-<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 2.07, 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→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
-<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>View→Show Sequence Features</strong></p>\r
-<p>Toggle the display of sequence features in this alignment.</p>\r
-<p><strong>View→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>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→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>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>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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>. You can also <a href="creatinFeatures.html">create
+ features</a> from the results of searches or the current selection,
+ and <a href="editingFeatures.html">edit features</a> by double
+ clicking on them.
+ </p>
+ <p>
+ <strong>Sequence Feature Colouring Styles</strong>
+ </p>
+ <p>
+ By default, Jalview will assign a color to each feature based on its
+ type. These colours can be changed from the <a
+ href="featuresettings.html"
+ >feature settings</a> and <a href="editingFeatures.html">amend
+ features</a> dialog boxes. Since Jalview 2.5, it is also possible to
+ define <a href="featureschemes.html">feature colourschemes</a> to
+ shade features based on their associated scores or text labels.
+ </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