Merge branch 'feature/JAL-3121gffAttributeMap' into develop

diff --git a/.cvsignore b/.cvsignore
deleted file mode 100644 (file)
index 51ece2d..0000000
--- a/.cvsignore
+++ /dev/null
@@ -1,58 +0,0 @@
-NOBACK
-Old_bak
-bak
-classes
-das-obert-src
-old_lib_signed
-temp
-tmpextvamsas
-.#JalviewX.jpx.1.2
-.#JalviewX.jpx.1.4
-.#JalviewX.jpx.1.7
-.#build.xml.1.23
-.#build.xml.1.24
-.#build.xml.1.25
-.#build.xml.1.27
-1
-FeatureRequests.txt
-JalviewApplet.jpx.local
-JalviewApplet_jims.jpx
-JalviewApplet_jims.jpx.local
-JalviewX.jpx.jimpCVS
-JalviewX_cvs.jpx
-JalviewX_jimsApplet.jpx
-JalviewX_jimsApplet.jpx.local
-JalviewX_jimsOwn.jpx
-JalviewX_jimsOwn.jpx.local
-Old.activation.jar
-TODO
-axis.library
-axiskeys
-jalview-jim-jalopy.xml
-jalview.html
-jalview.jpx
-jalview.jpx.local
-jalviewApplet.jar
-jalviewres.library
-javah.library
-log4j-1.2.8.jar
-minimum.library
-new.activation.jar
-prj.el
-regex.library
-test.tree
-jsrc
-keys
-Run Jalview Release.launch
-Run Jalview Release HugeMem.launch
-Run Jalview Groovy Vamsas Release (1).launch
-Run Jalview Lite From Jar (1).launch
-Run Jalview Groovy Vamsas Release.launch
-Run Jalview Lite.launch
-Run Jalview Lite From Jar.launch
-Run Jalview Questionnaire.launch
-Run Jalview Groovy Release.launch
-lib-old
-statcvs
-statcvs_out
-jp_gEHhZay.results_files

diff --git a/RELEASE b/RELEASE
index 1960368..f6e3b96 100644 (file)
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
-jalview.release=releases/Release_2_11_Branch
-jalview.version=2.11.0
+jalview.release=releases/Release_2_11_1_Branch
+jalview.version=2.11.1

diff --git a/dist/.cvsignore b/dist/.cvsignore
deleted file mode 100644 (file)
index 00a0187..0000000
--- a/dist/.cvsignore
+++ /dev/null
@@ -1,3 +0,0 @@
-?*.*
-*.jar
-*.jnlp

diff --git a/help/help/html/.cvsignore b/help/help/html/.cvsignore
deleted file mode 100644 (file)
index 085e8ba..0000000
--- a/help/help/html/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-Thumbs.db

diff --git a/help/help/html/colourSchemes/.cvsignore b/help/help/html/colourSchemes/.cvsignore
deleted file mode 100644 (file)
index 085e8ba..0000000
--- a/help/help/html/colourSchemes/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-Thumbs.db

diff --git a/help/help/html/editing/.cvsignore b/help/help/html/editing/.cvsignore
deleted file mode 100644 (file)
index 085e8ba..0000000
--- a/help/help/html/editing/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-Thumbs.db

diff --git a/help/help/html/features/.cvsignore b/help/help/html/features/.cvsignore
deleted file mode 100644 (file)
index 085e8ba..0000000
--- a/help/help/html/features/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-Thumbs.db

diff --git a/help/help/html/index.html b/help/help/html/index.html
index 62b46a9..36ed33a 100755 (executable)
--- a/help/help/html/index.html
+++ b/help/help/html/index.html
@@ -83,9 +83,11 @@
     <li>Jalview 2
       <ul>
         <li>Jim Procter</li>
-        <li>Andrew Waterhouse</li>
         <li>Mungo Carstairs</li>
+        <li>Ben Soares</li>
+        <li>Kira Mour&atilde;o</li>
         <li>Tochukwu 'Charles' Ofoegbu</li>
+        <li>Andrew Waterhouse</li>
         <li>Jan Engelhardt</li>
         <li>Lauren Lui</li>
         <li>Anne Menard</li>

