\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
+ f</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
</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 can now read and write \r
+ PIR files with sequence descriptions compatible with the program <a href="http://salilab.org/modeller/">Modeller</a>. \r
+ If this option is selected Jalview will write the sequence description in the \r
+ following format:</p>\r
+<pre>>P1;O80429_MAIZE\r
+sequence:O80429_MAIZE:1:.:140:.:.</pre>\r
+If a sequence description existed before the file was saved, it will be appended \r
+to the new Modeller style desciption. The Jalview id/start-end option is ignored \r
+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> </p>\r
<p> </p>\r
</body>\r
git://source.jalview.org / jalview.git / commitdiff