\r
<body>\r
<p><strong>Preferences</strong></p>\r
-<p>The "Visual" tab on the preferences window allows you to configure \r
- 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
+ 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 the chosen \r
- option is "User Defined" then the last User Defined Colour loaded \r
- or saved via the User Defined Colours panel will be loaded. </p>\r
-<p><em>Open file</em> - If this is selected then the default alignment file will be opened \r
- when Jalview is started. You can change the default file by clicking on file \r
- name and either typing in the file path or selecting it from the file chooser \r
- window. </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
+ loaded or saved via the User Defined Colours panel will be loaded. </p>\r
+<p><em>Sort by</em> - When the alignment is loaded in, it will can be sorted by \r
+ Id or pairwise identity.</p>\r
+<p><em>Open file</em> - If this is selected then the default alignment file will \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><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
+ link will show a web page in your default browser with the selected sequence \r
+ id as part of the URL.<br>\r
+ Jalview allows you to add your own custom links to other web pages. Click new \r
+ to add a new link. You can name the link, this will be displayed on a new menu \r
+ item under the "Link" menu when you right click on a sequence id. \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
+ browser application. </p>\r
+<p><em>Proxy Server</em><br>\r
+ If you normally use a proxy server for using the internet, you must tick the \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><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><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
</html>\r
git://source.jalview.org / jalview.git / blobdiff