JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 0a9d35f..d26ba89 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -36,7 +36,6 @@ 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;
@@ -51,23 +50,20 @@ 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;
 import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.GroupSet;
 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.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
@@ -312,7 +308,6 @@ public class AnnotationLabels extends JPanel
         ap.av.getAlignment().setAnnotationIndex(annotation, 0);
       }
       ap.refresh(true);
-      return null;
     });
   }
 
@@ -422,33 +417,140 @@ public class AnnotationLabels extends JPanel
         consclipbrd.addActionListener(this);
         pop.add(consclipbrd);
       }
-      if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP
-              && PAEContactMatrix.PAEMATRIX
-                      .equals(aa[selectedRow].getCalcId()))
+
+      addColourOrFilterByOptions(ap,aa[selectedRow],pop);
+      
+      if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP)
       {
-        final PAEContactMatrix cm = (PAEContactMatrix) av
-                .getContactMatrix(aa[selectedRow]);
-        if (cm != null && cm.hasTree())
+        addContactMatrixOptions(ap,aa[selectedRow],pop);
+          // Set/adjust threshold for grouping ?
+          // colour alignment by this [type]
+          // select/hide columns by this row
+          
+        }
+      }
+    
+    pop.show(this, evt.getX(), evt.getY());
+  }
+
+  static void addColourOrFilterByOptions(final AlignmentPanel ap,
+          final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+  {
+    JMenuItem item;
+    item = new JMenuItem(MessageManager.getString("label.colour_by_annotation"));
+    item.addActionListener(new ActionListener()
+    {
+      
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,false);
+      };
+    });
+    pop.add(item);
+    if (alignmentAnnotation.sequenceRef!=null)
+    {
+      item = new JMenuItem(MessageManager.getString("label.colour_by_annotation")+" ("+MessageManager.getString("label.per_seq")+")");
+      item.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
         {
-          item = new JMenuItem("Show Tree for Matrix");
-          item.addActionListener(new ActionListener()
-          {
+          AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,true);
+        };
+      });
+      pop.add(item);
+    }
+    item = new JMenuItem(MessageManager.getString("action.select_by_annotation"));
+    item.addActionListener(new ActionListener()
+    {
+      
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        AnnotationColumnChooser.displayFor(ap.av,ap,alignmentAnnotation);
+      };
+    });
+    pop.add(item);
+  }
+  static void addContactMatrixOptions(final AlignmentPanel ap,
+          final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+  {
+    
+    final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation);
+    JMenuItem item;
+    if (cm != null)
+    {
+      pop.addSeparator();
 
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
+      if (cm.hasGroups())
+      {
+        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);
+        chitem.addActionListener(new ActionListener()
+        {
 
-              ap.alignFrame.showContactMapTree(aa[selectedRow], cm);
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            sel_row.setShowGroupsForContactMatrix(chitem.getState());
+            // 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(MessageManager.getString("action.show_tree_for_matrix"));
+        item.setToolTipText(MessageManager.getString("action.show_tree_for_matrix_tooltip"));
+        item.addActionListener(new ActionListener()
+        {
 
-            }
-          });
-          pop.addSeparator();
-          pop.add(item);
-        }
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
 
+            ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
+
+          }
+        });
+        pop.add(item);
+      }
+      else
+      {
+        item = new JMenuItem(MessageManager.getString("action.cluster_matrix"));
+        item.setToolTipText(MessageManager.getString("action.cluster_matrix_tooltip"));
+        item.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            new Thread(new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                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();
+          }
+        });
+        pop.add(item);
       }
     }
-    pop.show(this, evt.getX(), evt.getY());
   }
 
   /**
@@ -1135,7 +1237,7 @@ public class AnnotationLabels extends JPanel
             {
               if (debugRedraw)
               {
-                System.out.println("before vis: " + i);
+                jalview.bin.Console.outPrintln("before vis: " + i);
               }
               before = true;
             }
@@ -1149,7 +1251,7 @@ public class AnnotationLabels extends JPanel
             {
               if (debugRedraw)
               {
-                System.out.println(
+                jalview.bin.Console.outPrintln(
                         "Scroll offset: " + sOffset + " after vis: " + i);
               }
               after = true;