<html>
-
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 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>Preferences</title>
</head>
<body>
<p><strong>Preferences</strong></p>
-<p>There are four tabs in the Preferences dialog box:
+<p>There are six tabs in the Preferences dialog box:
<ul>
<li>The <a href="#visual"><strong>"Visual"</strong>
Preferences</a> tab allows you to configure the default display for a new
alignment window.</li>
+ <li>The <a href="#colours"><strong>"Colours"</strong>
+ Preferences</a> tab allows you to configure default colourschemes for a new
+ alignment window.</li>
<li>The <a href="#connections"><strong>"Connections"</strong>
Preferences</a> tab allows you to change the links made from Jalview to
your default web browser.</li>
<li>The <a href="#editing"><strong>"Editing"</strong>
Preferences</a> tab contains settings affecting the export of sequence
alignments and EPS files.</li>
- <li>The <a href="#editing"><strong>"DAS
+ <li>The <a href="dassettings.html"><strong>"DAS
Settings"</strong> Preferences</a> tab allows you to select which DAS sources
to use when fetching DAS Features.</li>
+ <li>The <a href="../webServices/webServicesPrefs.html"><strong>"Web Service"</strong> Preferences</a> tab allows you to configure the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a> servers that Jalview uses, and change the layout of the alignment's Web Services menu.</li>
</ul>
</p>
<p><strong><a name="visual">Visual</a> Preferences tab</strong></p>
will display an annotation panel below the sequences. This annotation
panel may have several rows describing the whole alignment. The 3
standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
- may be shown or hidden by default.</p>
+for the alignment may be shown or hidden by default using the checkboxes
+below.</p>
+<p><em>Show group: Conservation and Consensus</em> controls the
+display of per-group automatic annotation.</p>
+<p><em>Consensus: Histogram and Logo</em> checkboxes control the
+display of the consensus histogram and sequence logo for consensus
+annotation rows.</p>
<p><em>Full Sequence ID</em> - If selected the ID panel will display
the name of a sequence plus the start and end residues in the format
name/start-end. If not selected, the displayed ID will be the name of
edge of the alignment display window.</p>
<p><em>Font</em> - The default font name, size and style can be set
for a new alignment window.</p>
+<p><em>Sequence ID Tooltip</em>: Control the display of Database
+References and Non-positional annotation in the tooltip displayed when
+the mouse is over a sequence's ID.</p>
<p><em>Sequence Name Italics</em> - select to apply the italicised
vbersion of the font to sequence labels.</p>
<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
windows in wrapped mode or not.</p>
<p><em>Gap Symbol</em> - The default gap symbol may be set to either
"-" or "."</p>
-<p><em>Colour</em> - The default colour scheme for a new alignment
-window. If the chosen option is "User Defined" then the last
-User Defined Colour loaded or saved via the User Defined Colours panel
-will be loaded.</p>
<p><em>Sort by</em> - When the alignment is loaded in, it will can
be sorted by Id or pairwise identity.</p>
<p><em>Open file</em> - If this is selected then the default
alignment file will be opened when Jalview is started. You can change
the default file by clicking on file name and either typing in the file
path or selecting it from the file chooser window.</p>
+<p><a name="colours"><strong>"Colours" Preferences tab</strong></p>
+<p><em>Alignment Colour</em> - The default colour scheme for a new alignment
+window. If the chosen option is "User Defined" then the last
+User Defined Colour loaded or saved via the User Defined Colours panel
+will be loaded.</p>
+ <p>
+ <em>Annotation Shading Default</em> - set the default minimum
+ and maximum colours used when <a
+ href="../colourSchemes/annotationColouring.html">Colour by
+ Annotation ..</a> is selected from the alignment window's colours menu.
+ </p>
+ <br>
+ </p>
<p><a name="connections"><strong>"Connections"
Preferences tab</strong></a></p>
<p><em>URL Link From Sequence ID</em><br>
make an EPS file.</li>
</ul>
</p>
+<p><em>Automatically set ID width</em><br>
+When enabled, the column containing sequence and annotation labels at the left hand side of an exported figure will be made large enough to display each sequence ID and annotation label in its own line. Enable this if you have particularly long sequence IDs and need to generate EPS or PNG figures or web pages.</p>
+<p><em>Figure ID column width</em><br>
+Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if <em>"Automatically set ID width"</em> is set.
+</p>
<p><em>Sequence//Start-End Numbering</em><br>
The output tab also has a group of checkboxes for each file format. If
these are ticked, then Jalview will write files with the start and end
-sequence positions appended to each sequence id:
-<pre>
+sequence positions appended to each sequence id: <pre>
>ID/1-10
AACDEAAFEA
</pre>
Consensus" option set according to this setting.</p>
<p><em>Pad gaps when editing</em> - New alignment windows will
"Pad Gaps" according to this setting.</p>
-<p><a name="editing"><strong>DAS Settings </strong></a></p>
-<p>See <a href="dassettings.html">DAS Settings</a></p>
<p> </p>
<p> </p>
</body>
git://source.jalview.org / jalview.git / blobdiff