From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 4 Jun 2014 08:36:30 +0000 (+0100)
Subject: JAL-1503 tidying docs
X-Git-Tag: Release_2_8_1~4^2~2^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8bc6bb1e8aaa61bd6f1e63d65c5799263063e582;p=jalview.git

JAL-1503 tidying docs
---

diff --git a/help/help.jhm b/help/help.jhm
index cc272e8..20f3c88 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -49,6 +49,7 @@
    <mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>
    <mapID target="seqfeatures.settings.selcols" url="html/features/featuresettings.html#selectbyfeature"/>
    <mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
+   <mapID target="viewingpdbs.reps" url="html/features/viewingpdbs.html#viewreps"/>
    <mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
    <mapID target="pdbjmol" url="html/features/jmol.html"/>
    <mapID target="varna" url="html/features/varna.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index a65cafe..626a244 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -23,6 +23,7 @@
  <tocitem text="What's new" target="new" expand="true">
     <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
     <tocitem text="Select columns containing sequence features" target="seqfeatures.settings.selcols"/>
+    <tocitem text="View all representative PDB structures" target="viewingpdbs.reps"/>
     <tocitem text="Support for PAM250 for trees and PCA calculations" target="subtMatrices.pam250"/>
   </tocitem>
   <tocitem text="Editing Alignments" target ="edit"/>	
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 048f0ef..c2143a3 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -38,7 +38,7 @@ sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.</p>
       with the current selection, superposed according to the currently selected region of the alignment.<br/><em>This
       capability was added in Jalview 2.7</em>
     </li>
-    <li>The <strong>&quot;Structure&#8594;View all <em>N</em>
+    <li><a name="viewreps"/>The <strong>&quot;Structure&#8594;View all <em>N</em>
         representative structures
     </strong> option will open a new window containing exactly one structure per
       currently selected sequence.<br />
diff --git a/help/html/releases.html b/help/html/releases.html
index 1eb7abf..35c522a 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -36,10 +36,11 @@
 	</tr>
 		<tr>
 			<td><div align="center">
-					<strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>3/6/2014</em></strong>
+					<strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
 				</div></td>
 			<td>
 				<!--  New features --> <!--  For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
+				<em>General</em>
 				<ul>
 					<li>Internationalisation of user interface (usually called
 						i18n support) and translation for Spanish locale</li>
@@ -47,7 +48,10 @@
 						Ctrl-G/Shift Ctrl-G</li>
 					<li>Improved group creation/removal options in
 						alignment/sequence Popup menu</li>
-
+					<li>Sensible precision for symbol distribution percentages
+						shown in logo tooltip.</li>
+					<li>Annotation panel height set according to amount of
+						annotation when alignment first opened</li>
 				</ul> <em>Application</em>
 				<ul>
 					<li>Interactive consensus RNA secondary structure prediction
@@ -68,14 +72,6 @@
 						(PAM250)</li>
 					<li>Experimental support for retrieval and viewing of flanking
 						regions for an alignment</li>
-				</ul> <em>Applet</em>
-				<ul>
-
-				</ul> <em>Other improvements</em>
-				<li>Sensible precision for symbol distribution percentages
-					shown in logo tooltip.</li>
-				<li>Annotation panel height set according to amount of
-					annotation when alignment first opened</li>
 				</ul>
 			</td>
 			<td>