diff --git a/help/help/html/io/.cvsignore b/help/help/html/io/.cvsignore
deleted file mode 100644 (file)
index 085e8ba..0000000
--- a/help/help/html/io/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-Thumbs.db

diff --git a/help/help/html/misc/.cvsignore b/help/help/html/misc/.cvsignore
deleted file mode 100644 (file)
index 085e8ba..0000000
--- a/help/help/html/misc/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-Thumbs.db

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 0a20650..0f4dd9b 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,6 +57,37 @@ li:before {
     </tr>
     <tr>
       <td width="60" align="center" nowrap>
+          <strong><a name="Jalview.2.11.1">2.11.1</a><br />
+            <em>16/2/2020</em></strong>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+          <li><!-- -->
+          </li>
+        </ul>
+        <em>Deprecations</em>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+        </ul>
+        <em>Java 11 Compatibility issues</em>
+        <ul>
+          <li>
+            <!-- JAL-2987 -->OSX - Can't view results in PDB/Uniprot FTS
+          </li>
+        </ul>
+        
+        <em>Repository and Source Release</em>
+        <ul>
+          <li>
+            <!-- JAL-3474 -->removed redundant .gitignore files from
+            repository
+          </li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td width="60" align="center" nowrap>
           <strong><a name="Jalview.2.11.0">2.11.0</a><br />
             <em>04/07/2019</em></strong>
       </td>
@@ -486,51 +517,51 @@ li:before {
                                <li>
                                <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
                                </li>
-                                       <li>
-                                               <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
-                                               regions of protein alignment.
-                                       </li>
-                                       <li>
-                                               <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
-                                               is restored from a Jalview 2.11 project
-                                       </li>
-                                       <li>
-                                               <!-- JAL-3213 -->Alignment panel height can be too small after
-                                               'New View'
-                                       </li>
-                                       <li>
-                                               <!-- JAL-3240 -->Display is incorrect after removing gapped
-                                               columns within hidden columns
-                                       </li>
-                                       <li>
-                                               <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
-                                               window after dragging left to select columns to left of visible
-                                               region
-                                       </li>
-                                       <li>
-                                               <!-- JAL-2876 -->Features coloured according to their description
-                                               string and thresholded by score in earlier versions of Jalview are
-                                               not shown as thresholded features in 2.11. To workaround please
-                                               create a Score filter instead.
-                                       </li>
-                                       <li>
-                                       <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li> 
-                                       <li>
-                                       <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
-                                       </li>
-          <li>
-            <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
-            alignments with multiple views can close views unexpectedly
-          </li>
-          </ul>
-          <em>Java 11 Specific defects</em>
-            <ul>
-              <li>
-                <!-- JAL-3235 -->Jalview Properties file is not sorted
-                alphabetically when saved
-              </li>
-          </ul>
-                       </td>
+                               <li>
+                                       <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
+                                       regions of protein alignment.
+                               </li>
+                               <li>
+                                       <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
+                                       is restored from a Jalview 2.11 project
+                               </li>
+                               <li>
+                                       <!-- JAL-3213 -->Alignment panel height can be too small after
+                                       'New View'
+                               </li>
+                               <li>
+                                       <!-- JAL-3240 -->Display is incorrect after removing gapped
+                                       columns within hidden columns
+                               </li>
+                               <li>
+                                       <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
+                                       window after dragging left to select columns to left of visible
+                                       region
+                               </li>
+                               <li>
+                                       <!-- JAL-2876 -->Features coloured according to their description
+                                       string and thresholded by score in earlier versions of Jalview are
+                                       not shown as thresholded features in 2.11. To workaround please
+                                       create a Score filter instead.
+                               </li>
+                               <li>
+                               <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li> 
+                               <li>
+                               <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
+                               </li>
+        <li>
+          <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
+          alignments with multiple views can close views unexpectedly
+        </li>
+        </ul>
+        <em>Java 11 Specific defects</em>
+          <ul>
+            <li>
+              <!-- JAL-3235 -->Jalview Properties file is not sorted
+              alphabetically when saved
+            </li>
+        </ul>
+      </td>
                </tr>
     <tr>
     <td width="60" nowrap>

