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+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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>Alignment Window Menus</title>
</head>
<li><strong>Undefine Groups (Control U)<br>
</strong><em>The alignment will be reset with no defined groups.<br>
<strong>WARNING</strong>: This cannot be undone.</em></li>
+ <li><strong>Make Groups<br/></strong>
+ <em>The currently selected groups of the alignment will be
+ subdivided according to the contents of the currently selected region.
+ <br/>Use this to subdivide an alignment based on the
+ different combinations of residues observed at specific
+ positions. (new in jalview 2.5)</em></li>
</ul>
</li>
<li><strong>View</strong>
<li><strong>Gather Views (G)</strong><em><br>
Each view associated with the alignment will be displayed within its
own tab on the current alignment window. </em></li>
- <li><strong>Show→(all Columns / Sequences)</strong><em><br>
- All hidden Columns / Sequences will be revealed. </em></li>
- <li><strong>Hide→(all Columns / Sequences)</strong><em><br>
- Hides the all the currently selected Columns / Sequences</em></li>
+ <li><strong>Show→(all Columns / Sequences / Sequences and Columns)</strong><em><br>
+ All hidden Columns / Sequences / Sequences and Columns will be revealed. </em></li>
+ <li><strong>Hide→(all Columns / Sequences / Selected Region / All but Selected Region )</strong><em><br>
+ Hides the all the currently selected Columns / Sequences / Region or everything but the selected Region.</em></li>
+ <li><strong>Automatic Scrolling<br>
+ </strong><em>When selected, the view will automatically scroll to display the
+ highlighted sequence position corresponding to the position under the mouse
+ pointer in a linked alignment or structure view.</em>
+ </li>
<li><strong>Show Annotations<br>
</strong><em>If this is selected the "Annotation Panel" will be
displayed below the alignment. The default setting is to display the
conservation calculation, quality calculation and consensus values as
bar charts. </em></li>
- <li><strong>Show Sequence Features</strong><br>
+ <li><strong>Autocalculated Annotation<br></strong>Settings for the display of autocalculated annotation.
+ <ul><li>
+ <strong>Apply to all groups<br></strong>
+ When ticked, any modification to the current settings will be applied to all autocalculated annotation.
+ </li>
+ <li>
+ <strong>Show Consensus Histogram<br></strong>
+ Enable or disable the display of the histogram above the consensus sequence.
+ </li>
+ <li>
+ <strong>Show Consensus Profile<br></strong>
+ Enable or disable the display of the sequence logo above the consensus sequence.
+ </li>
+ <li>
+ <strong>Group Conservation<br></strong>
+ When ticked, display a conservation row for all groups (only available for protein alignments).
+ </li>
+ <li>
+ <strong>Apply to all groups<br></strong>
+ When ticked, display a consensus row for all groups.
+ </li>
+ </ul>
+ </li>
+ <li><strong>Show Sequence Features</strong><br>
<em>Show or hide sequence features on this alignment.</em></li>
<li><strong><a href="../features/featuresettings.html">Seqence
Feature Settings...</a></strong><em><br>
<br>This submenu's options allow the inclusion or exclusion of
non-positional sequence features or database cross references
from the tooltip shown when the mouse hovers over the sequence ID panel.</em></li>
-
+ <li><strong>Alignment Properties...<br/>
+ </strong><em>Displays some simple statistics computed for the
+ current alignment view and any named properties defined on the
+ whole alignment.</em></li>
<li><strong><a href="../features/overview.html">Overview
Window</a><br>
</strong><em>A scaled version of the alignment will be displayed in a
<li><strong>Centre Annotation Labels<br>
</strong><em>Select this to center labels along an annotation row
relative to their associated column (default is off, i.e. left-justified).</em></li>
+ <li><strong>Show Unconserved<br>
+ </strong><em>When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
+ </em></li>
+
</ul>
<li><strong>Colour</strong>
<ul>
<li><strong>by ID</strong><em><br>
This will sort the sequences according to sequence name. If the sort
is repeated, the order of the sorted sequences will be inverted. </em></li>
- <li><strong>by Group</strong><strong><br>
+ <li><strong>by Length</strong><em><br>
+ This will sort the sequences according to their length (excluding gap characters). If the sort is
+ repeated, the order of the sorted sequences will be inverted. </em></li>
+ <li><strong>by Group</strong><strong><br>
</strong><em>This will sort the sequences according to sequence name. If
the sort is repeated, the order of the sorted sequences will be
inverted. </em><strong></strong></li>
git://source.jalview.org / jalview.git / blobdiff