\r
<body>\r
<p><strong>Preferences</strong></p>\r
-<p>There are three tabs in the Preferences dialog box:\r
-<ul><li>The <a href="#visual"><strong>"Visual"</strong>\r
- Preferences</a> tab allows \r
- you to configure the default display for a new alignment\r
- window. </li>\r
-<li>The <a\r
- href="#connections"><strong>"Connections"</strong>\r
- Preferences</a> tab allows you to change the links \r
- made from Jalview to your default web browser.\r
-</li>\r
-<li>The <a href="#output"><strong>"Output"</strong>\r
- Preferences</a> tab contains settings affecting the export of sequence\r
-alignments and EPS files.\r
-</li>\r
-</ul></p>\r
+<p>There are four tabs in the Preferences dialog box: \r
+<ul>\r
+ <li>The <a href="#visual"><strong>"Visual"</strong> Preferences</a> \r
+ tab allows you to configure the default display for a new alignment window. \r
+ </li>\r
+ <li>The <a\r
+ href="#connections"><strong>"Connections"</strong> Preferences</a> \r
+ tab allows you to change the links made from Jalview to your default web browser. \r
+ </li>\r
+ <li>The <a href="#output"><strong>"Output"</strong> Preferences</a> \r
+ tab contains settings affecting the export of sequence alignments and EPS \r
+ files. </li>\r
+ <li>The <a href="#editing"><strong>"Editing"</strong> Preferences</a> \r
+ tab contains settings affecting the export of sequence alignments and EPS \r
+ files.</li>\r
+ <li>The <a href="#editing"><strong>"DAS Settings"</strong> Preferences</a> \r
+ tab allows you to select which DAS sources to use when fetching DAS Features.</li>\r
+</ul>\r
+</p>\r
<p><strong><a name="visual">Visual</a> Preferences tab</strong></p>\r
<p><em>Maximise Window</em> - If this is selected, a new alignment window will stretch \r
to fit the available space.</p>\r
+<p><em>Show Overview Window</em> - When this is selected, the <a\r
+ href="overview.html">alignment overview</a> panel is opened by\r
+ default for a new alignment window.</p>\r
<p><em>Show Annotations</em> - If this is selected the new window will display an annotation \r
panel below the sequences. This annotation panel may have several rows describing \r
the whole alignment. The 3 standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em> \r
<p><em>Full Sequence ID</em> - If selected the ID panel will display the name of a sequence \r
plus the start and end residues in the format name/start-end. If not selected, \r
the displayed ID will be the name of the sequence.</p>\r
-<p><em>Font</em> - The default font name, size and style can be set for a new alignment \r
- window. </p>\r
+<p><em>Font</em> - The default font name, size and style can be set for a new \r
+ alignment window. </p>\r
+<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster rendering \r
+ of the alignment.</p>\r
+<p><em>Wrap Alignment</em> - Select whether to open new alignment windows in wrapped \r
+ mode or not.</p>\r
<p><em>Gap Symbol</em> - The default gap symbol may be set to either "-" or "."</p>\r
<p><em>Colour</em> - The default colour scheme for a new alignment window. If \r
the chosen option is "User Defined" then the last User Defined Colour \r
<br>\r
You must enter $SEQUENCE_ID$ within your URL. This will be replaced by the chosen \r
sequence id when you click on it. </p>\r
+<p>eg.<br>\r
+ UniRef100 = http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100<br>\r
+ Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$</p>\r
<p><em>Default Browser (Unix)</em><br>\r
Its difficult in Java to detect the default web browser for Unix users. If Jalview \r
can't find your default web browser, enter the name or full path to your web \r
</ul>\r
</p>\r
<p><em>Sequence//Start-End Numbering</em><br>\r
-The output tab also has a group of checkboxes for each file format. If these \r
+ The output tab also has a group of checkboxes for each file format. If these \r
are ticked, then Jalview will write files with the start and end sequence positions \r
- appended to each sequence id:<br>\r
+ appended to each sequence id:\r
<pre>\r
- >ID//1-10\r
+ >ID/1-10\r
AACDEAAFEA\r
</pre>\r
-<br>If the boxes are left unchecked for a particular \r
- format, the sequence limits will not be appended to the sequence id. </p>\r
+<p>If the boxes are left unchecked for a particular format, the sequence limits \r
+ will not be appended to the sequence id. </p>\r
+</p>\r
+<p><em>Use Modeller Output</em></p>\r
+<p>This option only applies to PIR format output. Jalview\r
+ automatically reads PIR files with sequence descriptions compatible\r
+ with the program <a\r
+ href="http://salilab.org/modeller/">Modeller</a>.\r
+ If this option is selected <a href="../io/modellerpir.html">Jalview will write Modeller style PIR\r
+ files</a> with correct start/end numbering and PDB file association (if\r
+ available). The Jalview id/start-end option is ignored if Modeller output is selected.\r
+<p><a name="editing"><strong>Editing Preferences tab</strong></a></p>\r
+<p>There are currently 2 options available which can be selected / deselected. \r
+</p>\r
+<p><em>AutoCalculate Consensus</em> - For large alignments it can be useful to \r
+ deselect "Autocalculate Consensus" when editing. This prevents lengthy \r
+ calculations which are performed after each sequence edit. New alignment windows \r
+ will have their "Autocalculate Consensus" option set according to \r
+ this setting. </p>\r
+<p><em>Pad gaps when editing</em> - New alignment windows will "Pad Gaps" \r
+ according to this setting.</p>\r
+<p><a name="editing"><strong>DAS Settings </strong></a></p>\r
+<p>See <a href="dassettings.html">DAS Settings</a></p>\r
<p> </p>\r
<p> </p>\r
</body>\r
git://source.jalview.org / jalview.git / blobdiff