Commit 0bb8b194 authored by Filippo Rusconi's avatar Filippo Rusconi
Browse files

Re-reading of the doc.

parent cfa8c37f
......@@ -31,17 +31,11 @@ xml:lang="en">
<xi:include href="generalities.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
</xi:include>
<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="main-program-window.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="exploring-identification-data.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">
</xi:include>
......
......@@ -157,9 +157,9 @@ xml:id="chap_main-program-window" version="5.0">
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.
scrutiny of the FIXME : peptide|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>
......@@ -171,9 +171,9 @@ xml:id="chap_main-program-window" version="5.0">
<para>
In this chapter, &xtpcpp;'s main window user interface is described in detail,
in particular in the way it is a starting point for the main tasks described
above. Each specific task will be described in a chapter on its own.
In this chapter, &xtpcpp;'s main window's user interface is described in
detail, in particular in the way it is a starting point for the main tasks
described above.
</para>
......@@ -251,7 +251,7 @@ xml:id="chap_main-program-window" version="5.0">
<para>
<guilabel>Load an X!TandemPipeline project</guilabel>. See <xref
linkend="chap_loading-xtandempipeline-project"/>.
linkend="sec_loading-xtandempipeline-projects"/>.
</para>
......@@ -343,9 +343,9 @@ xml:id="chap_main-program-window" version="5.0">
<guilabel>Choose presets</guilabel>: This setting defines the
parameters that &xtandem; must use. Either load already known presets
from the drop-down list or edit them (or create a new set) by clicking
onto the <guilabel>Edit</guilabel> button. Note that to load a
preexisting presets file, it might be necessary to point &xtpcpp; to
from the drop-down list widget or edit them (or create a new set) by
clicking onto the <guilabel>Edit</guilabel> button. Note that to load
a preexisting presets file, it might be necessary to point &xtpcpp; to
the presets file-containing directory. Use the folder icon for this.
</para>
......@@ -379,7 +379,7 @@ xml:id="chap_main-program-window" version="5.0">
&xtandem; software. As many files as necessary might be added in the
list.
<note>
<tip>
<para>
......@@ -390,7 +390,7 @@ xml:id="chap_main-program-window" version="5.0">
</para>
</note>
</tip>
</para>
......@@ -415,7 +415,11 @@ xml:id="chap_main-program-window" version="5.0">
<guilabel>Number of threads</guilabel>: This setting defines the
maximum number of execution threads that &xtandem; might be using
during its run. </para> </listitem>
during its run.
</para>
</listitem>
</itemizedlist>
......@@ -457,7 +461,7 @@ xml:id="chap_main-program-window" version="5.0">
The configuration of the &xtandem; presets is performed in this
configuration window. Each parameter is associated to a manual page
that can be displayed by clicking on the interrogation mark button
next to it. It is possible to load existing presets from file or
next to it. It is possible to load existing presets from file or to
create brand new ones.
</para>
......@@ -475,15 +479,16 @@ xml:id="chap_main-program-window" version="5.0">
<para>
It is possible to load existing &xtandem; presets configurations (in
particular if the samples most often come from the same instrument using
the same configuration) by first pointing &xtpcpp; to the right directory
that contains the presets configuration file of interest (folder icon in <xref
It is possible to load existing &xtandem; presets configurations (which is
useful in particular if the samples most often come from the same
instrument using the same configuration) by first pointing &xtpcpp; to the
right directory that contains the presets configuration file of interest
(folder icon in <xref
linkend="fig_xtpcpp-xtandem-presets-configuration-spectrum-tab"/>). The
presets configuration files in the chosen directory are automatically
detected and listed in the drop-down list. At this point, select the file
of interest from that list and click onto the <guilabel>Load</guilabel>
button.
detected and listed in the drop-down list widget. At this point, select
from that list the file of interest and click onto the
<guilabel>Load</guilabel> button.
<warning>
......@@ -508,9 +513,9 @@ xml:id="chap_main-program-window" version="5.0">
It is possible to create a new presets configuration in a new file by
clicking onto the <guilabel>New</guilabel> button. This open an input
dialog window into which the user defines a new file name (the edit widget
is preset with the currently loaded file's name augmented with the
<emphasis>_copy</emphasis> suffix).
dialog window for the user to define a new file name (the edit widget is
preset with the currently loaded file's name suffixed with
<emphasis>_copy</emphasis>).
