Commit 7ebd9a46 authored by Filippo Rusconi's avatar Filippo Rusconi
Browse files

Going forward with doc, but modifs to the GUI also.

parent e3b5b110
......@@ -39,5 +39,5 @@ STYLEROOT="xslt"
#PROFOS=""
#PROFVENDOR=""
FOP_CMD_OPTIONS="-c /home/langella/developpement/git/xtandempipeline/doc/user-manual/fop.xconf"
FOP_CMD_OPTIONS="-c /home/rusconi/devel/xtpcpp/development/doc/user-manual/fop.xconf"
......@@ -31,7 +31,16 @@ xml:lang="en">
<xi:include href="generalities.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
</xi:include>
<xi:include href="graphical-user-interface.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
<xi:include href="main-program-window.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
</xi:include>
<xi:include href="running-xtandem-identifications.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
</xi:include>
<xi:include href="loading-identification-results.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
</xi:include>
<xi:include href="loading-xtandempipeline-project.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
</xi:include>
<xi:include href="gpl-3.0.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
......
......@@ -83,6 +83,61 @@ xml:id="chap_graphical-user-interface" version="5.0">
</listitem>
<listitem>
<para>
Load the data produced during the previous step;
<note>
<para>
&xtpcpp; can also handle peptide vs spectrum matches data (peptide
identification data) from other software with the following formats:
<itemizedlist>
<listitem>
<para>
mzIdentML;
</para>
</listitem>
<listitem>
<para>
pepXML;
</para>
</listitem>
<listitem>
<para>
FIXME: quels autres ? Soyons exhaustifs.
</para>
</listitem>
</itemizedlist>
</para>
</note>
</para>
</listitem>
<listitem>
<para>
......@@ -120,52 +175,88 @@ xml:id="chap_graphical-user-interface" version="5.0">
</para>
<sect1 xml:id="sec_starting-xtpcpp-working-session">
<title>Starting a new &xtpcpp; working session</title>
<para>
To start a session, run &xtpcpp; and the main program windows shows up as
described in <xref linkend="fig_xtpcpp-main-program-window"/>.
<figure xml:id="fig_xtpcpp-main-program-window">
<sect1 xml:id="sec_opening-mass-spectrometry-data-files">
<title>Main program window</title>
<title>Opening Mass Spectrometry Data Files</title>
<mediaobject>
<imageobject role="fo">
<imagedata fileref="print-xtpcpp-main-program-window.png" format="PNG" scale="100"/>
</imageobject>
<imageobject role="html">
<imagedata fileref="web-xtpcpp-main-program-window.png" format="PNG" scale="100"/>
</imageobject>
<caption>
<para>
The main program window contains three buttons described in detail in the text.
</para>
</caption>
</mediaobject>
</figure>
</para>
<para>
To start a session, open one or more mass spectra using the menu
The main program window contains three buttons that start the following functions:
<itemizedlist>
<listitem>
<para>
<guilabel> Run X!Tandem identifications</guilabel>. See <xref
linkend="chap_running-xtandem-identifications"/>.
<menuchoice>
</para>
<guimenu>File</guimenu>
</listitem>
<guimenuitem>Open mass spectrum file(s) in streamed mode</guimenuitem>
<listitem>
</menuchoice>
<para>
menu. &mineXp2; understands the mzML, mzXML and MGF formats. The file
loading procedures, for these formats, are delegated to the excellent
<filename class="libraryfile">libpwiz</filename> library from the
<application>ProteoWizard</application> project.<footnote><para>
<guilabel>Load identification results (mzIdentML, pepXML,
X!Tandem)</guilabel>. See <xref
linkend="chap_loading-identification-results"/>.
Please, see <link
xlink:href="http://proteowizard.sourceforge.net/"/></para></footnote>
Simple txt,&nbsp;asc data where &mz; and intensity values are separated
by any character that is neither a newline nor a dot nor a digit
(loading is handled by a private parser) can be loaded either from file
or directly from the clipboard.
