From a990c2c6facfd04d61d316dcafba31d03747d162 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 3 Sep 2017 13:35:45 +0100
Subject: [PATCH] JAL-2588 overview tab docs, whats new and release notes

---
 help/help.jhm                       |    1 +
 help/helpTOC.xml                    |    1 +
 help/html/features/preferences.html |   30 ++++++++++++++++++++++++++++++
 help/html/releases.html             |    1 +
 4 files changed, 33 insertions(+)

diff --git a/help/help.jhm b/help/help.jhm
index c12436f..8e4961f 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -163,4 +163,5 @@
    <mapID target="printSetupIcon" url="icons/setup.png" />
    
    <mapID target="overview" url="html/features/overview.html" />
+   <mapID target="overviewprefs" url="html/features/preferences.html#overview" />
 </map>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index f3311a7..4636ea3 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -28,6 +28,7 @@
 				<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
 				<tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
 				<tocitem text="Omit hidden regions in Overview" target="overview"/>
+				<tocitem text="Show gaps as grey in overview" target="overviewprefs"/>
 				<tocitem text="identifers.org for URL Links" target="linksprefs" />
 				<tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
 		</tocitem>
diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index acd7ba6..b29b66b 100755
--- 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.
@@ -181,6 +184,33 @@
       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>
diff --git a/help/html/releases.html b/help/html/releases.html
index bab2bac..81e75ea 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -82,6 +82,7 @@ li:before {
               in grey (sequences used to be coloured grey, and gaps were
               white)
             </li>
+            <li><!-- JAL-2588 -->Overview tab in Jalview Desktop Preferences</li>
           </ul>
         </div></td>
       <td><div align="left">
-- 
1.7.10.2