-<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="#overview"><strong>"Overview"</strong>
+ Preferences</a> tab configures defaults for the overview 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 configure Jalview's internet
+ settings and specify your default web browser.
+ </li>
+ <li>The <a href="#links"><strong>"Links"</strong>
+ Preferences</a> tab shows the currently configured <em>URL
+ Links</em> shown in the <strong>Link</strong> submenu in the Sequence
+ ID popup menu.
+ </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 4
+ standard annotations <em>Conservation</em>, <em>Quality</em>,
+ <em>Occupancy</em> and <em>Consensus</em> for the alignment may
+ be shown or hidden by default using the checkboxes adjacent and
+ 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="overview"><strong>"Overview"
+ Preferences tab</strong>
+ </p>
+ <p>
+ <em>Use legacy gap colouring (gaps are white)</em> - when enabled,
+ Jalview's overview shows gaps as white, and sequences with no
+ colourscheme applied as grey.
+ </p>
+ <p>
+ <em>Show Hidden regions when opening overview</em> - default setting
+ for inclusion of hidden regions.
+ </p>
+ <p>
+ <em>Gap Colour</em> - When legacy gap colouring is not enabled, this
+ configures the default colour for gaps in the overview.
+ </p>
+ <p>
+ <em>Hidden Colour</em> - colour used to highlight regions in the
+ overview that are hidden in the alignment.
+ </p>
+ <p>
+ <em>Gap 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>
+ <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>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="links"><strong>The "Links" Preferences
+ tab</strong></a>
+ </p>
+ <p>
+ This panel shows a table, and two sections - <em>Edit</em> and <em>Filter</em>.
+ The table shows the available URL link definitions (consisting of a
+ database, Name, and URL template string), a checkbox <em>In
+ Menu</em> which indicates if the link is enabled, and <em>Double
+ Click</em> which marks the link that will be opened if a sequence's ID
+ is double clicked. The table can be sorted by clicking on the column headers.
+ </p>
+ <p><em>Edit Links</em><br /> This section contains three buttons,
+ <em>New</em>, <em>Edit</em> and <em>Delete</em>, which allow you to
+ create, modify and remove user-defined URL links from the Sequence
+ ID's links submenu.
+ </p>
+ <p>
+ <em>Filter</em><br /> The <em>Filter text</em> box allows you to
+ quickly show rows in the table containing a particular text string.
+ The <em>Custom only</em> button limits the entries in the table to
+ just those you have configured yourself <em>via</em> the <em>Edit
+ Links</em> buttons. Press <em>Show all</em> to clear any filters.
+ </p>
+ <p>The links table is prepoulated with persistent URLs for many common
+ bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
+ the <em>identifiers.org</em> website, and the names and URLs are not
+ user editable.
+ <a href="../webServices/urllinks.html#urllinks">Read more about configuring
+ URL links.</a>
+ </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>