diff --git a/help/help/html/webServices/.cvsignore b/help/help/html/webServices/.cvsignore
deleted file mode 100644 (file)
index 085e8ba..0000000
--- a/help/help/html/webServices/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-Thumbs.db

diff --git a/resources/.cvsignore b/resources/.cvsignore
deleted file mode 100644 (file)
index 43d40c0..0000000
--- a/resources/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-axisCommons
-jalview_mapping.xml

diff --git a/resources/images/.cvsignore b/resources/images/.cvsignore
deleted file mode 100644 (file)
index 1d13d05..0000000
--- a/resources/images/.cvsignore
+++ /dev/null
@@ -1,10 +0,0 @@
-dna.gif
-dna1.gif
-dna2.gif
-dna3.gif
-dna4.gif
-dna5.gif
-dna6.gif
-dna7.gif
-dna8.gif
-dna9.gif

diff --git a/schemas/.cvsignore b/schemas/.cvsignore
deleted file mode 100644 (file)
index 83ef99a..0000000
--- a/schemas/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-.#jalview.xsd.1.5
\ No newline at end of file

diff --git a/src/MCview/.cvsignore b/src/MCview/.cvsignore
deleted file mode 100644 (file)
index 5ee52a6..0000000
--- a/src/MCview/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-.#PDBViewer.java.1.3
\ No newline at end of file

diff --git a/src/jalview/.cvsignore b/src/jalview/.cvsignore
deleted file mode 100644 (file)
index f436451..0000000
--- a/src/jalview/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-vamsas
\ No newline at end of file

diff --git a/src/jalview/analysis/.cvsignore b/src/jalview/analysis/.cvsignore
deleted file mode 100644 (file)
index 33989c8..0000000
--- a/src/jalview/analysis/.cvsignore
+++ /dev/null
@@ -1,3 +0,0 @@
-.#NJTree.java.1.22
-.#NJTree.java.1.23
-.#SeqsetUtils.java.1.8

diff --git a/src/jalview/datamodel/.cvsignore b/src/jalview/datamodel/.cvsignore
deleted file mode 100644 (file)
index a4d99ef..0000000
--- a/src/jalview/datamodel/.cvsignore
+++ /dev/null
@@ -1,5 +0,0 @@
-.#Alignment.java.1.41
-.#Alignment.java.1.42
-.#Alignment.java.1.43
-.#Alignment.java.1.44
-.#AlignmentI.java.1.21

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 247f5e5..026061b 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1885,15 +1885,6 @@ public class Sequence extends ASequence implements SequenceI
 
     List<SequenceFeature> result = getFeatures().findFeatures(startPos,
             endPos, types);
-    if (datasetSequence != null)
-    {
-      result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
-              types);
-    }
-    else
-    {
-      result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
-    }
 
     /*
      * if end column is gapped, endPos may be to the right, 

diff --git a/src/jalview/gui/.cvsignore b/src/jalview/gui/.cvsignore
deleted file mode 100644 (file)
index a1659ce..0000000
--- a/src/jalview/gui/.cvsignore
+++ /dev/null
@@ -1,11 +0,0 @@
-.#AlignViewport.java.1.62
-.#AlignViewport.java.1.63
-.#AnnotationPanel.java.1.57
-.#FeatureRenderer.java.1.22
-.#OverviewPanel.java.1.26
-.#Preferences.java.1.26
-.#Preferences.java.1.28
-.#Preferences.java.1.29
-.#SequenceFetcher.java.1.23
-.#SequenceFetcher.java.1.24
-.#TreePanel.java.1.33

