From 67594472bd8920efa45169478981b700b79ae683 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 9 Feb 2007 18:00:40 +0000
Subject: [PATCH] added command line help documentation and preferences help
 to contents. Documented SHOW_OVERVIEW property in
 preferences.

---
 help/help.jhm                       |    2 ++
 help/helpTOC.xml                    |    6 +++++-
 help/html/features/preferences.html |    3 +++
 help/html/releases.html             |    7 ++++++-
 help/html/whatsNew.html             |    1 +
 5 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/help/help.jhm b/help/help.jhm
index 1ff788f..056a813 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -23,6 +23,8 @@
    <mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>
    <mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
    <mapID target="preferences" url="html/features/preferences.html"/>     
+   <mapID target="commandline" url="html/features/commandline.html"/>
+   <mapID target="clarguments" url="html/features/clarguments.html"/>
    <mapID target="io" url="html/io/index.html"/>
    <mapID target="io.modellerpir" url="html/io/modellerpir.html"/>
    <mapID target="export" url="html/io/export.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index fc52348..7d9e595 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -76,11 +76,15 @@
 		<tocitem text="Popup Menu" target="popMenu"/>
                 </tocitem>
 	</tocitem>
+        <tocitem text="Preferences" target="preferences"/>
 	<tocitem text="Memory Settings" target="memory" expand="false">
           <tocitem text="JNLP with extra memory parameters" target="jalviewjnlp"/>
           </tocitem>
+        <tocitem text="Command Line" target="commandline" expand="false">
+          <tocitem text="Command Line Arguments" target="clarguments"/>
+        </tocitem>
 </tocitem>
-<tocitem text="Useful information" expand="true">
+<tocitem text="Useful information" expa nd="true">
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>
 	<tocitem text="Amino Acid Properties" target="aaProperties"/>
 	<tocitem text="The Genetic Code" target="geneticCode"/>
diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 55ccf51..0abce06 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -26,6 +26,9 @@
 <p><strong><a name="visual">Visual</a> Preferences tab</strong></p>
 <p><em>Maximise Window</em> - If this is selected, a new alignment window will stretch 
   to fit the available space.</p>
+<p><em>Show Overview Window</em> - When this is selected, the <a
+  href="overview.html">alignment overview</a> panel is opened by
+  default for a new alignment window.</p>
 <p><em>Show Annotations</em> - If this is selected the new window will display an annotation 
   panel below the sequences. This annotation panel may have several rows describing 
   the whole alignment. The 3 standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em> 
diff --git a/help/html/releases.html b/help/html/releases.html
index 8026219..5cdf8a5 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -16,7 +16,12 @@
         <li>Annotations/Features can be imported/exported to the applet via textbox
         <li>Applet allows editing of sequence/annotation/group name &amp; description
         <li>Preference setting to display sequence name in italics
-        <li>Annotation file format extended to allow Sequence_groups to be defined</ul></td>
+        <li>Annotation file format extended to allow Sequence_groups
+        to be defined
+        <li>Default opening of alignment overview panel can be specified in
+        preferences
+        <li>PDB residue numbering annotation added to associated sequences
+        </ul></td>
     <td> <ul>
         <li>Applet crash under certain Linux OS with Java 1.6 installed
         <li>Annotation file export / import bugs fixed
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index c6389d9..6989dd4 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -11,6 +11,7 @@
 <p>Applet allows editing of sequence/annotation/group name &amp; description </p>
 <p>Preference setting to display sequence name in italics </p>
 <p>Annotation file format extended to allow Sequence_groups to be defined</p>
+<p>Default opening of alignment overview panel can be specified in preferences</p>
 <p>&nbsp;</p>
 <p><strong>Issues Resolved</strong></p>
 <p><br>
-- 
1.7.10.2