Merge branch 'develop' into features/JAL-2446NCList

diff --git a/help/help.jhm b/help/help.jhm
index 54cce2a..363f549 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -153,7 +153,7 @@
    <mapID target="uniprotfetcher" url="html/features/uniprotsequencefetcher.html" />
    
    <mapID target="urllinks" url="html/webServices/urllinks.html" />
-   <mapID target="linksprefs" url="html/features/Preferences.html#links" />
+   <mapID target="linksprefs" url="html/features/preferences.html#links" />
 
    <mapID target="backIcon" url="icons/back.png" />
    <mapID target="forwardIcon" url="icons/forward.png" />
@@ -161,5 +161,5 @@
    <mapID target="printIcon" url="icons/print.png" />
    <mapID target="printSetupIcon" url="icons/setup.png" />
    
-   <mapID target="overview" url="features/overview.html" />
+   <mapID target="overview" url="html/features/overview.html" />
 </map>

diff --git a/help/html/releases.html b/help/html/releases.html
index e39a4c1..86a1100 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -71,7 +71,7 @@ li:before {
       <td width="60" nowrap>
         <div align="center">
           <strong><a name="Jalview.2.10.2">2.10.2</a><br />
-            <em>20/6/2017</em></strong>
+            <em>8/8/2017</em></strong>
         </div>
       </td>
       <td><div align="left">
@@ -91,7 +91,8 @@ li:before {
               extension when importing structure files without embedded
               names or PDB accessions
             </li>
-            <li><!-- JAL-2547 -->Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent</li>
+          <li><!-- JAL-2547 -->Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent</li>
+         <li><!-- JAL-2631 -->Graduated feature colour style example included in the example feature file</li>
           </ul>
           <em>Application</em>
           <ul>
@@ -163,7 +164,13 @@ li:before {
           <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
           <li><!-- JAL-2547 -->Sequence features shown in tooltip for gaps before start of features</li>
           <li><!-- JAL-2576 -->Very large alignments take a long time to load</li>
-          <li><!-- JAL-2590 -->Cannot load Newick trees from eggnog ortholog database</li>
+           <li><!-- JAL-2623 -->Graduated feature colour threshold not restored to UI when feature colour is edited</li>
+           <li><!-- JAL-2624 -->Feature colour thresholds not respected when rendered on overview and structures when opacity at 100%</li>
+           <li><!-- JAL-2630 -->Structure and alignment overview update as graduate feature colour settings are modified via the dialog box</li>
+           <li><!-- JAL-147 -->Vertical scrollbar jumps one page-width at a time when scrolling vertically in wrapped mode.</li>
+           <li><!-- JAL-2034 -->Overview window doesn't always update when a group defined on the alignment is resized</li>
+           <li><!-- JAL-2605 -->Mouseovers on left/right scale region in wrapped view result in positional status updates</li>
+           <li><!-- JAL-2563 -->Status bar shows position for ambiguous amino acid and nucleotide symbols</li>
           </ul>
           <em>Application</em>
           <ul>
@@ -198,6 +205,7 @@ li:before {
           <ul>
           <li><!--  JAL-2566 -->Protein/CDS view scrolling not always in phase after a sequence motif find operation</li>
           <li><!-- JAL-2550 -->Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols</li>  
+            <li><!-- JAL-2590 -->Cannot load Newick trees from eggnog ortholog database</li>
           </ul>
           
           </div>

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e5d550f..162d100 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2944,7 +2944,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void showAllColumns_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenColumns();
-    repaint();
+    alignPanel.paintAlignment(true);
     viewport.sendSelection();
   }
 
@@ -2952,7 +2952,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelSequences_actionPerformed(ActionEvent e)
   {
     viewport.hideAllSelectedSeqs();
-    // alignPanel.paintAlignment(true);
   }
 
   /**