</para>
......@@ -531,9 +536,9 @@ xml:id="chap_main-program-window" version="5.0">
</sect2>
<sect2 xml:id="sec_actual-xtandem-configuration-settings">
<sect2 xml:id="sec_actual-xtandem-presets-configuration">
<title>Actual &xtandem; configuration settings</title>
<title>Actual &xtandem; presets configuration</title>
<para>
......@@ -625,7 +630,7 @@ xml:id="chap_main-program-window" version="5.0">
</sect1>
<sect1 xml:id="sec_loading-identification-results">
<title>Loading identification results</title>
<para>
......@@ -633,42 +638,108 @@ xml:id="chap_main-program-window" version="5.0">
The loading of identification results comes with a minimal set of
configuration required to instruct &xtpcpp; on the way to handle contaminant
proteins, for example. This process is pictured in <xref
linkend="fig_xtpcpp-load-identification-results-window"/> and described in this
section.
linkend="fig_xtpcpp-load-identification-results-window"/> and described in
this section.
</para>
<figure xml:id="fig_xtpcpp-load-identification-results-window">
<figure xml:id="fig_xtpcpp-load-identification-results-window">
<title>&xtandem; presets configuration window</title>
<title>&xtandem; presets configuration window</title>
<mediaobject>
<mediaobject>
<imageobject role="fo">
<imagedata fileref="print-xtpcpp-load-identification-results-window.png" format="PNG" scale="80"/>
</imageobject>
<imageobject role="html">
<imagedata fileref="web-xtpcpp-load-identification-results-window.png" format="PNG" scale="100"/>
</imageobject>
<imageobject role="fo">
<caption>
<imagedata
fileref="print-xtpcpp-load-identification-results-window.png"
format="PNG" scale="80"/>
<para>
</imageobject>
Loading identification results comes with some configuration that is
described in the text.
<imageobject role="html">
</para>
<imagedata fileref="web-xtpcpp-load-identification-results-window.png"
format="PNG" scale="100"/>
</caption>
</imageobject>
</mediaobject>
<caption>
</figure>
<para>
Loading identification results comes with some configuration that is
described in the text.
</para>
</caption>
</mediaobject>
</figure>
<sect2 xml:id="sec_saving-xtandempipeline-projects">
<title>Saving &xtpcpp; projects</title>
<para>
Once exploration and optional modication of the identification data have
been performed, the user can save the resulting data set into a &xtpcpp;
project by selecting the <guimenuitem>Save project</guimenuitem> menu item
of the <guimenu>File</guimenu> menu in the main program window (the
extension of the file name typically should be <filename
class="extension">xpip</filename>). See <xref
linkend="sec_loading-xtandempipeline-projects"/> for loading such a
project.
</para>
</sect2>
</sect1>
<sect1 xml:id="sec_loading-xtandempipeline-projects">
<title>Loading &xtpcpp; projects</title>
<para>
Loading of &xtpcpp; project files (file of <filename
class="extension">xpip</filename>) extension) is only possible if the user
has previously
<itemizedlist>
<listitem>
<para>
Loaded identification results;
</para>
</listitem>
<listitem>
<para>
Saved the data to an &xtpcpp; project file using the <guimenuitem>Save
project</guimenuitem> menu item of the <guimenu>File</guimenu> menu in
the main program window.
</para>
</listitem>
</itemizedlist>
</para>
</sect1>
</chapter>
......@@ -15,7 +15,7 @@
<!ENTITY xpm "<application>XpertMiner</application>">
<!ENTITY emdash "—">
<!ENTITY ellipsis "&#8230;">
<!ENTITY ellip "&#8230;">
<!-- nbnsp is non breaking *no* space, that is a non breaking no-width space-->
<!ENTITY nbnsp "&#xFEFF;">
......
<?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_running-xtandem-identifications" version="5.0">
<info>
<title>Running &xtandem; identifications</title>
<keywordset>
<keyword>identifications</keyword>
<keyword>peptide vs mass spectrum match</keyword>
</keywordset>
</info>
<para>
This chapter describes in detail all the steps that are required to perform
&xtandem;-based identifications, starting from mass spectrometry data files
and protein databases.
</para>
<para>
Clicking onto the <guilabel>Run X!Tandem identifcations</guilabel> button (see
<xref linkend="sec_starting-xtpcpp-working-session"/>), opens the
configuration window shown in <xref
linkend="fig_xtpcpp-xtandem-configuration-window"/>.
</para>
<sect1 xml:id="sec_configuration-xtandem-run">
<title>Configuration of the &xtandem; run</title>
<para>
Text
</para>
</sect1>
</chapter>
......@@ -435,6 +435,9 @@
<layout class="QHBoxLayout" name="horizontalLayout">
<item>
<widget class="QLabel" name="label">
<property name="toolTip">
<string>Max. number of threads that X!Tandem is allowed to use</string>
</property>
<property name="text">
<string>Number of threads</string>
</property>
......@@ -442,6 +445,9 @@
</item>
<item>
<widget class="QSpinBox" name="thread_spin_box">
<property name="toolTip">
<string>Max. number of threads that X!Tandem is allowed to use</string>
</property>
<property name="minimum">
<number>1</number>
</property>
......
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