<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- *
+ * 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/>.
--->
+ * 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>Preferences</title>
</head>
<body>
<p><strong>Preferences</strong></p>
-<p>There are six tabs in the Preferences dialog box:
+<p>The preferences panel is opened from the Jalview Desktop’s <strong><em>Tools</em></strong> menu.</p>
+<p>There are eight 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
<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="#structure"><strong>"Structure"</strong>
+ Preferences</a> tab allows you to configure options for obtaining and displaying structure information.</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>
<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>Show Unconserved</em> - When this is selected, all consensus sequence
+symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.</p>
<p><em>Sequence Name Italics</em> - select to apply the italicised
-vbersion of the font to sequence labels.</p>
+version of the font to sequence labels.</p>
<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
rendering of the alignment.</p>
-<p><em>Wrap Alignment</em> - Select whether to open new alignment
-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>Sort by</em> - When the alignment is loaded in, it will can
-be sorted by Id or pairwise identity.</p>
+<p><em>Wrap Alignment</em> - Select whether to open new alignment
+windows in wrapped mode or not.</p>
+<p><em>Sort alignment by</em> - When the alignment is loaded in, it can
+be ordered as read (No sort), or sorted by Id or pairwise identity.</p>
+<p><em>Sort annotations by</em> - Annotations can be unsorted, sorted by the order of the related sequences in
+the alignment, or by label. Autocalculated annotations (e.g. Consensus) can be shown either last (below sequence
+annotations) or first (above sequence annotations). <em>Since Jalview 2.8.2.</em></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>
+path or selecting it from the file chooser window.<br/><em>Note: The default example alignment is updated periodically to demonstrate new features in Jalview.</em></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
<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>
+ Annotation...</a> is selected from the alignment window's colours menu.
</p>
+<p><a name="structure"><strong>"Structure"
+Preferences tab</strong></a><em> added in Jalview 2.8.2</em></p>
+<p><em>Process secondary structure from PDB</em> - if selected, then structure information
+read from PDB will be processed and annotation added to associated sequences.
+<p><em>Use RNAView for secondary structure</em> - if selected, the pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>) will be
+called to derive secondary structure information for RNA chains.
+<p><em>Add secondary structure annotation to alignment</em> - if selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's implementation DSSP</a> will be used to add annotation to polypeptide chains in the structure.
+<p><em>Add Temperature Factor annotation to alignment</em> - if selected, values extracted from the Temperature Factor
+column for the backbone atoms in the PDB file will be extracted as annotation lines shown on the alignment.
+<p><em>Default structure viewer</em> - choose JMOL or CHIMERA for viewing 3D structures.
+<p><em>Path to Chimera program</em> - Optional, as Jalview will search standard installation paths for Windows, Linux or MacOS.
+If you have installed Chimera in a non-standard location, you can specify it here, by entering the full path to the Chimera executable program.
+Double-click this field to open a file chooser dialog.
+
<p><a name="connections"><strong>"Connections"
Preferences tab</strong></a></p>
<p><em>URL Link From Sequence ID</em><br>
This is a selection box which allows the user to set a default rendering
style for EPS export:
<ul>
+ <li>"Prompt each time"<br>
+ Choose this to be asked select between Lineart and Text each time you
+ make an EPS file.</li>
<li>"Lineart"<br>
EPS files will accurately reproduce the alignment view in Jalview and
all characters will be converted into line art. Files generated in this
files that can be edited easily in programs like Microsoft Word and
Adobe Illustrator, but can be problematic if the fonts available to
jalview are not accessible by the program reading the EPS file.
- <li>"Prompt each time"<br>
- Choose this to be asked select between Lineart and Text each time you
- make an EPS file.</li>
</ul>
+<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
</pre>
<p>If the boxes are left unchecked for a particular format, the
sequence limits will not be appended to the sequence id.</p>
-</p>
<p><em>Use Modeller Output</em></p>
<p>This option only applies to PIR format output. Jalview
automatically reads PIR files with sequence descriptions compatible with
write Modeller style PIR files</a> with correct start/end numbering and PDB
file association (if available). The Jalview id/start-end option is
ignored if Modeller output is selected.
+
<p><a name="editing"><strong>Editing Preferences tab</strong></a></p>
-<p>There are currently 2 options available which can be selected /
+<p>There are currently three options available which can be selected /
deselected.</p>
<p><em>AutoCalculate Consensus</em> - For large alignments it can be
useful to deselect "Autocalculate Consensus" when editing.
This prevents lengthy calculations which are performed after each
sequence edit. New alignment windows will have their "Autocalculate
Consensus" option set according to this setting.</p>
-<p><em>Pad gaps when editing</em> - New alignment windows will
+<p><em>Pad Gaps when Editing</em> - New alignment windows will
"Pad Gaps" according to this setting.</p>
+<p><em>Sort with New Tree</em> - When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.</p>
<p> </p>
<p> </p>
</body>
git://source.jalview.org / jalview.git / blobdiff