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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> 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><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>The <strong>"Connections"</strong> tab allows you to change the links \r
+ made from Jalview to your default web browser.</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>The "<strong>Output</strong>" tab has a selection box allowing the \r
+ user to set a default rendering style for EPS export. "Lineart" will \r
+ produce an accurate representation of the visible alignment in Jalview, all \r
+ the characters will be graphics objects. "Text" will produce a much \r
+ smaller file and will rely on the software you use to view the EPS file, such \r
+ as Adobe Illustrator, having the same font as the file was created with. You \r
+ will only be able to edit text in an EPS file if you select the "Text" \r
+ option.<br>\r
+ Choose "Prompt each time" to select between Lineart and Text each \r
+ time you make an EPS file.</p>\r
+<p>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. If the boxes are left unchecked for a paritcular \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