored by Filippo Rusconi's avatar Filippo Rusconi
Browse files

Fix all typos as reported by lintian.

parent 7380562b
......@@ -2,7 +2,7 @@
* \file /core/tandem_run/tandemcondorprocess.cpp
* \date 5/9/2017
* \author Olivier Langella
* \brief handles execution of a bunch of X!Tandem process throught condor job
* \brief handles execution of a bunch of X!Tandem process through condor job
*/
/*******************************************************************************
......
......@@ -2,7 +2,7 @@
* \file /core/tandem_run/tandemcondorprocess.h
* \date 5/9/2017
* \author Olivier Langella
* \brief handles execution of a bunch of X!Tandem process throught condor job
* \brief handles execution of a bunch of X!Tandem process through condor job
*/
/*******************************************************************************
......
......@@ -75,7 +75,7 @@
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Cantarell'; font-size:11pt; font-weight:400; font-style:normal;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">X!TandemPipeline C++ is developped by PAPPSO team (<a href="http://pappso.inra.fr"><span style=" text-decoration: underline; color:#0000ff;">http://pappso.inra.fr</span></a>).</p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">X!TandemPipeline C++ is developed by PAPPSO team (<a href="http://pappso.inra.fr"><span style=" text-decoration: underline; color:#0000ff;">http://pappso.inra.fr</span></a>).</p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">This software is distributed under the terms of the GNU General Public License.</p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
......
......@@ -3479,7 +3479,7 @@
<item row="7" column="0">
<widget class="QLabel" name="label_71">
<property name="text">
<string>Write spectrum informations</string>
<string>Write spectrum information</string>
</property>
</widget>
</item>
......
......@@ -2,7 +2,7 @@
* \file gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
* \date 25/01/2019
* \author Olivier Langella
* \brief all needed informations to write a MassChroqML file
* \brief all needed information to write a MassChroqML file
*/
/*******************************************************************************
......
......@@ -2,7 +2,7 @@
* \file gui/export/export_masschroq_dialog/masschroqfileparameters.h
* \date 25/01/2019
* \author Olivier Langella
* \brief all needed informations to write a MassChroqML file
* \brief all needed information to write a MassChroqML file
*/
/*******************************************************************************
......
......@@ -103,7 +103,7 @@
<item>
<widget class="QGroupBox" name="use_htcondor_groupbox">
<property name="title">
<string>&amp;run X!Tandem throught HTCondor</string>
<string>&amp;run X!Tandem through HTCondor</string>
</property>
<property name="checkable">
<bool>true</bool>
......
......@@ -438,7 +438,7 @@ TandemRunDialog::selectTdfFolder()
{
throw pappso::PappsoException(
tr(
"The directory %1/ dosent contain the mandatory analysis.tdf "
"The directory %1/ does not contain the mandatory analysis.tdf "
"file")
.arg(directory_name));
}
......
......@@ -3338,7 +3338,7 @@
<item row="7" column="0">
<widget class="QLabel" name="writeSpectrumInformationsLabel">
<property name="text">
<string>Write spectrum informations</string>
<string>Write spectrum information</string>
</property>
</widget>
</item>
......
......@@ -392,7 +392,7 @@ XtandemSaxHandler::startElement_domain(QXmlAttributes attributes)
_p_peptide_evidence->setChecked(true);
// missing informations
// missing information
// peptide.set_hypercorr(Float.valueOf(attrs.getValue("hyperscore")));
// peptide.set_pre(attrs.getValue("pre"));
// peptide.set_post(attrs.getValue("post"));
......
......@@ -41,7 +41,7 @@ InfoSheet::InfoSheet(OdsExport *p_ods_export,
{
_p_ods_export = p_ods_export;
_p_writer = p_writer;
p_writer->writeSheet("X!TandemPipeline informations");
p_writer->writeSheet("X!TandemPipeline information");
p_writer->writeCell("X!TandemPipeline version :");
p_writer->writeLine();
......
......@@ -412,7 +412,7 @@ ProticdbMl::writeIdentificationRun(IdentificationGroup *p_identification)
*/
_output_stream->writeEndElement(); // admin
// if we can retrieve original informations in xml xtandem results
// if we can retrieve original information in xml xtandem results
//
for(IdentificationDataSource *p_identification_data_source :
p_identification->getIdentificationDataSourceList())
......
......@@ -149,7 +149,7 @@ has been added. To specify additional sets of modifications, use the same parame
<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 &quot;1&quot;
but no &quot;2&quot; then processing stops at &quot;1&quot; even if there is a &quot;3&quot; 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
Processing is also stopped 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>
......
......@@ -130,7 +130,7 @@ below.</p>
</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
modification. Many biologically relevant 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>
......
......@@ -143,7 +143,7 @@ has been added. To specify additional sets of modifications, use the same parame
<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 &quot;1&quot;
but no &quot;2&quot; then processing stops at &quot;1&quot; even if there is a &quot;3&quot; 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
Processing is also stopped 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>
......
......@@ -116,7 +116,7 @@ X<sub>i</sub></span> is a single letter abbreviation for a type of amino acid re
<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
residues are often oxidized). Additionally, other residues may be have been modified in the original
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
......
......@@ -129,7 +129,7 @@ below.</p>
</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
modification. Many biologically relevant 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>
......
......@@ -116,7 +116,7 @@ sequence file, in valid BIOML format.</p>
<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
not included. The input file can either be an X! Tandem BIOML output 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
......
......@@ -115,7 +115,7 @@ td {
<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 &quot;.&quot; 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>,
been finished. For example, 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>
......
......@@ -112,7 +112,7 @@ td {
<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 &quot;mass&quot; of the molecule.
<p>Naturally occurring organic molecules do not have a single value corresponding to the &quot;mass&quot; 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 &quot;chemical&quot; or &quot;average&quot; mass of the
......@@ -120,8 +120,8 @@ molecule. When this parameter is set to <span class="v">average</span>, this wei
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 &quot;monoisotopic&quot; mass for the molecule (also refered to as the A0 peak). When this parameter is
only <sup>12</sup>C atoms. This lowest mass peak in the isotopic distribution measured is commonly referred to
as the &quot;monoisotopic&quot; mass for the molecule (also referred 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> |
......
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