-<html>\r
-<head><title>Sequence Features</title></head>\r
-<body>\r
-<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\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 2.08, 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→Show Sequence Features</strong></p>\r
-<p>Toggle the display of sequence features in this alignment. If\r
-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→Sequence Feature Settings...</strong>\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 "File->Load Features / Annotations"\r
- menu item. See the <a href="featuresFormat.html">Features File Format</a> for\r
- more details.</p>\r
-</body>\r
-</html>\r
+<html>
+<head><title>Sequence Features</title></head>
+<body>
+<p><strong>Sequence Features</strong></p>
+<p>Jalview can colour parts of a sequence based on the presence of
+sequence features - which may be retrieved from database records (such
+as Uniprot), the result of <a href="search.html">sequence motif
+searches</a> or simply read from a <a
+href="featuresFormat.html">sequence features file</a>.</p>
+<p><strong>Sequence Feature Groups</strong></p>
+<p>Since Jalview 2.08, sequence features assigned to a sequence can be
+organised into groups, which may indicate that the features were all retrieved
+from the same database (such as Uniprot features), or generated by the
+same analysis process (as might be specified in a <a
+href="featuresFormat.html">sequence features file</a>).</p>
+<p><strong>Sequence Feature Inheritance</strong></p>
+<p>Since Jalview 2.08, sequence features are <em>global</em> to a set of
+sequences appearing (independently or together) in many different
+alignments. Practically, this means features loaded onto one alignment
+can be viewed in any alignments involving the same sequences. The same
+sequence appears in different alignments when a new alignment is
+generated by submitting an existing set of sequences to one of the
+alignment or prediction web services, and when sequences are copied
+and pasted into other alignment windows.</p>
+<p><strong>View→Show Sequence Features</strong></p>
+<p>Toggle the display of sequence features in this alignment. If
+feature retrieval has not already been carried out, then Jalview will
+automatically try to fetch sequence features (as described below).</p>
+<p><strong>View→Sequence Feature Settings...</strong></p>
+<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><strong>View→Sequence ID Tooltip→Show Non-Positional features</strong><br>
+ <em>Only available in application</em></br></p>
+<p>Toggles the display of non-positional features in the sequence ID tooltip,
+ and whether they will be included when sequence features are exported using
+ "File→Export Features".</p>
+<p>Precalculated Sequence Features may be added to an alignment from the command
+ line, drag and drop, or from the "File→Load Features / Annotations"
+ menu item. See the <a href="featuresFormat.html">Features File Format</a> for
+ more details.</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff