From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 14 Aug 2006 15:22:36 +0000 (+0000)
Subject: 2.1 updates
X-Git-Tag: Release_2_1~68
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3b58e33030c6cfe56564d17edcb9d81b750398fe;p=jalview.git

2.1 updates
---

diff --git a/help/help.jhm b/help/help.jhm
index 3790abe..8c314d3 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -26,6 +26,7 @@
    <mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>
    <mapID target="features.fileformat" url="html/features/featuresFormat.html"/>
    <mapID target="das.settings" url="html/features/dassettings.html"/>
+   <mapID target="das.viewing" url="html/features/dasfeatures.html"/>
    <mapID target="edit" url="html/editing/index.html"/>
    <mapID target="jalarchive" url="html/features/jalarchive.html"/>
    <mapID target="trees" url="html/calculations/tree.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 9265599..d08e3d2 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -19,7 +19,7 @@
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
           <tocitem text="User Defined Sequence Features" target="search"/>
-          <tocitem text="DAS Features Settings" target="das.settings"/>
+          <tocitem text="DAS Features Settings" target="das.viewing"/>
         </tocitem>
 	<tocitem text="Web Services" target="webservice" expand="false">
 		<tocitem text="Clustal Alignment" target="clustal"/>
diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html
index 5283e38..9efa19f 100755
--- 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
 automatically try to fetch sequence features (as described below).</p>
 <p><strong>View&#8594;Sequence Feature Settings...</strong>
-<p>Once sequence features have been loaded, their display can be fully
-  controlled using the alignment window's <a
-  href="featuresettings.html">Sequence Feature Settings</a> dialog
-  box. Feature colour schemes and display parameters are unique to a
-  particular alignment, so it is possible to colour the same sequence
-  features differently in different alignment views.</p>
-<p><strong>View&#8594;Fetch Sequence Features</strong></p>
-<p>When this option is selected, sequence features extracted from the
-  <a href="http://www.ebi.uniprot.org/index.html">Uniprot (http://www.ebi.unprot.org/index.html)</a>
-  record for each sequence are displayed on the alignment.</p>
-<p>Jalview will attempt to retrieve sequence features from Uniprot files using
-  the EBI dbFetch web service using the given sequence names (or
-  Uniprot ID, if available). A 100% match with
-  the Uniprot record is required for Uniprot features to be view on a sequence.</p>
-<p>More information about the feature is given in a tooltip, which is viewed by
-  moving the mouse pointer over a sequence feature. The description associated
-  with the feature will then be displayed in a small label near the pointer.</p>
-<p><strong>The Sequence Identification Process</strong>
-
-  </p>
-<p>The first step in the procedure for matching uniprot IDs to
-  sequences is to use the ID (name) of
-  each sequence to retrieve Uniprot records directly.</p>
-<p>
-  If a uniprot record (or set of records) is found for a sequence,
-  then the sequence is aligned to the one in the Uniprot record
-  to determine the correct start and end residue positions (which are
-  displayed when the 'Show Full Sequence ID' option is set).
-</p>
-
-<p>If the alignment reveals differences between the sequence in the
-  alignment and the one in the record, then Jalview will assume that
-  the aligned sequence is not the one in the uniprot record.
-
-  </p>
-
-  <p>
-  In some cases, the ID used to retrieve Uniprot records may be out of
-  date and you will be notified of that a 100% match between the
-  sequence and a Uniprot record was identified, but the sequence name
-  must be manually changed (by right clicking on the sequence ID and selecting
-  <strong>Sequence&#8594;Edit Name</strong>), before Jalview will show its sequence
-  features.
-<ul>
-  <li>remember to save your alignment if you have updated any of the sequence
-    IDs! </li>
-</ul>
+<p>Once sequence features have been loaded, their display can be fully controlled 
+  using the alignment window's <a
+  href="featuresettings.html">Sequence Feature Settings</a> dialog box. Feature 
+  colour schemes and display parameters are unique to a particular alignment, 
+  so it is possible to colour the same sequence features differently in different 
+  alignment views.<br>
+  Since Jalview 2.1, it is possible to add <a href="dassettings.html">DAS features</a> 
+  to an alignment via the DAS tabbed pane of the feature settings window. </p>
 <p>Precalculated Sequence Features may be added to an alignment from the command
   line, drag and drop, or from the &quot;File-&gt;Load Features / Annotations&quot;
   menu item. See the <a href="featuresFormat.html">Features File Format</a> for