+++ /dev/null
-<html>
-
-<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>
- >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>
-</body>
-</html>
git://source.jalview.org / jalview.git / blobdiff