added command line help documentation and preferences help to

contents. Documented SHOW_OVERVIEW property in preferences.

diff --git a/help/help.jhm b/help/help.jhm
index 1ff788f..056a813 100755 (executable)
--- 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 (executable)
--- 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 (executable)
--- 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>\r
 <p><em>Maximise Window</em> - If this is selected, a new alignment window will stretch \r
   to fit the available space.</p>\r
+<p><em>Show Overview Window</em> - When this is selected, the <a\r
+  href="overview.html">alignment overview</a> panel is opened by\r
+  default for a new alignment window.</p>\r
 <p><em>Show Annotations</em> - If this is selected the new window will display an annotation \r
   panel below the sequences. This annotation panel may have several rows describing \r
   the whole alignment. The 3 standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em> \r

diff --git a/help/html/releases.html b/help/html/releases.html
index 8026219..5cdf8a5 100755 (executable)
--- 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\r
         <li>Applet allows editing of sequence/annotation/group name &amp; description\r
         <li>Preference setting to display sequence name in italics\r
-        <li>Annotation file format extended to allow Sequence_groups to be defined</ul></td>\r
+        <li>Annotation file format extended to allow Sequence_groups\r
+        to be defined\r
+        <li>Default opening of alignment overview panel can be specified in\r
+        preferences\r
+        <li>PDB residue numbering annotation added to associated sequences\r
+        </ul></td>\r
     <td> <ul>\r
         <li>Applet crash under certain Linux OS with Java 1.6 installed\r
         <li>Annotation file export / import bugs fixed\r

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index c6389d9..6989dd4 100755 (executable)
--- 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>\r
 <p>Preference setting to display sequence name in italics </p>\r
 <p>Annotation file format extended to allow Sequence_groups to be defined</p>\r
+<p>Default opening of alignment overview panel can be specified in preferences</p>\r
 <p>&nbsp;</p>\r
 <p><strong>Issues Resolved</strong></p>\r
 <p><br>\r