Another progress.

doc/user-manual/xml/main-program-window.xml

@@ -228,7 +228,7 @@ xml:id="chap_main-program-window" version="5.0">
         <para>
 
           <guilabel>Run X!Tandem identifications</guilabel>. See <xref
-          linkend="chap_running-xtandem-identifications"/>.
+          linkend="sec_running-xtandem-identifications"/>.
 
         </para>
 
@@ -240,7 +240,7 @@ xml:id="chap_main-program-window" version="5.0">
 
           <guilabel>Load identification results (mzIdentML, pepXML,
           X!Tandem)</guilabel>. See <xref
-          linkend="chap_loading-identification-results"/>.
+          linkend="sec_loading-identification-results"/>.
 
         </para>
 
@@ -614,7 +614,9 @@ xml:id="chap_main-program-window" version="5.0">
       linkend="fig_xtpcpp-main-program-window"/>). From there, it is possible to
       open the &xtandem; results file located in the output directory configured
       above. There are as many output files (XML-based format, and xml
-      extension) as there were mass spectrometry data files to process.
+      extension) as there were mass spectrometry data files to process. The
+      loading of the results files is described in <xref
+      linkend="sec_loading-identification-results"/>.
 
     </para>
 
@@ -622,5 +624,51 @@ xml:id="chap_main-program-window" version="5.0">
 
 </sect1>
 
+<sect1 xml:id="sec_loading-identification-results">
+  
+  <title>Loading identification results</title>
+
+  <para>
+
+    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.
+
+  </para>
+
+
+    <figure xml:id="fig_xtpcpp-load-identification-results-window">
+
+      <title>&xtandem; presets configuration window</title>
+
+      <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>
+
+        <caption>
+
+          <para>
+
+            Loading identification results comes with some configuration that is
+            described in the text. 
+
+          </para>
+
+        </caption>
+
+      </mediaobject>
+
+    </figure>
+
+
+
+</sect1>
 
 </chapter>