+++ /dev/null
-<html>\r
-\r
-<head><title>Preferences</title></head>\r
-\r
-<body>\r
-<p><strong>Preferences</strong></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
- 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
- may be shown or hidden by default.</p>\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 \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
- 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:\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 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
-</html>\r
git://source.jalview.org / jalview.git / blobdiff