doco changes.

[jalview.git] / help / html / features / seqfeatures.html

diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html
index 2a57e63..2217c29 100755 (executable)
--- a/help/html/features/seqfeatures.html
+++ b/help/html/features/seqfeatures.html
@@ -4,8 +4,24 @@
 <p><strong>Sequence Features</strong></p>\r
 <p>Jalview can colour parts of a sequence based on the presence of\r
 sequence features - which may be retrieved from database records (such\r
-as Uniprot), the result of <a href="../search.html">sequence motif\r
-searches</a> or simply read from a <a href="featuresFormat.html">sequence features file</a>.</p>\r
+as Uniprot), the result of <a href="search.html">sequence motif\r
+searches</a> or simply read from a <a\r
+href="featuresFormat.html">sequence features file</a>.</p>\r
+<p><strong>Sequence Feature Groups</strong></p>\r
+<p>Since Jalview 2.08, sequence features assigned to a sequence can be\r
+organised into groups, which may indicate that the features were all retrieved\r
+from the same database (such as Uniprot features), or generated by the\r
+same analysis process (as might be specified in a <a\r
+href="featuresFormat.html">sequence features file</a>).</p>\r
+<p><strong>Sequence Feature Inheritance</strong></p>\r
+<p>Since Jalview 2.07, sequence features are <em>global</em> to a set of\r
+sequences appearing (independently or together) in many different\r
+alignments. Practically, this means features loaded onto one alignment\r
+can be viewed in any alignments involving the same sequences. The same\r
+sequence appears in different alignments when a new alignment is\r
+generated by submitting an existing set of sequences to one of the\r
+alignment or prediction web services, and when sequences are copied\r
+and pasted into other alignment windows.</p>\r
 <p><strong>View&#8594;Fetch Sequence Features</strong></p>\r
 <p>When this option is selected, sequence features extracted from the <a href="http://www.ebi.uniprot.org/">Uniprot</a> \r
   record for each sequence are displayed on the alignment.</p>\r
@@ -20,22 +36,11 @@ searches</a> or simply read from a <a href="featuresFormat.html">sequence featur
 <p>Toggle the display of sequence features in this alignment.</p>\r
 <p><strong>View&#8594;Feature Settings...</strong>\r
 <p>Once sequence features have been loaded, their display can be fully\r
-  controlled using the alignment window's Feature Settings dialog box\r
-  :</p>\r
-<img src="appFeatureSettings.gif" align="left"/>\r
-\r
-<p> features can be hidden \r
-  or have their rendering priority changed using the Feature Settings dialog. \r
-  This displays all the features loaded, the colour and whether to display the \r
-  feature or not. You can easily change the colour by clicking the colour box.<br>\r
-  It is important to realise that the order in which features are drawn to the \r
-  alignment may result in overlapping features being hidden. Features at the foot \r
-  of the table are rendered first. Therefore features higher up the table will \r
-  be drawn over the top of lower featrues. You can change the order of the feature \r
-  priority by dragging the feature with your mouse. <br>\r
-  Use the transparency setting as another way to visualise overlapping features. \r
-<p><strong><em>You can save all features, with their current colours and visibility \r
-  in a Jalview format file. </em></strong>\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>The Sequence Identification Process</strong>\r
 \r
   </p>\r