From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 23 Nov 2016 11:45:33 +0000 (+0000)
Subject: Merge branch 'documentation/JAL-2325_release2101' into develop
X-Git-Tag: Release_2_10_1~10^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=940b2a9de4b6d750944a7d915eda70c5d2e024b0;hp=c605ffeba9f0df32f111c418763122a1b1ad42ec;p=jalview.git

Merge branch 'documentation/JAL-2325_release2101' into develop
---

diff --git a/help/html/releases.html b/help/html/releases.html
index 2d0c4e8..30aa7f2 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -55,7 +55,9 @@
 	    <em>General</em>
             <ul>
 	      <li><!-- JAL-98 -->Improved memory usage: sparse arrays used for all consensus calculations</li>
-	      <li><!-- JAL- --></li>
+	      <li><!-- JAL-2177 -->Updated Jmol shipped with applet and desktop to 14.6.4</li>
+          <li><!--  --></li>
+        
           </ul>
           <em>Application</em>
           <ul>
@@ -63,7 +65,8 @@
    	    <li><!-- JAL-2282-->New replacement token for creating URLs <em>just</em> from database cross references. Users with custom links will receive a warning dialog asking them to update their preferences.</li>
 	    <li><!-- JAL-2287-->Cancel button and escape listener on dialog warning user about disconnecting Jalview from a Chimera session</li>
 	    <li><!-- JAL-2281-->Custom URL links for database cross-references are matched to database name regardless of case</li>
-	    <li></li>
+	    <li><!-- JAL-1738-->Select highlighted columns menu item and keystroke (B) to mark columns containing highlighted regions from structure selections or results of a Find operation</li>
+        <li><!-- JAL-2284-->Command line option for batch-generation of HTML pages rendering alignment data with the BioJS MSAviewer</li>
 	    
 
           </ul>
@@ -84,16 +87,28 @@
 	    <li><!-- JAL-2301 -->Threonine incorrectly reported as not hydrophobic</li>
 	    <li><!-- JAL-2318 -->Updates to documentation pages (above PID threshold, amino acid properties)</li>
 	    <li><!-- JAL-2292 -->Lower case residues in sequences are not reported as mapped to residues in a structure file in the View Mapping report</li>
+        <li><!--JAL-2324 -->Identical features with non-numeric scores could be added multiple times to a sequence</li>
+        
           </ul>
           <em>Application</em>
           <ul>
-	    <li><!-- JAL-2282-->Custom URL links for specific database names without regular expressions also offer invalid links from Sequence ID</li>
+	    <li><!-- JAL-2282-->Custom URL links for specific database names without regular expressions also offer links from Sequence ID</li>
 	    <li><!-- JAL-2315-->Removing a single configured link in the URL links pane in Connections preferences doesn't actually update Jalview configuration</li>
 	    <li><!-- JAL-2272-->CTRL-Click on a selected region to open the alignment area popup menu doesn't work on El-Capitan</li>
 	    <li><!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF files with similarly named sequences if dropped onto the alignment</li>
 	    <li><!-- JAL-2312 -->Additional mappings are shown for PDB entries where more chains exist in the PDB accession than are reported in the SIFTS file</li>
 	    <li><!-- JAL-2317-->Certain structures do not get mapped to the structure view when displayed with Chimera</li>
 	    <li><!-- JAL-2317-->No chains shown in the Chimera view panel's View->Show Chains submenu</li>
+        <li><!--JAL-2277 -->Export as HTML with embedded SVG doesn't work for wrapped alignment views</li>
+            <li>
+              <!--JAL-2335 -->Disulphide bond features shown as two
+              highlighted residues rather than a range in linked
+              structure views, and treated correctly when selecting and
+              computing trees from features
+            </li>
+        <li><!--JAL-2197 -->Rename UI components for running JPred predictions from 'JNet' to 'JPred'</li>
+
+            <li><!--JAL- --></li>
       
       <li><!-- --></li>
 	    <li><!-- --></li>
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index d5593e3..3feae5d 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -192,13 +192,13 @@ public class JnetAnnotationMaker
           if (id.equals("JNETCONF"))
           {
             annot = new AlignmentAnnotation(preds[i].getName(),
-                    "JNet Output", annotations, 0f, 10f,
+                    "JPred Output", annotations, 0f, 10f,
                     AlignmentAnnotation.BAR_GRAPH);
           }
           else
           {
             annot = new AlignmentAnnotation(preds[i].getName(),
-                    "JNet Output", annotations);
+                    "JPred Output", annotations);
           }
 
           if (seqRef != null)