2.1 updates

diff --git a/help/help.jhm b/help/help.jhm
index 16e620f..210933b 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -53,6 +53,7 @@
    \r
    <mapID target="calcs.alquality" url="html/calculations/quality.html"/>   \r
    <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>\r
+   <mapID target="calcs.consensus" url="html/calculations/consensus.html"/>\r
    \r
    <mapID target="menus" url="html/menus/index.html"/>\r
    <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>\r

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 6630a0a..09c7125 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -17,6 +17,7 @@
        <tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
           <tocitem text="Conservation" target="calcs.alconserv"/>\r
           <tocitem text="Quality" target="calcs.alquality"/>\r
+          <tocitem text="Consensus" target="calcs.consensus"/>\r
           <tocitem text="Annotations File Format" target="annotations.fileformat"/>\r
         </tocitem>\r
        <tocitem text="Input / Output" target="io"/>\r

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 0390e25..e5c08ed 100755 (executable)
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -18,7 +18,9 @@
     files. </li>\r
   <li>The <a href="#editing"><strong>&quot;Editing&quot;</strong> Preferences</a> \r
     tab contains settings affecting the export of sequence alignments and EPS \r
-    f</li>\r
+    files.</li>\r
+  <li>The <a href="#editing"><strong>&quot;DAS Settings&quot;</strong> Preferences</a> \r
+    tab allows you to select which DAS sources to use when fetching DAS Features.</li>\r
 </ul>\r
 </p>\r
 <p><strong><a name="visual">Visual</a> Preferences tab</strong></p>\r
@@ -35,6 +37,8 @@
   alignment window. </p>\r
 <p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster rendering \r
   of the alignment.</p>\r
+<p><em>Wrap Alignment</em> - Select whether to open new alignment windows in wrapped \r
+  mode or not.</p>\r
 <p><em>Gap Symbol</em> - The default gap symbol may be set to either &quot;-&quot; or &quot;.&quot;</p>\r
 <p><em>Colour</em> - The default colour scheme for a new alignment window. If \r
   the chosen option is &quot;User Defined&quot; then the last User Defined Colour \r
@@ -111,6 +115,8 @@ the program reading the EPS file.
   this setting. </p>\r
 <p><em>Pad gaps when editing</em> - New alignment windows will &quot;Pad Gaps&quot; \r
   according to this setting.</p>\r
+<p><a name="editing"><strong>DAS Settings </strong></a></p>\r
+<p>See <a href="dassettings.html">DAS Settings</a></p>\r
 <p>&nbsp;</p>\r
 <p>&nbsp;</p>\r
 </body>\r