</para>
</para>
</listitem>
<listitem>
<para>
<para>
There are two variants of the mass spectrometry file opening menu, one for
which the mass data are read from file and stored <emphasis>totally</emphasis>
in memory and one for which the mass data are read from file in
<emphasis>streamed mode</emphasis>, used to compute the TIC chromatogram and
discarded. The latter mode is useful when the mass data are so large that they
cannot fit in memory. Optionally, a table view can be displayed with all the
data in the MS run data set that was loaded from disk. The TIC chromatogram
or the table view can then be used to access the mass data in the file
according to criteria set by the user (retention time range, for example).
<guilabel>Load an X!TandemPipeline project</guilabel>. See <xref
linkend="chap_loading-xtandempipeline-project"/>.
</para>
</para>
</listitem>
</itemizedlist>
</para>
</sect1>
......@@ -315,11 +406,13 @@ xml:id="chap_graphical-user-interface" version="5.0">
<sect1 xml:id="sec_main-program-window-menu">
<title>The Main Program Window Menu</title>
<para>
The menu bar in the main program window displays a number of menu
items, reviewed below: </para>
items, reviewed below:
<itemizedlist>
......@@ -491,6 +584,9 @@ xml:id="chap_graphical-user-interface" version="5.0">
</itemizedlist>
</para>
</sect1>
......
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE chapter [
<!ENTITY % entities SYSTEM "pappso-user-manuals.ent">
%entities;
<!ENTITY % xtpcpp-entities SYSTEM "xtpcpp-entities.ent">
%xtpcpp-entities;
<!ENTITY % sgml.features "IGNORE">
<!ENTITY % xml.features "INCLUDE">
<!ENTITY % dbcent PUBLIC "-//OASIS//ENTITIES DocBook Character Entities V4.5//EN" "/usr/share/xml/docbook/schema/dtd/4.5/dbcentx.mod">
%dbcent;
]>
<chapter xmlns="http://docbook.org/ns/docbook"
xmlns:xlink="http://www.w3.org/1999/xlink"
xml:id="chap_loading-identification-results" version="5.0">
<info>
<title>Loading identification results</title>
<keywordset>
<keyword>identifications</keyword>
<keyword>peptide vs mass spectrum match</keyword>
</keywordset>
</info>
<para>
Text
</para>
</chapter>
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE chapter [
<!ENTITY % entities SYSTEM "pappso-user-manuals.ent">
%entities;
<!ENTITY % xtpcpp-entities SYSTEM "xtpcpp-entities.ent">
%xtpcpp-entities;
<!ENTITY % sgml.features "IGNORE">
<!ENTITY % xml.features "INCLUDE">
<!ENTITY % dbcent PUBLIC "-//OASIS//ENTITIES DocBook Character Entities V4.5//EN" "/usr/share/xml/docbook/schema/dtd/4.5/dbcentx.mod">
%dbcent;
]>
<chapter xmlns="http://docbook.org/ns/docbook"
xmlns:xlink="http://www.w3.org/1999/xlink"
xml:id="chap_loading-xtandempipeline-project" version="5.0">
<info>
<title>Loading an &xtpcpp; project</title>
<keywordset>
<keyword>identifications</keyword>
<keyword>peptide vs mass spectrum match</keyword>
</keywordset>
</info>
<para>
Text
</para>
</chapter>
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE chapter [
<!ENTITY % entities SYSTEM "pappso-user-manuals.ent">
%entities;
<!ENTITY % xtpcpp-entities SYSTEM "xtpcpp-entities.ent">
%xtpcpp-entities;
<!ENTITY % sgml.features "IGNORE">
<!ENTITY % xml.features "INCLUDE">
<!ENTITY % dbcent PUBLIC "-//OASIS//ENTITIES DocBook Character Entities V4.5//EN" "/usr/share/xml/docbook/schema/dtd/4.5/dbcentx.mod">
%dbcent;
]>
<chapter xmlns="http://docbook.org/ns/docbook"
xmlns:xlink="http://www.w3.org/1999/xlink"
xml:id="chap_main-program-window" version="5.0">
<info>
<title>The main program window</title>
<keywordset>
<keyword>graphical user interface</keyword>
<keyword>GUI</keyword>
</keywordset>
</info>
<para>
Proteomics data explorations, with &xtpcpp;, entail, for a large part, the
following steps:
<itemizedlist>
<listitem>
<para>
Configuration of the &xtandem; external software that runs the database
