From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 11 Aug 2006 14:20:21 +0000 (+0000)
Subject: 2.1 updates
X-Git-Tag: Release_2_1~103
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9fb80b5bf530d18172a8e01d31d8c3555591a1bb;hp=c0a695cebfd9a86be228472be431096fa9dc281d;p=jalview.git

2.1 updates
---

diff --git a/help/help.jhm b/help/help.jhm
index 16e620f..210933b 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -53,6 +53,7 @@
    
    <mapID target="calcs.alquality" url="html/calculations/quality.html"/>   
    <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
+   <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>
    
    <mapID target="menus" url="html/menus/index.html"/>
    <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 6630a0a..09c7125 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -17,6 +17,7 @@
       	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
           <tocitem text="Conservation" target="calcs.alconserv"/>
           <tocitem text="Quality" target="calcs.alquality"/>
+          <tocitem text="Consensus" target="calcs.consensus"/>
           <tocitem text="Annotations File Format" target="annotations.fileformat"/>
         </tocitem>
 	<tocitem text="Input / Output" target="io"/>
diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 0390e25..e5c08ed 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -18,7 +18,9 @@
     files. </li>
   <li>The <a href="#editing"><strong>&quot;Editing&quot;</strong> Preferences</a> 
     tab contains settings affecting the export of sequence alignments and EPS 
-    f</li>
+    files.</li>
+  <li>The <a href="#editing"><strong>&quot;DAS Settings&quot;</strong> Preferences</a> 
+    tab allows you to select which DAS sources to use when fetching DAS Features.</li>
 </ul>
 </p>
 <p><strong><a name="visual">Visual</a> Preferences tab</strong></p>
@@ -35,6 +37,8 @@
   alignment window. </p>
 <p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster rendering 
   of the alignment.</p>
+<p><em>Wrap Alignment</em> - Select whether to open new alignment windows in wrapped 
+  mode or not.</p>
 <p><em>Gap Symbol</em> - The default gap symbol may be set to either &quot;-&quot; or &quot;.&quot;</p>
 <p><em>Colour</em> - The default colour scheme for a new alignment window. If 
   the chosen option is &quot;User Defined&quot; then the last User Defined Colour 
@@ -111,6 +115,8 @@ the program reading the EPS file.
   this setting. </p>
 <p><em>Pad gaps when editing</em> - New alignment windows will &quot;Pad Gaps&quot; 
   according to this setting.</p>
+<p><a name="editing"><strong>DAS Settings </strong></a></p>
+<p>See <a href="dassettings.html">DAS Settings</a></p>
 <p>&nbsp;</p>
 <p>&nbsp;</p>
 </body>