JAL-4134 only build tree when showing it in the tree viewer..

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 4702f2a..e3cc36e 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -36,10 +36,12 @@ 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;
@@ -50,18 +52,24 @@ 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
@@ -416,6 +424,61 @@ public class AnnotationLabels extends JPanel
         consclipbrd.addActionListener(this);
         pop.add(consclipbrd);
       }
+      if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP)
+      {
+        
+        final ContactMatrixI cm = av.getContactMatrix(aa[selectedRow]);
+        if (cm != null)
+        {
+          pop.addSeparator();
+
+          if (cm.hasTree())
+          {
+            item = new JMenuItem("Show Tree for Matrix");
+            item.addActionListener(new ActionListener()
+            {
+
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+
+                ap.alignFrame.showContactMapTree(aa[selectedRow], cm);
+
+              }
+            });
+            pop.add(item);
+          }
+          else
+          {
+            item = new JMenuItem("Calculate Tree for Matrix");
+            item.addActionListener(new ActionListener()
+            {
+              // TODO - refactor to analysis background thread
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                new Thread(new Runnable()
+                {
+                  @Override
+                  public void run()
+                  {
+                    AlignmentAnnotation alan = aa[selectedRow];
+                    cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true));
+                    ap.alignFrame.showContactMapTree(alan, cm);
+                  }
+                }).start();
+              }
+            });
+            pop.add(item);
+
+          }
+          // Show/Hide group shading on matrix view
+          // Set/adjust threshold for grouping ?
+          // colour alignment by this [type]
+          // select/hide columns by this row
+          
+        }
+      }
     }
     pop.show(this, evt.getX(), evt.getY());
   }
@@ -1055,7 +1118,8 @@ public class AnnotationLabels extends JPanel
 
     g.translate(0, getScrollOffset());
     g.setColor(Color.black);
-
+    SequenceI lastSeqRef = null;
+    String lastLabel = null;
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
     int fontHeight = g.getFont().getSize();
     int y = 0;
@@ -1080,6 +1144,7 @@ public class AnnotationLabels extends JPanel
     {
       hasHiddenRows = false;
       int olY = 0;
+      int nexAA = 0;
       for (int i = 0; i < aa.length; i++)
       {
         visible = true;
@@ -1089,6 +1154,10 @@ public class AnnotationLabels extends JPanel
           continue;
         }
         olY = y;
+        // look ahead to next annotation
+        for (nexAA = i + 1; nexAA < aa.length
+                && !aa[nexAA].visible; nexAA++)
+          ;
         y += aa[i].height;
         if (clip)
         {
@@ -1134,8 +1203,40 @@ public class AnnotationLabels extends JPanel
         {
           offset += fm.getDescent();
         }
-
-        x = width - fm.stringWidth(aa[i].label) - 3;
+        String label = aa[i].label;
+        boolean vertBar = false;
+        if ((lastLabel != null && lastLabel.equals(label)))
+        {
+          label = aa[i].description;
+        }
+        else
+        {
+          if (nexAA < aa.length && label.equals(aa[nexAA].label)) // &&
+                                                                  // aa[nexY].sequenceRef==aa[i].sequenceRef)
+          {
+            lastLabel = label;
+            // next label is the same as this label
+            label = aa[i].description;
+          }
+          else
+          {
+            lastLabel = label;
+          }
+        }
+        if (aa[i].sequenceRef != null)
+        {
+          if (aa[i].sequenceRef != lastSeqRef)
+          {
+            label = aa[i].sequenceRef.getName() + " " + label;
+            // TODO record relationship between sequence and this annotation and
+            // display it here
+          }
+          else
+          {
+            vertBar = true;
+          }
+        }
+        x = width - fm.stringWidth(label) - 3;
 
         if (aa[i].graphGroup > -1)
         {
@@ -1203,16 +1304,27 @@ public class AnnotationLabels extends JPanel
         }
         else
         {
-          g.drawString(aa[i].label, x, y + offset);
+          if (vertBar)
+          {
+            g.drawLine(width - 3, y + offset - fontHeight, width - 3,
+                    (int) (y - 1.5 * aa[i].height - offset - fontHeight));
+            // g.drawLine(20, y + offset, x - 20, y + offset);
+
+          }
+          g.drawString(label, x, y + offset);
         }
+        lastSeqRef = aa[i].sequenceRef;
       }
     }
 
     if (!resizePanel && dragEvent != null && aa != null)
     {
       g.setColor(Color.lightGray);
-      g.drawString(aa[selectedRow].label, dragEvent.getX(),
-              dragEvent.getY() - getScrollOffset());
+      g.drawString(
+              (aa[selectedRow].sequenceRef == null ? ""
+                      : aa[selectedRow].sequenceRef.getName())
+                      + aa[selectedRow].label,
+              dragEvent.getX(), dragEvent.getY() - getScrollOffset());
     }
 
     if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))