searches (producing peptide vs mass spectrum matches, leading to the
peptide identifications);
</para>
</listitem>
<listitem>
<para>
Configuration of the protein database files (both the organism-specific
protein databases and optional contaminant-containing databases);
</para>
</listitem>
<listitem>
<para>
Loading of the mass spectrometry data acquisition files (the mzML format
is recommended);
</para>
</listitem>
<listitem>
<para>
Running of &xtandem; from inside of &xtpcpp;, with production of a set of
peptide vs mass spectrum matches (peptide identification results);
</para>
</listitem>
<listitem>
<para>
Loading of the identification results produced during the previous step
(or by another protein database searching program);
<note>
<para>
&xtpcpp; can also handle peptide vs spectrum matches data (peptide
identification data) from other software with the following formats:
<itemizedlist>
<listitem>
<para>
mzIdentML;
</para>
</listitem>
<listitem>
<para>
pepXML;
</para>
</listitem>
<listitem>
<para>
FIXME: quels autres ? Soyons exhaustifs.
</para>
</listitem>
</itemizedlist>
</para>
</note>
</para>
</listitem>
<listitem>
<para>
Relentless scrutiny of the peptide identification results. Optional
modification of the results;
</para>
</listitem>
<listitem>
<para>
Protein inference, that is, protein identification on the basis of the
peptide identifications. &xtpcpp; has a powerful interface to ease the
scrutiny of the protein groups (<quote>grouping</quote>) that leads
ultimately to protein identification. The protein groups, as calculated
by &xtpcpp;, can be modified by the user.
</para>
</listitem>
</itemizedlist>
</para>
<para>
In this chapter, &xtpcpp;'s main window user interface is described in detail.
</para>
<sect1 xml:id="sec_starting-xtpcpp-working-session">
<title>Starting a new &xtpcpp; working session</title>
<para>
To start a session, run &xtpcpp; and the main program windows shows up as
described in <xref linkend="fig_xtpcpp-main-program-window"/>.
<figure xml:id="fig_xtpcpp-main-program-window">
<title>Main program window</title>
<mediaobject>
<imageobject role="fo">
<imagedata fileref="print-xtpcpp-main-program-window.png" format="PNG" scale="100"/>
</imageobject>
<imageobject role="html">
<imagedata fileref="web-xtpcpp-main-program-window.png" format="PNG" scale="100"/>
</imageobject>
<caption>
<para>
The main program window contains three buttons described in detail in the text.
</para>
</caption>
</mediaobject>
</figure>
</para>
<para>
The main program window contains three buttons that start the following functions:
<itemizedlist>
<listitem>
<para>
<guilabel> Run X!Tandem identifications</guilabel>. See <xref
linkend="chap_running-xtandem-identifications"/>.
</para>
</listitem>
<listitem>
<para>
<guilabel>Load identification results (mzIdentML, pepXML,
X!Tandem)</guilabel>. See <xref
linkend="chap_loading-identification-results"/>.
</para>
</listitem>
<listitem>
<para>
<guilabel>Load an X!TandemPipeline project</guilabel>. See <xref
linkend="chap_loading-xtandempipeline-project"/>.
</para>
</listitem>
</itemizedlist>
</para>
</sect1>
<sect1>
<title>The Window Layout</title>
<para>The graphical interface of comprises a number of windows where data
and informations are displayed. When first started, the program shows the
main program window. Upon loading of a MS run data set from file, new
windows do show up as described below (see <xref
linkend="fig_minexpert-whole-window-set"/>):</para>
<itemizedlist>
<listitem>
<para>
<guilabel>mineXpert2</guilabel> main program window: this is an unintrusive
window sporting the main menu; </para>
</listitem>
<listitem>
<para>
The <guilabel>Task monitors</guilabel> window, that displays all the
ongoing tasks, always providing the user the ability to cancel an
ongoing task; </para> </listitem>