<mapID target="clarguments" url="html/features/clarguments.html"/>
<mapID target="io" url="html/io/index.html"/>
<mapID target="io.modellerpir" url="html/io/modellerpir.html"/>
+ <mapID target="io.seqreport" url="html/io/exportseqreport.html"/>
<mapID target="export" url="html/io/export.html"/>
<mapID target="alformats" url="html/io/fileformats.html"/>
<mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>
<tocitem text="Viewing RNA structure" target="varna" />
<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
<tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
+ <tocitem text="HTML annotation report" target="io.seqreport"/>
</tocitem>
<tocitem text="Editing Alignments" target ="edit"/>
<tocitem text="Cursor Mode" target="cursor"/>
<tocitem text="Editing Sequence Features" target="seqfeatedit"/>
<tocitem text="DAS Feature Retrieval" target="das.viewing"/>
<tocitem text="DAS Feature Settings" target="das.settings"/>
+ <tocitem text="HTML annotation report" target="io.seqreport"/>
</tocitem>
<tocitem text="Web Services" target="webservice" expand="false">
<tocitem text="JABAWS" target="jabaws"/>
</tocitem>
<tocitem text="Privacy" target="privacy"/>
</tocitem>
-<tocitem text="Useful information" expa nd="true">
+<tocitem text="Useful information" expand="true">
<tocitem text="Amino Acid Table" target="aminoAcids"/>
<tocitem text="Amino Acid Properties" target="aaProperties"/>
<tocitem text="The Genetic Code" target="geneticCode"/>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<head>
+<title>Viewing and exporting sequence annotation reports</title>
+</head>
+<body>
+<p><strong>Viewing and exporting sequence annotation reports</strong>
+<br/>
+Much of the information retrieved by Jalview about a sequence is visualized on the alignment.
+Often, however, there are a huge number of ontology terms, cross-references, links to publications and other kinds of data shown
+ in the sequence ID tooltip that cannot be examined. In this case, you can view and export the information shown in a sequence's ID tooltip by right-clicking and
+selecting the <strong>"<em>(sequence's name)</em></em>→Sequence Details ..."</strong> entry from the <a href="../menus/popupMenu.html">pop-up menu</a>.
+</p>
+<p><strong>Annotation Reports for a range of sequences</strong><br/>
+If you would like to view the tooltips for a number of sequences, simply select them all and then use the <strong>Selection→Sequence Details ...</strong> entry in the <a href="../menus/popupMenu.html">pop-up menu</a>.
+</p>
+<img src="seqreport.gif" alt="Sequence Annotation is displayed as HTML in a report window"/>
+<p><strong>Copying and pasting annotation to other programs</strong><br>
+The <strong>File→Save</strong> option in the sequence annotation report window allows the report to be saved as HTML, which will preserve links and any other metadata. It is also possible to copy and paste the text to other programs, but in some cases, the HTML will not be preserved. In that case, you can toggle the display of HTML source code with the <strong>Edit→Show HTML Source</strong> drop down menu entry.
+</p>
+</body>
+</html>
<ul>
<li><strong>Selection</strong>
<ul>
+ <li><a name="sqreport"><strong>Sequence Details ...<br>
+ </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
+ and database cross references</a> normally shown in the sequence's
+ tooltip.</em></li>
<li><strong>Edit </strong>
<ul>
<li><strong>Copy</strong><br>
</strong><em>This menu is only visible if you right-click on a sequence name.
</em>
<ul>
- <li><strong>Edit Name/Description<br>
+ <li><a name="sqreport"><strong>Sequence Details ...<br>
+ </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
+ and database cross references</a> normally shown in the sequence's
+ tooltip.</em></li>
+ <li><strong>Edit Name/Description<br>
</strong><em>You may edit the name and description of each sequence. A
window will be displayed asking for a new sequence name and sequence description
to be entered. Press OK to accept your edit. To save sequence descriptions,
git://source.jalview.org / jalview.git / commitdiff