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 441dca7..11d5e39 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -282,7 +282,8 @@ public class FeatureSettings extends JPanel
       @Override
       public void mousePressed(MouseEvent evt)
       {
-        selectedRow = table.rowAtPoint(evt.getPoint());
+        Point pt = evt.getPoint();
+        selectedRow = table.rowAtPoint(pt);
         String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
         if (evt.isPopupTrigger())
         {
@@ -290,7 +291,8 @@ public class FeatureSettings extends JPanel
           popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
                   evt.getY());
         }
-        else if (evt.getClickCount() == 2)
+        else if (evt.getClickCount() == 2
+                && table.columnAtPoint(pt) == TYPE_COLUMN)
         {
           boolean invertSelection = evt.isAltDown();
           boolean toggleSelection = Platform.isControlDown(evt);

diff --git a/src/jalview/io/.cvsignore b/src/jalview/io/.cvsignore
deleted file mode 100644 (file)
index 485d807..0000000
--- a/src/jalview/io/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-.#DasSequenceFeatureFetcher.java.1.17
-cli

diff --git a/src/jalview/jbgui/.cvsignore b/src/jalview/jbgui/.cvsignore
deleted file mode 100644 (file)
index 1cb80c3..0000000
--- a/src/jalview/jbgui/.cvsignore
+++ /dev/null
@@ -1,3 +0,0 @@
-#GPreferences.java#
-.#GPreferences.java.1.20
-.#GPreferences.java.1.22

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 9f98ffa..1b4a8bd 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -2487,7 +2487,7 @@ public class GPreferences extends JPanel
     {
       try
       {
-        i = Integer.parseInt((String) s.getValue());
+        i = ((Integer) s.getValue()).intValue();
       } catch (Exception e)
       {
         Cache.log.error(
@@ -2506,6 +2506,10 @@ public class GPreferences extends JPanel
     {
       max = def;
     }
+    if (def < min)
+    {
+      def = min;
+    }
     SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
     s.setModel(sModel);
 

diff --git a/src/jalview/util/.cvsignore b/src/jalview/util/.cvsignore
deleted file mode 100644 (file)
index c5b8965..0000000
--- a/src/jalview/util/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-InstanceDiscoverer.java
\ No newline at end of file

diff --git a/src/jalview/ws/.cvsignore b/src/jalview/ws/.cvsignore
deleted file mode 100644 (file)
index be25ffb..0000000
--- a/src/jalview/ws/.cvsignore
+++ /dev/null
@@ -1,3 +0,0 @@
-.#JPredClient.java.1.25
-.#JPredClient.java.1.31
-.#MsaWSClient.java.1.26

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 81ec443..a262147 100644 (file)
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -410,7 +410,7 @@ public class CrossRefTest
    * Test for finding 'product' sequences for the case where the selected
    * sequence has a dbref with no mapping, triggering a fetch from database
    */
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Functional_Failing" })
   public void testFindXrefSequences_withFetch()
   {
     SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
@@ -464,7 +464,7 @@ public class CrossRefTest
    * Test for finding 'product' sequences for the case where both gene and
    * transcript sequences have dbrefs to Uniprot.
    */
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Functional_Failing" })
   public void testFindXrefSequences_forGeneAndTranscripts()
   {
     /*
@@ -561,7 +561,7 @@ public class CrossRefTest
    * - X06707 dbrefs to P0CE19/20 mapped to original Uniprot sequences
    * </pre>
    */
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Functional_Failing" })
   public void testFindXrefSequences_uniprotEmblManyToMany()
   {
     /*

diff --git a/utils/.cvsignore b/utils/.cvsignore
deleted file mode 100644 (file)
index 823caeb..0000000
--- a/utils/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-help2Website.class
-getJavaVersion.class

diff --git a/utils/InstallAnywhere/.cvsignore b/utils/InstallAnywhere/.cvsignore
deleted file mode 100644 (file)
index a44ca6b..0000000
--- a/utils/InstallAnywhere/.cvsignore
+++ /dev/null
@@ -1 +0,0 @@
-Jalview_modified.iap_xml