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<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 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><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>Font</em> - The default font name, size and style can be set for a new alignment \r
window. </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><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:<br>\r
+<pre>\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> </p>\r
+<p> </p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff