JAL-3855 auto select clusters and fix up colouring/propagation on calculation & tree...

[jalview.git] / src / jalview / gui / AnnotationLabels.java

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 8930629..28065c3 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -36,12 +36,10 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.geom.AffineTransform;
-import java.io.IOException;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.Iterator;
 import java.util.Locale;
-import java.util.concurrent.Callable;
 
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JMenuItem;
@@ -52,7 +50,6 @@ import javax.swing.ToolTipManager;
 
 import jalview.analysis.AlignSeq;
 import jalview.analysis.AlignmentUtils;
-import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -62,15 +59,11 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
-import jalview.io.NewickFile;
-import jalview.schemes.AnnotationColourGradient;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 
 /**
  * The panel that holds the labels for alignment annotations, providing
@@ -315,7 +308,6 @@ public class AnnotationLabels extends JPanel
         ap.av.getAlignment().setAnnotationIndex(annotation, 0);
       }
       ap.refresh(true);
-      return null;
     });
   }
 
@@ -493,7 +485,8 @@ public class AnnotationLabels extends JPanel
 
       if (cm.hasGroups())
       {
-        JCheckBoxMenuItem chitem = new JCheckBoxMenuItem("Show Groups on Matrix");
+        JCheckBoxMenuItem chitem = new JCheckBoxMenuItem(MessageManager.getString("action.show_groups_on_matrix"));
+        chitem.setToolTipText(MessageManager.getString("action.show_groups_on_matrix_tooltip"));
         boolean showGroups = alignmentAnnotation.isShowGroupsForContactMatrix();
         final AlignmentAnnotation sel_row=alignmentAnnotation;
         chitem.setState(showGroups);
@@ -504,15 +497,18 @@ public class AnnotationLabels extends JPanel
           public void actionPerformed(ActionEvent e)
           {
             sel_row.setShowGroupsForContactMatrix(chitem.getState());
-            ap.getAnnotationPanel()
-            .paint(ap.getAnnotationPanel().getGraphics());
+            // so any annotation colour changes are propagated - though they
+            // probably won't be unless the annotation row colours are removed
+            // too!
+            ap.alignmentChanged();
           }
         });
         pop.add(chitem);
       }
       if (cm.hasTree())
       {
-        item = new JMenuItem("Show Tree for Matrix");
+        item = new JMenuItem(MessageManager.getString("action.show_tree_for_matrix"));
+        item.setToolTipText(MessageManager.getString("action.show_tree_for_matrix_tooltip"));
         item.addActionListener(new ActionListener()
         {
 
@@ -528,10 +524,10 @@ public class AnnotationLabels extends JPanel
       }
       else
       {
-        item = new JMenuItem("Calculate Tree for Matrix");
+        item = new JMenuItem(MessageManager.getString("action.cluster_matrix"));
+        item.setToolTipText(MessageManager.getString("action.cluster_matrix_tooltip"));
         item.addActionListener(new ActionListener()
         {
-          // TODO - refactor to analysis background thread
           @Override
           public void actionPerformed(ActionEvent e)
           {
@@ -540,9 +536,14 @@ public class AnnotationLabels extends JPanel
               @Override
               public void run()
               {
-                AlignmentAnnotation alan = alignmentAnnotation;
-                cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true));
-                ap.alignFrame.showContactMapTree(alan, cm);
+                final long progBar;
+                ap.alignFrame.setProgressBar(MessageManager.formatMessage("action.clustering_matrix_for",cm.getAnnotDescr(),5f), progBar = System.currentTimeMillis());
+                cm.setGroupSet(GroupSet.makeGroups(cm, true));
+                cm.randomlyReColourGroups();
+                cm.transferGroupColorsTo(alignmentAnnotation);
+                ap.alignmentChanged();
+                ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
+                ap.alignFrame.setProgressBar(null, progBar);
               }
             }).start();
           }