2.1 updates

diff --git a/help/help.jhm b/help/help.jhm
index 3790abe..8c314d3 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -26,6 +26,7 @@
    <mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>\r
    <mapID target="features.fileformat" url="html/features/featuresFormat.html"/>\r
    <mapID target="das.settings" url="html/features/dassettings.html"/>\r
+   <mapID target="das.viewing" url="html/features/dasfeatures.html"/>\r
    <mapID target="edit" url="html/editing/index.html"/>\r
    <mapID target="jalarchive" url="html/features/jalarchive.html"/>\r
    <mapID target="trees" url="html/calculations/tree.html"/>\r

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 9265599..d08e3d2 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -19,7 +19,7 @@
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
           <tocitem text="Sequence Features File" target="features.fileformat"/>\r
           <tocitem text="User Defined Sequence Features" target="search"/>\r
-          <tocitem text="DAS Features Settings" target="das.settings"/>\r
+          <tocitem text="DAS Features Settings" target="das.viewing"/>\r
         </tocitem>\r
        <tocitem text="Web Services" target="webservice" expand="false">\r
                <tocitem text="Clustal Alignment" target="clustal"/>\r

diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html
index 5283e38..9efa19f 100755 (executable)
--- a/help/html/features/seqfeatures.html
+++ b/help/html/features/seqfeatures.html
@@ -27,53 +27,14 @@ and pasted into other alignment windows.</p>
 feature retrieval has not already been carried out, then Jalview will\r
 automatically try to fetch sequence features (as described below).</p>\r
 <p><strong>View&#8594;Sequence Feature Settings...</strong>\r
-<p>Once sequence features have been loaded, their display can be fully\r
-  controlled using the alignment window's <a\r
-  href="featuresettings.html">Sequence Feature Settings</a> dialog\r
-  box. Feature colour schemes and display parameters are unique to a\r
-  particular alignment, so it is possible to colour the same sequence\r
-  features differently in different alignment views.</p>\r
-<p><strong>View&#8594;Fetch Sequence Features</strong></p>\r
-<p>When this option is selected, sequence features extracted from the\r
-  <a href="http://www.ebi.uniprot.org/index.html">Uniprot (http://www.ebi.unprot.org/index.html)</a>\r
-  record for each sequence are displayed on the alignment.</p>\r
-<p>Jalview will attempt to retrieve sequence features from Uniprot files using\r
-  the EBI dbFetch web service using the given sequence names (or\r
-  Uniprot ID, if available). A 100% match with\r
-  the Uniprot record is required for Uniprot features to be view on a sequence.</p>\r
-<p>More information about the feature is given in a tooltip, which is viewed by\r
-  moving the mouse pointer over a sequence feature. The description associated\r
-  with the feature will then be displayed in a small label near the pointer.</p>\r
-<p><strong>The Sequence Identification Process</strong>\r
-\r
-  </p>\r
-<p>The first step in the procedure for matching uniprot IDs to\r
-  sequences is to use the ID (name) of\r
-  each sequence to retrieve Uniprot records directly.</p>\r
-<p>\r
-  If a uniprot record (or set of records) is found for a sequence,\r
-  then the sequence is aligned to the one in the Uniprot record\r
-  to determine the correct start and end residue positions (which are\r
-  displayed when the 'Show Full Sequence ID' option is set).\r
-</p>\r
-\r
-<p>If the alignment reveals differences between the sequence in the\r
-  alignment and the one in the record, then Jalview will assume that\r
-  the aligned sequence is not the one in the uniprot record.\r
-\r
-  </p>\r
-\r
-  <p>\r
-  In some cases, the ID used to retrieve Uniprot records may be out of\r
-  date and you will be notified of that a 100% match between the\r
-  sequence and a Uniprot record was identified, but the sequence name\r
-  must be manually changed (by right clicking on the sequence ID and selecting\r
-  <strong>Sequence&#8594;Edit Name</strong>), before Jalview will show its sequence\r
-  features.\r
-<ul>\r
-  <li>remember to save your alignment if you have updated any of the sequence\r
-    IDs! </li>\r
-</ul>\r
+<p>Once sequence features have been loaded, their display can be fully controlled \r
+  using the alignment window's <a\r
+  href="featuresettings.html">Sequence Feature Settings</a> dialog box. Feature \r
+  colour schemes and display parameters are unique to a particular alignment, \r
+  so it is possible to colour the same sequence features differently in different \r
+  alignment views.<br>\r
+  Since Jalview 2.1, it is possible to add <a href="dassettings.html">DAS features</a> \r
+  to an alignment via the DAS tabbed pane of the feature settings window. </p>\r
 <p>Precalculated Sequence Features may be added to an alignment from the command\r
   line, drag and drop, or from the &quot;File-&gt;Load Features / Annotations&quot;\r
   menu item. See the <a href="featuresFormat.html">Features File Format</a> for\r