<html>
-
-<head><title>Preferences</title></head>
+<!--
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Preferences</title>
+</head>
<body>
-<p><strong>Preferences</strong></p>
-<p>There are four 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="#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="#editing"><strong>"DAS Settings"</strong> Preferences</a>
- tab allows you to select which DAS sources to use when fetching DAS Features.</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>
- may be shown or hidden by default.</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 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>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="connections"><strong>"Connections" Preferences tab</strong></a></p>
-<p><em>URL Link From Sequence ID</em><br>
- Right click a sequence id to see a popup menu with "Link" as one of
- the items. By default the item "SRS" is added to this link menu. This
- link will show a web page in your default browser with the selected sequence
- id as part of the URL.<br>
- Jalview allows you to add your own custom links to other web pages. Click new
- to add a new link. You can name the link, this will be displayed on a new menu
- item under the "Link" menu when you right click on a sequence id.
- <br>
- You must enter $SEQUENCE_ID$ within your URL. This will be replaced by the chosen
- sequence id when you click on it. </p>
-<p>eg.<br>
- UniRef100 = http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100<br>
- Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$</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><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>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><a name="editing"><strong>DAS Settings </strong></a></p>
-<p>See <a href="dassettings.html">DAS Settings</a></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