<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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>
<body>
<p><strong>Alignment Window Menus</strong></p>
-<ul>
<li><strong>File</strong>
<ul>
<li><strong>Fetch Sequence</strong><br>
determine which <a href="../io/index.html">alignment format</a> to
save as.</em></li>
<li><strong>Output to Textbox<br>
- </strong><em>The alignment will be displayed in plain text in a new window
- which you can "Copy and Paste" using the pull down menu, or
- your standard operating system copy and paste keys. <br>
+ </strong><em>The alignment will be displayed in plain text in a new
+ window, which you can "Copy and Paste" using the pull down
+ menu, or your standard operating system copy and paste keys. The
+ output window also has a <strong>"New Window"</strong>
+ button to import the (possibly edited) text as a new alignment.<br>
Select the format of the text by selecting one of the following menu
items.</em>
<ul>
<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>
<em>Opens the Sequence Feature Settings dialog box to control the
colour and display of sequence features on the alignment, and
configure and retrieve features from DAS annotation servers.</em></li>
+ <li><strong>Sequence ID Tooltip</strong><em> (application only)
+ <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>Scale Right</strong><br>
Show the sequence position for the last aligned residue in each row
in the right-most column of the alignment.</li>
- </em></li>
<li><strong>Show Sequence Limits<br>
</strong><em>If this box is selected the sequence name will have the start
and end position of the sequence appended to the name, in the format
will appear as blank spaces. <br>
You may set the default gap character in <a
href="../features/preferences.html">preferences</a>.</em></li>
+ <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>
<li><strong>Colour</strong>
<ul>
<li><strong>Apply Colour To All Groups<br>
<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>
BLOSUM62 scores in the alignment. See <a
href="../calculations/pca.html">Principal Component Analysis</a>.</em> <br>
</li>
+ <li><strong>Extract Scores ... (optional)</strong><br>
+ <em>This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.<br>
+ When selected, these numbers are parsed into sequence associated annotation which can
+ then be used to sort the alignment via the Sort by→Score menu.</em> <br>
+ </li>
<li><strong>Autocalculate Consensus</strong><br>
<em>For large alignments it can be useful to deselect
"Autocalculate Consensus" when editing. This prevents the
</ul>
</li>
<li><strong>Web Service<br>
- </strong> <em>Selecting one of the following menu items starts a remote
+ </strong>
+ <ul><li><strong>Fetch DB References</strong><br>
+ <em>This will use any of the database services that Jalview is aware
+ of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI)
+ to verify the sequence and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.</em><br>
+ </li>
+ </ul>
+ <em>Selecting one of the following menu items starts a remote
service on compute facilities at the University of Dundee. You need a
continuous network connection in order to use these services through
Jalview. </em>
git://source.jalview.org / jalview.git / blobdiff