<html>
-<head><title>Preferences</title></head>
+<head>
+<title>Preferences</title>
+</head>
<body>
<p><strong>Preferences</strong></p>
-<p>There are four tabs in the Preferences dialog box:
+<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>
+ <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>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
+ 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>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>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/$SEQUENCE_ID$
- <br>
- Links will also be made for any database cross references
- associated with the sequence where the database name exactly
- matches a URL link name. In this case, the $SEQUENCE_ID$ string will be replaced with
- the accession string for the database cross-reference, rather than the
- sequence ID for the sequence (<em>since Jalview 2.4</em>).
- <br>
- <strong>Regular Expression Substitution</strong><br>
- A url may contain a string of the form $SEQUENCE_ID=/<em>regular expression</em>/=$. In this case, the regular expression will be applied to the full sequence ID string and the resulting match will be inserted into the URL.
- Groups of parentheseses can be used to specify which regions of the regular expression will be used to generate the URL:
- <ul>
- <li>Each top level parenthesis will yield a URL containing the text matched within that parenthesis.
- </li>
- <li>Regions matching sub-parentheseses within a top-level parenthesis will be concatenated to form the text inserted into the URL for the top-level parenthesis.</li>
- <em>Please Note:
- <ul><li>The regular expressions supported by Jalview are those provided by the <a href="www.javaregex.com">Stevesoft javaregex package</a>.
- </li><li>Some characters must be escaped when specifying them as a match within a regular expression.</li></ul>
- <br>Many Thanks to Bernd Brand of the Free University of Amsterdam for testing this new regular-expression expansion feature!
- </em>
- <em>
- </ul>
- </p>
+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>
+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>
+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>
+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>
+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:
+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>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.
+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>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>
--- /dev/null
+<html>
+<head>
+Opening URLs from Jalview
+</head>
+<body>
+<p>
+<p><strong>Opening URLs from Jalview</strong><br>
+Both the applet and the desktop application are able to open URLs as
+'popups' in your web browser. <br>
+Double-clicking on the ID of a sequence will open the first URL that can
+be generated from its sequence ID. This is often the SRS site, but you
+can easily configure your own <a href="#urllinks>sequence URL links</a>.</p>
+<p>Other links for a sequence either derived from any other
+configured URL links, or imported from the sequence's annotation, are
+accessed by right clicking to open the sequence pop-up menu, and
+selecting from the <em>Links</em> submenu.</p>
+<p><strong><a name="urllinks">Configuring URL Links</a></strong>
+<br>URL links are defined in the "Connections" tab of the <a
+ href="../features/preferences.html">Jalview desktop preferences</a>, or
+specified as <a
+ href="http://www.jalview.org/examples/appletParameters.html#parameters">applet
+parameters</a>. <br>
+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>
+In the preferences dialog box, click <strong>new</strong> to add a new
+link, and <strong>edit</strong> to modify an existing link, or <strong>delete</strong>
+to remove it.<br>
+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>
+The URL string must contain a token that can be replaced with a sequence
+ID. The simplest token is "$SEQUENCE_ID$", which 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/$SEQUENCE_ID$ <br>
+<br>
+Links will also be made for any database cross references associated
+with the sequence where the database name exactly matches a URL link
+name. In this case, the $SEQUENCE_ID$ string will be replaced with the
+accession string for the database cross-reference, rather than the
+sequence ID for the sequence (<em>since Jalview 2.4</em>).</p>
+<p><strong>Regular Expression Substitution</strong><br>
+A url may contain a string of the form $SEQUENCE_ID=/<em>regular
+expression</em>/=$. In this case, the regular expression will be applied to
+the full sequence ID string and the resulting match will be inserted
+into the URL. Groups of parentheses can be used to specify which regions
+of the regular expression will be used to generate the URL:
+<ul>
+ <li>Each top level parenthesis will yield a URL containing the
+ text matched within that parenthesis.</li>
+ <li>Regions matching sub-parentheses within a top-level
+ parenthesis will be concatenated to form the text inserted into the URL
+ for the top-level parenthesis.</li>
+ <em>Please Note:
+ <ul>
+ <li>The regular expressions supported by Jalview are those
+ provided by the <a href="www.javaregex.com">Stevesoft javaregex
+ package</a>.</li>
+ <li>Some characters must be escaped when specifying them as a
+ match within a regular expression.</li>
+ </ul>
+ <br>
+ Many Thanks to Bernd Brandt of the Free University of Amsterdam for
+ testing this new regular-expression expansion feature! </em>
+ <em>
+</ul>
+</p>
+<p
+</body>
+</html>
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