New help

[jalview.git] / help / html / features / preferences.html

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index e9ec458..802c22a 100755 (executable)
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -18,15 +18,17 @@
 <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 &quot;-&quot; or &quot;.&quot;</p>\r
-<p><em>Colour</em> - The default colour scheme for a new alignment window. If the chosen \r
-  option is &quot;User Defined&quot; then the last User Defined Colour loaded \r
-  or saved via the User Defined Colours panel will be loaded. </p>\r
+<p><em>Colour</em> - The default colour scheme for a new alignment window. If \r
+  the chosen option is &quot;User Defined&quot; 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 &quot;Connections&quot; tab allows you to change the links made from Jalview \r
-  to your default web browser.</p>\r
+<p>The <strong>&quot;Connections&quot;</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 &quot;Link&quot; as one of \r
   the items. By default the item &quot;SRS&quot; is added to this link menu. This \r
@@ -47,5 +49,21 @@
   box &quot;Use a Proxy Server&quot; 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 &quot;<strong>Output</strong>&quot; tab has a selection box allowing the \r
+  user to set a default rendering style for EPS export. &quot;Lineart&quot; will \r
+  produce an accurate representation of the visible alignment in Jalview, all \r
+  the characters will be graphics objects. &quot;Text&quot; 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 &quot;Text&quot; \r
+  option.<br>\r
+  Choose &quot;Prompt each time&quot; 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>&nbsp;</p>\r
+<p>&nbsp;</p>\r
 </body>\r
 </html>\r