-<html>\r
-<head><title>Sequence Features</title></head>\r
-<body>\r
-<p><strong>View→Sequence Features</strong></p>\r
-<p>When this option is selected, sequence features extracted from the\r
- <a href="http://www.ebi.uniprot.org/">Uniprot</a> record for each\r
- sequence are displayed on the alignment.</p>\r
-<p>Currently, sequence features are rendered in red or blue, dependent\r
- upon their type:</p><ul>\r
- <li>Features associated with a particular residue are coloured\r
- red<br><italic>e.g. an active site residue</italic></li>\r
- <li>Features which span a region are coloured blue<br>\r
-<italic>e.g. a region of sequence with known structure</italic></p>\r
-<p>More information about the feature is given in a tooltip, which are\r
- viewed by moving the mouse pointer over a sequence feature. The\r
- associated text for the feature will then be displayed in a small\r
- label will appear near the pointer.</p>\r
-<p>After the Sequence Features option is selected, there may be some delay before\r
- the features are actually rendered, as jalview must first determine if a\r
- sequence is contained in uniprot and then retrieve its sequence\r
- record. This delay should only happen once for a particular\r
- alignment, as jalview caches uniprot records in a file in your home\r
- directory called '.jalview.uniprot.xml'.\r
-\r
-<p>The first step in this process is to try to use the ID (name) of\r
- each sequence as an ID search in Uniprot. If there is no match, The\r
- EBI Blast search is used in an attempt to obtain the Uniprot Id for\r
- each sequence. You will be notified of any 100% matches with\r
- Uniprot, but you must then manually change the name of the sequence,\r
- by right clicking on the sequence ID and selecting\r
- Sequence→Edit Name, before Jalview will show its sequence\r
- features.<ul>\r
- <li>remember to save your alignment if you have updated any of the\r
- sequence IDs!\r
- </li>\r
- </ul></p>\r
-<p>\r
- If a uniprot record (or set of records) is found for a sequence,\r
- then the sequence in aligned to the one in the Uniprot record\r
- to determine the correct start and end residue positions that will be\r
- displayed when the 'Show Full Sequence ID' option is set.</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * 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