Merge branch 'develop' into developtomchmmer

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

diff --git a/help/html/features/preferences.html b/help/help/html/features/preferences.html
similarity index 96%
rename from help/html/features/preferences.html
rename to help/help/html/features/preferences.html
index 5bca358..5bb0b8a 100755 (executable)
--- a/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -62,15 +62,11 @@
       sequence alignments and EPS files.
     </li>
     <li>The <a href="#editing"><strong>&quot;Editing&quot;</strong>
-        Preferences</a> tab contains settings affecting the behaviour of alignments as you edit them.
+        Preferences</a> tab contains settings affecting behaviour when editing alignments.
     </li>
     <li>The <a href="#hmmer"><strong>&quot;HMMER&quot;</strong>
         Preferences</a> tab allows you to configure locally installed HMMER tools.
     </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.
-    </li>
     <li>The <a href="../webServices/webServicesPrefs.html"><strong>&quot;Web
           Service&quot;</strong> Preferences</a> tab allows you to configure the <a
       href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
@@ -237,7 +233,7 @@
     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
@@ -250,7 +246,7 @@
         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.
@@ -294,7 +290,7 @@
     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>The links table is prepoulated with persistent URLs for many common
+  <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.
@@ -309,7 +305,7 @@
     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
@@ -338,7 +334,7 @@
     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: