JAL-3033 always run the toJs core file build before building core files from classlis...

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

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 6e8d3e4..8c6b699 100755 (executable)
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -41,6 +41,9 @@
         Preferences</a> tab allows you to configure default colourschemes
       for a new alignment window.
     </li>
+    <li>The <a href="#overview"><strong>&quot;Overview&quot;</strong>
+        Preferences</a> tab configures defaults for the overview window.
+    </li>
     <li>The <a href="#structure"><strong>&quot;Structure&quot;</strong>
         Preferences</a> tab allows you to configure options for obtaining
       and displaying structure information.
@@ -59,12 +62,7 @@
       sequence alignments and EPS files.
     </li>
     <li>The <a href="#editing"><strong>&quot;Editing&quot;</strong>
-        Preferences</a> tab contains settings affecting the export of
-      sequence alignments and EPS files.
-    </li>
-    <li>The <a href="dassettings.html"><strong>&quot;DAS
-          Settings&quot;</strong> Preferences</a> tab allows you to select which DAS
-      sources to use when fetching DAS Features.
+        Preferences</a> tab contains settings affecting behaviour when editing alignments.
     </li>
     <li>The <a href="../webServices/webServicesPrefs.html"><strong>&quot;Web
           Service&quot;</strong> Preferences</a> tab allows you to configure the <a
@@ -181,6 +179,33 @@
       by Annotation...</a> is selected from the alignment window's colours
     menu.
   </p>
+   <p>
+    <a name="overview"><strong>&quot;Overview&quot;
+        Preferences tab</strong>
+  </p>
+  <p>
+    <em>Use legacy gap colouring (gaps are white)</em> - when enabled,
+    Jalview's overview shows gaps as white, and sequences with no
+    colourscheme applied as grey.
+  </p>
+  <p>
+    <em>Show Hidden regions when opening overview</em> - default setting
+    for inclusion of hidden regions.
+  </p>
+  <p>
+    <em>Gap Colour</em> - When legacy gap colouring is not enabled, this
+    configures the default colour for gaps in the overview.
+  </p>
+  <p>
+    <em>Hidden Colour</em> - colour used to highlight regions in the
+    overview that are hidden in the alignment.
+  </p>
+  <p>
+    <em>Gap Colour</em> - The default colour scheme for a new alignment
+    window. If the chosen option is &quot;User Defined&quot; then the
+    last User Defined Colour loaded or saved via the User Defined
+    Colours panel will be loaded.
+  </p>
   <p>
     <a name="structure"><strong>&quot;Structure&quot;
         Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
@@ -205,7 +230,7 @@
     the backbone atoms in the PDB file will be extracted as annotation
     lines shown on the alignment.
   <p>
-    <em>Default structure viewer</em> - choose JMOL or CHIMERA for
+    <em>Default structure viewer</em> - choose Jmol or CHIMERA for
     viewing 3D structures.
   <p>
     <em>Path to Chimera program</em> - Optional, as Jalview will search
@@ -218,7 +243,7 @@
         Preferences tab</strong></a>
   </p>
   <p>
-    <em>Default Browser (Unix)</em><br> Its difficult in Java to
+    <em>Default Browser (Unix)</em><br> It's difficult in Java to
     detect the default web browser for Unix users. If Jalview can't find
     your default web browser, enter the name or full path to your web
     browser application.
@@ -261,7 +286,11 @@
     The <em>Custom only</em> button limits the entries in the table to
     just those you have configured yourself <em>via</em> the <em>Edit
       Links</em> buttons. Press <em>Show all</em> to clear any filters.
-  <p>
+  </p>
+  <p>The links table is prepopulated with persistent URLs for many common
+    bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
+    the <em>identifiers.org</em> website, and the names and URLs are not
+    user editable.
     <a href="../webServices/urllinks.html#urllinks">Read more about configuring
       URL links.</a>
   </p>
@@ -273,7 +302,7 @@
     allows the user to set a default rendering style for EPS export:
   <ul>
     <li>&quot;Prompt each time&quot;<br> Choose this to be
-      asked select between Lineart and Text each time you make an EPS
+      asked to select between Lineart and Text each time you make an EPS
       file.
     </li>
     <li>&quot;Lineart&quot;<br> EPS files will accurately
@@ -302,7 +331,7 @@
     ignored if <em>&quot;Automatically set ID width&quot;</em> is set.
   </p>
   <p>
-    <em>Sequence//Start-End Numbering</em><br> The output tab also
+    <em>Sequence/Start-End Numbering</em><br> The output tab also
     has a group of checkboxes for each file format. If these are ticked,
     then Jalview will write files with the start and end sequence
     positions appended to each sequence id:
@@ -333,7 +362,7 @@
     and PDB file association (if available). The Jalview id/start-end
     option is ignored if Modeller output is selected.
   <p>
-    <a name="editing"><strong>e&quot;Editinge&quot; Preferences tab</strong></a>
+    <a name="editing"><strong>&quot;Editing&quot; Preferences tab</strong></a>
   </p>
   <p>There are currently three options available which can be
     selected / deselected.</p>