<mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
<mapID target="seqfeatedit" url="html/features/editingFeatures.html"/>
<mapID target="seqfeatcreat" url="html/features/creatinFeatures.html"/>
+ <mapID target="seqfeatures.report" url="html/features/seqfeaturereport.html"/>
<mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>
<mapID target="seqfeatures.settings.selcols" url="html/features/featuresettings.html#selectbyfeature"/>
<mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
<tocitem text="Feature Colourschemes" target="features.featureschemes" />
<tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
<tocitem text="Editing Sequence Features" target="seqfeatedit" />
+ <tocitem text="HTML Feature Attributes report" target="seqfeatures.report" />
<tocitem text="HTML annotation report" target="io.seqreport" />
</tocitem>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 Feature Reports</title>
+</head>
+<body>
+ <p>
+ <strong>Sequence Feature Reports</strong> <br /> Sequence features
+ can carry a number of attributes. To view all the attributes for a
+ particular sequence feature, mouse over the feature and <em>right-click</em>
+ to open the <a href="../menus/popupMenu.html#featuredetails">Popup Menu</a> and
+ select the feature's entry from the <em>Feature Details</em>
+ submenu.
+ </p>
+ <img src="seqfeaturesrep.png" width="460"
+ alt="Full details for a particular Sequence Feature can be displayed as HTML in a report window" />
+ <p>
+ <em>Virtual Feature Reports</em><br /> When a sequence feature
+ report is shown for features mapped between CDS and Protein
+ sequences, the report will include both the original and mapped
+ feature's location.
+ </p>
+ <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>
+ <em>Feature Reports were added in Jalview 2.11.</em>
+</body>
+</html>
settings tabs and corresponding views showing 'Virtual Features'
from each view overlaid on the other (created with Jalview 2.11.1.0).</em>
</p>
- <p>When virtual features are enabled, they are also shown on any
- linked 3D structure views when 'Colour by Sequence' is enabled, and
+ <p>
+ When virtual features are enabled, they are also shown on any linked
+ 3D structure views when 'Colour by Sequence' is enabled, and
exported as GFF and Jalview Features files (mapped to their
- associated virtual coordinates).</p>
+ associated virtual coordinates). Both the original and the mapped
+ locations are also included in <a href="seqfeaturereport.html">Sequence
+ Feature Reports</a>.
+ </p>
<p>
<strong>Operations supported in Split Frame Mode</strong>
</p>
<p>
<strong>Popup Menu</strong><br> <em>This menu is visible
when right clicking either within a selected region on the
- alignment or on a selected sequence name. It may not be accessible
+ alignment, on a sequence name, and also when right-clicking a sequence feature. It may not be accessible
when in 'Cursor Mode' (toggled with the F2 key).</em><br /> <em><strong>Mac
Users:</strong> pressing CTRL whilst clicking the mouse/track pad is the
same as a right-click. See your system's settings to configure
your track-pad's corners to generate right-clicks.</em>
</p>
<ul>
- <li><strong>Selection</strong>
+ <li><strong>Selection<br/></strong>
+ <em>This menu is only visible when right-clicking a selected sequence or region of the alignment. </em>
<ul>
<li><a name="sqreport"><strong>Sequence
Details...<br>
according to gaps in just the current sequence)</em></li>
<li><strong>Hide Sequences</strong><br> <em>Hides the
currently selected sequences in this alignment view.</em><strong><br>
- </strong></li>
+ </strong><br/> <br/></li>
+
+ <li><strong><a name="featuredetails"> Feature Details</a><br /></strong>
+ <em>Each entry opens a <a
+ href="../features/seqfeaturereport.html">Sequence Feature
+ Report</a> for visible features under the mouse.<br />Only visible
+ when right-clicking a region where <a
+ href="../features/seqfeatures.html">Sequence Features</a> are
+ shown.
+ </em>
+ </li>
</ul>
+
</body>
</html>
<tr>
<td width="60" align="center" nowrap><strong><a
id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
- <em>16/04/2020</em></strong></td>
+ <em>22/04/2020</em></strong></td>
<td align="left" valign="top">
<ul>
<li>
- <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302 -->Map 'virtual'
+ <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map 'virtual'
codon features shown on protein (or vice versa) for display
- in alignments, on structure views and for export.
+ in alignments, on structure views, in feature reports and for export.
</li>
<li>
<!-- JAL-3121 -->Feature attributes from VCF files can be
git://source.jalview.org / jalview.git / commitdiff
