Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

diff --git a/RELEASE b/RELEASE
index c29c5d5..702d6e7 100644 (file)
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
-jalview.release=Release_2_10_Branch
-jalview.version=2.10.0
+jalview.release=Release_2_10_0_Branch
+jalview.version=2.10.0b1

diff --git a/examples/exampleFile.jar b/examples/exampleFile.jar
index 3231974..2f9000d 100755 (executable)
Binary files a/examples/exampleFile.jar and b/examples/exampleFile.jar differ

diff --git a/examples/exampleFile_2_3.jar b/examples/exampleFile_2_3.jar
index adf707e..1a8bef0 100644 (file)
Binary files a/examples/exampleFile_2_3.jar and b/examples/exampleFile_2_3.jar differ

diff --git a/examples/exampleFile_2_7.jar b/examples/exampleFile_2_7.jar
index 0b70e66..7cd9d77 100644 (file)
Binary files a/examples/exampleFile_2_7.jar and b/examples/exampleFile_2_7.jar differ

diff --git a/examples/ferredoxin.nw b/examples/ferredoxin.nw
index 0b949de..89ea348 100755 (executable)
--- a/examples/ferredoxin.nw
+++ b/examples/ferredoxin.nw
@@ -1 +1 @@
-(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);
+(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER1_ARATH:64.0,FER2_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);

diff --git a/examples/plantfdx.fa b/examples/plantfdx.fa
index f314c85..80d7133 100644 (file)
--- a/examples/plantfdx.fa
+++ b/examples/plantfdx.fa
@@ -34,18 +34,18 @@ IETHKEEELTA-
 ----------------------------------------------------------ATYKVKFITPEGEQ
 EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVT
 IETHREEDMV--
->FER1_ARATH/1-148
-----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
-EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
-IETHKEEAIM--
->FER_BRANA/1-96
-----------------------------------------------------------ATYKVKFITPEGEQ
-EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT
-IETHKEEELV--
 >FER2_ARATH/1-148
 ----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL
 EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT
 IETHKEEDIV--
+>FER_BRANA/1-96
+----------------------------------------------------------ATYKVKFITPEGEQ
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT
+IETHKEEELV--
+>FER1_ARATH/1-148
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
+IETHKEEAIM--
 >Q93Z60_ARATH/1-118
 ----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
 EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD--------------------

diff --git a/examples/uniref50.fa b/examples/uniref50.fa
index 4bdbfb4..6e6c670 100755 (executable)
--- a/examples/uniref50.fa
+++ b/examples/uniref50.fa
@@ -34,18 +34,18 @@ TIETHKEEELTA-
 -----------------------------------------------------------ATYKVKFITPEGE
 QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV
 TIETHREEDMV--
->FER1_ARATH Ferredoxin-1, chloroplast precursor
-MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
-QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV
-VIETHKEEAIM--
->FER_BRANA Ferredoxin
------------------------------------------------------------ATYKVKFITPEGE
-QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV
-TIETHKEEELV--
 >FER2_ARATH Ferredoxin-2, chloroplast precursor
 MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE
 LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV
 TIETHKEEDIV--
+>FER_BRANA Ferredoxin
+-----------------------------------------------------------ATYKVKFITPEGE
+QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV
+TIETHKEEELV--
+>FER1_ARATH Ferredoxin-1, chloroplast precursor
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV
+VIETHKEEAIM--
 >Q93Z60_ARATH At1g10960/T19D16_12
 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
 QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------

diff --git a/examples/uniref50_mz.fa b/examples/uniref50_mz.fa
index 9974fc7..725d210 100644 (file)
--- a/examples/uniref50_mz.fa
+++ b/examples/uniref50_mz.fa
@@ -18,11 +18,11 @@ AAYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDD
 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDD
 >FER3_RAPSA/1-66 Ferredoxin, leaf L-A
 ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDD
->FER1_ARATH/53-118 Ferredoxin-1, chloroplast precursor
+>FER2_ARATH/53-118 Ferredoxin-1, chloroplast precursor
 ATYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDD
 >FER_BRANA/1-66 Ferredoxin
 ATYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDD
->FER2_ARATH/53-118 Ferredoxin-2, chloroplast precursor
+>FER1_ARATH/53-118 Ferredoxin-2, chloroplast precursor
 ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD
 >Q93Z60_ARATH/53-118 At1g10960/T19D16_12
 ATYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD

diff --git a/help/html/editing/index.html b/help/html/editing/index.html
index 471e520..fd8c5a3 100755 (executable)
--- a/help/html/editing/index.html
+++ b/help/html/editing/index.html
@@ -49,9 +49,8 @@
     right to insert gaps and remove gaps.<br> If the current
     selection is a group over all sequences in the alignment, or a group
     over some sequences or all columns in the alignment, then hold down
-    either &quot;Control&quot; key (or the &quot;Alt;&quot; on OSX if
-    &quot;Control&quot; does not work) and drag the residue left or
-    right to edit all sequences in the defined group at once.
+    &quot;Control&quot; key (&quot;Cmd&quot; key on OSX) and drag the residue 
+    left or right to edit all sequences in the defined group at once.
   </p>
   <p>
     <em>Copy/paste/cut/delete</em> - any sequences which are in the

diff --git a/help/html/releases.html b/help/html/releases.html
index ee1318d..3fe08cb 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,29 +47,59 @@
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.9.0b2">2.10.0b1</a><br />
-            <em>20/10/2016</em></strong>
+          <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
+            <em>25/10/2016</em></strong>
         </div>
       </td>
       <td><em>Application</em>
         <ul>
-          <li>3D Structure chooser opens with 'Cached structures' view if structures already loaded</li>
+          <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 BLOSUM or PID shading applied</li>
+            <li>FER1_ARATH and FER2_ARATH labels were switched in
+              example sequences/projects/trees</li>
+          </ul>
           <em>Application</em>
           <ul>
-            <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>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>
+            <li>OSX right-click fixed for group selections:
+              CMD-click to insert/remove gaps in groups and CTRL-click
+              to open group pop-up menu</li>
           </ul>
-          <em>New Known Issues</em>
-          <ul><li>Drag and drop from URL links in browsers do not work on Windows</li></ul>
           <em>Build and deployment</em>
-          <ul><li>URL link checker now copes with multi-line anchor tags</li></ul>
+          <ul>
+            <li>URL link checker now copes with multi-line anchor
+              tags</li>
+          </ul>
+          <em>New Known Issues</em>
+          <ul>
+            <li>Drag and drop from URL links in browsers do not
+              work on Windows</li>
+          </ul>
         </div>
       </td>
     </tr>

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index bae80db..3266fab 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -616,13 +616,14 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+    boolean isControlDown = Platform.isControlDown(evt);
+    if (evt.isShiftDown() || isControlDown)
     {
-      if (evt.isAltDown() || evt.isControlDown())
+      editingSeqs = true;
+      if (isControlDown)
       {
         groupEditing = true;
       }
-      editingSeqs = true;
     }
     else
     {

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3a92e4b..c1c88c1 100644 (file)
--- 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..00c52ed 100644 (file)
--- 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 +331,20 @@ 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("DEFAULT_COLOUR_PROT", "NONE");
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+            Boolean.TRUE.toString());
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", FormatAdapter.FILE);
+    ColourSchemeI cs = new PIDColourScheme();
+    af.getViewport().setGlobalColourScheme(cs);
+    assertFalse(cs.conservationApplied());
+  }
 }