JAL-4134 popup menu and annotation row property to control display of display of...

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index b5987f4..de98c64 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -308,6 +308,11 @@ public class AlignmentAnnotation
 
   public static final int CONTACT_MAP = 4;
 
+  /**
+   * property that when set to non-empty string disables display of column groups defined on the contact matrix
+   */
+  public static final String CONTACT_MAP_NOGROUPS = "CMNOGRPS";
+
   public boolean belowAlignment = true;
 
   public SequenceGroup groupRef = null;
@@ -1745,5 +1750,23 @@ public class AlignmentAnnotation
     }
     return aa;
   }
+  
+  /**
+   * convenience method to check for the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row
+   * @return true if no CONTACT_MAP_NOGROUPS property is found, or it is set to ""
+   */
+  public boolean isShowGroupsForContactMatrix()
+  {
+    return getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS)==null || "".equals(getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS));
+  }
+  /**
+   * set the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row
+   * @see isShowGroupsForContactMatrix
+   */
+  public void setShowGroupsForContactMatrix(boolean showGroups)
+  {
+    setProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS, showGroups ? "" : "nogroups");
+  }
+
 
 }

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3b7420f..53dec93 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -45,6 +45,7 @@ import jalview.bin.Console;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactMatrixI;
@@ -1161,4 +1162,5 @@ public class AlignViewport extends AlignmentViewport
   {
     this.viewName = viewName;
   }
+
 }

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index e3cc36e..f4c37fd 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -432,6 +432,25 @@ public class AnnotationLabels extends JPanel
         {
           pop.addSeparator();
 
+          if (cm.hasGroups())
+          {
+            JCheckBoxMenuItem chitem = new JCheckBoxMenuItem("Show Groups on Matrix");
+            boolean showGroups = aa[selectedRow].isShowGroupsForContactMatrix();
+            final AlignmentAnnotation sel_row=aa[selectedRow];
+            chitem.setState(showGroups);
+            chitem.addActionListener(new ActionListener()
+            {
+
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                sel_row.setShowGroupsForContactMatrix(chitem.getState());
+                ap.getAnnotationPanel()
+                .paint(ap.getAnnotationPanel().getGraphics());
+              }
+            });
+            pop.add(chitem);
+          }
           if (cm.hasTree())
           {
             item = new JMenuItem("Show Tree for Matrix");

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index a8f6c1b..8f38d02 100644 (file)
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -102,7 +102,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
           HiddenColumns hiddenColumns, ColumnSelection columnSelection,
           AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
           int eRes, float min, float max, int y)
-  {
+  {    
     if (sRes > aa_annotations.length)
     {
       return;
@@ -114,7 +114,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
     g.setColor(shade.no_data);
 
     g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
-
+    boolean showGroups = _aa.isShowGroupsForContactMatrix();
     int column;
     int aaMax = aa_annotations.length - 1;
     ContactMatrixI cm = viewport.getContactMatrix(_aa);
@@ -204,7 +204,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         {
           col = shade.hidden;
         }
-        if (gpcol != null && gpcol != Color.white)
+        if (showGroups && gpcol != null && gpcol != Color.white)
         {
           // todo - could overlay group as a transparent rectangle ?
           col = new Color(

diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index 2f46eca..4615204 100644 (file)
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -20,7 +20,9 @@
  */
 package jalview.datamodel;
 
+import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
 import static org.testng.AssertJUnit.assertEquals;
 
 import jalview.analysis.AlignSeq;
@@ -426,4 +428,23 @@ public class AlignmentAnnotationTests
     assertNull(ann.annotations[0]);
     assertNull(ann.annotations[4]);
   }
+  /**
+   * test the contact matrix nogroups property methods
+   */
+  @Test(groups= {"Functional"})
+  public void test_contactMatrixGroups()
+  {
+    AlignmentAnnotation aa = new AlignmentAnnotation("foo","foo desc",null);
+    assertTrue(aa.isShowGroupsForContactMatrix());
+    aa.setShowGroupsForContactMatrix(false);
+    assertFalse(aa.isShowGroupsForContactMatrix());
+    AlignmentAnnotation copy = new AlignmentAnnotation(aa);
+    assertFalse(copy.isShowGroupsForContactMatrix());
+    aa.setShowGroupsForContactMatrix(true);
+    assertTrue(aa.isShowGroupsForContactMatrix());
+    // copy should not be updated
+    assertFalse(copy.isShowGroupsForContactMatrix());
+    
+    
+  }
 }