\r
<body>\r
<p><strong>Preferences</strong></p>\r
-<p> The <strong>"Visual" </strong>tab on the preferences window allows \r
- you to configure the default display for a new alignment window. </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
<p><em>Show Annotations</em> - If this is selected the new window will display an annotation \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>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
be opened when Jalview is started. You can change the default file by clicking \r
on file name and either typing in the file path or selecting it from the file \r
chooser window. </p>\r
-<p>The "Connections" tab allows you to change the links made from Jalview \r
- to your default web browser.</p>\r
+<p><a name="connections"><strong>"Connections" Preferences tab</strong></a></p>\r
<p><em>URL Link From Sequence ID</em><br>\r
Right click a sequence id to see a popup menu with "Link" as one of \r
the items. By default the item "SRS" is added to this link menu. This \r
box "Use a Proxy Server" and enter the address and port details as \r
necessary. Web Services will not work if you are using a proxy server and do \r
not enter the settings here.</p>\r
-<p>The "Export" tab has a selection box allowing the user to set a default \r
- rendering style for EPS export. "Lineart" will produce an accurate \r
- representation of the visible alignment in Jalview, all the characters will \r
- be graphics objects. "Text" will produce a much smaller file and will \r
- rely on the software you use to view the EPS file, such as Adobe Illustrator, \r
- having the same font as the file was created with. You will only be able to \r
- edit text in an EPS file if you select the "Text" option.<br>\r
- Choose "Prompt each time" to select between Lineart and Text each \r
- time you make an EPS file.</p>\r
+<p><a name="output"><strong>Output Preferences tab</strong></a></p>\r
+<p><em>EPS Rendering Style</em><br>\r
+This is a selection box which allows the \r
+ user to set a default rendering style for EPS export: \r
+<ul><li>"Lineart"<br>EPS files will accurately\r
+reproduce the alignment view in Jalview and all characters will be\r
+converted into line art. Files generated in this way are large and are\r
+not easily editable, but have no font table dependencies.</li>\r
+<li>"Text"<br>EPS files will be a mixture of text and\r
+lineart. This produces compact files that can be edited easily in\r
+programs like Microsoft Word and Adobe Illustrator, but can be\r
+problematic if the fonts available to jalview are not accessible by\r
+the program reading the EPS file.\r
+<li>"Prompt each time"<br>Choose this to be asked select between Lineart and Text each time you make an EPS file.</li>\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
+ are ticked, then Jalview will write files with the start and end sequence positions \r
+ appended to each sequence id:\r
+<pre>\r
+ >ID/1-10\r
+ AACDEAAFEA\r
+</pre>\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> </p>\r
<p> </p>\r
</body>\r
git://source.jalview.org / jalview.git / blobdiff