From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 24 Oct 2016 13:13:04 +0000 (+0100)
Subject: Merge branch 'develop' into releases/Release_2_10_0_Branch
X-Git-Tag: Release_2_10_0b1~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ea3d24d953af89ca95d4480371149b70abbfcc67;hp=63ac1681563e8abbc3b5fd06e4a6afa6d08dca90;p=jalview.git

Merge branch 'develop' into releases/Release_2_10_0_Branch
---

diff --git a/help/html/releases.html b/help/html/releases.html
index 11c7f58..5718926 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -54,17 +54,24 @@
       <td><em>Application</em>
         <ul>
           <li>3D Structure chooser opens with 'Cached structures' view if structures already loaded</li>
+          <li>Progress bar reports models as they are loaded to structure views</li> 
         </ul></td>
       <td>
         <div align="left">
+          <em>General</em>
+          <ul>
+            <li>Colour by conservation always enabled and no tick shown in menu when PID shading applied</li>
+          </ul>
           <em>Application</em>
           <ul>
+            <li>Jalview projects with views of local PDB structure files saved on Windows cannot be opened on OSX</li>
+            <li>Multiple structure views can be opened and superposed without timeout for structures with multiple models or multiple sequences in alignment</li>
             <li>Cannot import or associated local PDB files without a PDB ID HEADER line</li>
             <li>RMSD is not output in Jmol console when superposition is performed</li> 
             <li>Drag and drop of URL from Browser fails for Linux and OSX versions earlier than El Capitan</li>
             <li>ENA client ignores invalid content from ENA server</li>
-            <li>Exceptions are not raised when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option</li>
-            <li>Exceptions are not raised when a new view is created on the alignment</li>
+            <li>Exceptions are not raised in console when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option</li>
+            <li>Exceptions are not raised in console when a new view is created on the alignment</li>
           </ul>
           <em>New Known Issues</em>
           <ul><li>Drag and drop from URL links in browsers do not work on Windows</li></ul>
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3a92e4b..c1c88c1 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -612,7 +612,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     boolean recalc = false;
     if (cs != null)
     {
-      cs.setConservationApplied(recalc = getConservationSelected());
+      recalc = getConservationSelected();
       if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
               || cs instanceof Blosum62ColourScheme)
       {
@@ -629,6 +629,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         cs.setConsensus(hconsensus);
         cs.setConservation(hconservation);
       }
+      cs.setConservationApplied(getConservationSelected());
       cs.alignmentChanged(alignment, hiddenRepSequences);
     }
     if (getColourAppliesToAllGroups())
diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 341a814..d7b26b0 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -39,6 +39,8 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MapList;
 
@@ -329,4 +331,22 @@ public class AlignViewportTest
     assertNotNull("Quality in column 1 is null", annotations[0]);
     assertTrue("No quality value in column 1", annotations[0].value > 10f);
   }
+
+  @Test(groups = { "Functional" })
+  public void testSetGlobalColourScheme()
+  {
+    /*
+     * test for JAL-2283 don't inadvertently turn on colour by conservation
+     */
+    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+            Boolean.FALSE.toString());
+    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", FormatAdapter.FILE);
+    ColourSchemeI cs = new PIDColourScheme();
+    af.getViewport().setGlobalColourScheme(cs);
+    assertFalse(cs.conservationApplied());
+  }
 }