<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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>The preferences panel is opened from the Jalview Desktop’s <strong><em>Tools</em></strong> menu.</p>
-<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="#output"><strong>"Output"</strong>
- Preferences</a> tab contains settings affecting the export of sequence
- alignments and EPS files.</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="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>
-<p><em>Maximise Window</em> - If this is selected, a new alignment
-window will stretch to fit the available space.</p>
-<p><em>Open Overview Window</em> - When this is selected, the <a
- href="overview.html">alignment overview</a> panel is opened by default
-for a new alignment window.</p>
-<p><em>Show Annotations</em> - If this is selected the new window
-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>
-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
-the sequence.</p>
-<p><em>Right Align IDs</em> - select to align all sequence IDs to
-the left-hand edge of the sequence alignment, rather than the left-hand
-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
-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>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.<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
-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>
-These definitions are used to generate URLs from a sequence's ID or
-database cross references. Read more about <a
- href="../webServices/urllinks.html#urllinks">configuring URL links
-here</a>.</p>
-<p><em>Default Browser (Unix)</em><br>
-Its difficult in Java to detect the default web browser for Unix users.
-If Jalview can't find your default web browser, enter the name or full
-path to your web browser application.</p>
-<p><em>Proxy Server</em><br>
-If you normally use a proxy server for using the internet, you must tick
-the box "Use a Proxy Server" and enter the address and port
-details as necessary. Web Services will not work if you are using a
-proxy server and do not enter the settings here.</p>
-<p><em>Usage statistics, Questionnaire and Version checks</em><br>
-Uncheck these options to prevent Jalview from submitting usage
-statistics to google analytics, checking for jalview questionnaires or
-retrieving details of the latest release version (at www.jalview.org).
-See the <a href="../privacy.html">user privacy statement</a> for more
-information.</p>
-<p><a name="output"><strong>Output Preferences tab</strong></a></p>
-<p><em>EPS Rendering Style</em><br>
-This is a selection box which allows the user to set a default rendering
-style for EPS export:
-<ul>
- <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
- way are large and are not easily editable, but have no font table
- dependencies.</li>
- <li>"Text"<br>
- EPS files will be a mixture of text and lineart. This produces compact
- 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>
-<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>
+ <p>
+ <strong>Preferences</strong>
+ </p>
+ <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 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="#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>
+ <li>The <a href="#output"><strong>"Output"</strong>
+ Preferences</a> tab contains settings affecting the export of
+ sequence alignments and EPS files.
+ </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="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>
+ <p>
+ <em>Maximise Window</em> - If this is selected, a new alignment
+ window will stretch to fit the available space.
+ </p>
+ <p>
+ <em>Open Overview Window</em> - When this is selected, the <a
+ href="overview.html">alignment overview</a> panel is opened
+ by default for a new alignment window.
+ </p>
+ <p>
+ <em>Show Annotations</em> - If this is selected the new window 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>
+ 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 the sequence.
+ </p>
+ <p>
+ <em>Right Align IDs</em> - select to align all sequence IDs to the
+ left-hand edge of the sequence alignment, rather than the left-hand
+ 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>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
+ 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>Gap Symbol</em> - The default gap symbol may be set to either
+ "-" or "."
+ </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.<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 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>
+ <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> These definitions are
+ used to generate URLs from a sequence's ID or database cross
+ references. Read more about <a
+ href="../webServices/urllinks.html#urllinks">configuring
+ URL links here</a>.
+ </p>
+ <p>
+ <em>Default Browser (Unix)</em><br> Its difficult in Java to
+ detect the default web browser for Unix users. If Jalview can't find
+ your default web browser, enter the name or full path to your web
+ browser application.
+ </p>
+ <p>
+ <em>Proxy Server</em><br> If you normally use a proxy server
+ for using the internet, you must tick the box "Use a Proxy
+ Server" and enter the address and port details as necessary.
+ Web Services will not work if you are using a proxy server and do
+ not enter the settings here.
+ </p>
+ <p>
+ <em>Usage statistics, Questionnaire and Version checks</em><br>
+ Uncheck these options to prevent Jalview from submitting usage
+ statistics to google analytics, checking for Jalview questionnaires
+ or retrieving details of the latest release version (at
+ www.jalview.org). See the <a href="../privacy.html">user privacy
+ statement</a> for more information.
+ </p>
+ <p>
+ <a name="output"><strong>Output Preferences tab</strong></a>
+ </p>
+ <p>
+ <em>EPS Rendering Style</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 way are large and
+ are not easily editable, but have no font table dependencies.
+ </li>
+ <li>"Text"<br> EPS files will be a mixture of
+ text and lineart. This produces compact 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.
+ </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 these are ticked,
+ then Jalview will write files with the start and end sequence
+ positions appended to each sequence id:
+ <pre>
>ID/1-10
AACDEAAFEA
</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
-the program <a href="http://salilab.org/modeller/">Modeller</a>. If this
-option is selected <a href="../io/modellerpir.html">Jalview will
-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 /
-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
-"Pad Gaps" according to this setting.</p>
-<p> </p>
-<p> </p>
+ <p>If the boxes are left unchecked for a particular format, the
+ sequence limits will not be appended to the sequence id.</p>
+ <p>
+ <em>Embed BioJSON to HTML export</em>
+ </p>
+ <p>
+ When this option is enabled, Jalview embeds <a
+ href="bioJsonFormat.html">BioJSON</a> data within HTML files
+ exported from Jalview at generation time. This enables the exported
+ HTML files to be extracted and imported back into the Jalview
+ desktop application at a later time.
+ <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 the
+ program <a href="http://salilab.org/modeller/">Modeller</a>. If this
+ option is selected <a href="../io/modellerpir.html">Jalview will
+ 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 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
+ "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>
</html>
git://source.jalview.org / jalview.git / blobdiff