JAL-4134 repaint the tree or alignment view(s) when column selections change

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 425f710..2bdfc27 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -143,9 +143,43 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     scrollPane = scroller;
     addMouseListener(this);
     addMouseMotionListener(this);
+    
     ToolTipManager.sharedInstance().registerComponent(this);
   }
 
+  public void clearSelectedLeaves()
+  {
+    Vector<BinaryNode> leaves = tp.getTree()
+            .findLeaves(tp.getTree().getTopNode());
+    if (tp.isColumnWise())
+    {
+      markColumnsFor(getAssociatedPanels(), leaves, Color.white, true);
+    }
+    else
+    {
+      for (AlignmentPanel ap : getAssociatedPanels())
+      {
+        SequenceGroup selected = ap.av.getSelectionGroup();
+        if (selected != null)
+        {
+          {
+            for (int i = 0; i < leaves.size(); i++)
+            {
+              SequenceI seq = (SequenceI) leaves.elementAt(i).element();
+              if (selected.contains(seq))
+              {
+                selected.addOrRemove(seq, false);
+              }
+            }
+            selected.recalcConservation();
+          }
+        }
+        ap.av.sendSelection();
+      }
+    }
+    PaintRefresher.Refresh(tp, av.getSequenceSetId());
+    repaint();
+  }
   /**
    * DOCUMENT ME!
    * 
@@ -830,7 +864,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       Vector<BinaryNode> leaves = tree.findLeaves(highlightNode);
       if (tp.isColumnWise())
       {
-        markColumnsFor(getAssociatedPanels(), leaves, Color.red);
+        markColumnsFor(getAssociatedPanels(), leaves, Color.red,false);
       }
       else
       {
@@ -1117,29 +1151,26 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       if (cm instanceof MappableContactMatrixI)
       {
         MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
-        int pos[]=mcm.getMappedPositionsFor(rseq, colm);
+        int pos[]=mcm.getMappedPositionsFor(rseq, colm+1);
         if (pos!=null)
         {
-          offp=rseq.findIndex(pos[0])-1;
-        } else {
-          offp=-2;
+          offp=rseq.findIndex(pos[0]);
         }
       }
     }
-    if (offp==-1)
+    if (offp<=0)
     {
-      // assume a direct mapping to reference or column number
-        offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
-            : colm;
+      return false;
     }
 
+    offp-=2;
     if (!av.hasHiddenColumns())
     {
       return cs.contains(offp);
     }
-    if (hc.isVisible(offp - 1))
+    if (hc.isVisible(offp))
     {
-      return cs.contains(offp - 1);
+      return cs.contains(offp);
       // return cs.contains(hc.absoluteToVisibleColumn(offp));
     }
     return false;
@@ -1172,7 +1203,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   }
 
   private void markColumnsFor(AlignmentPanel[] aps, Vector<BinaryNode> l,
-          Color col)
+          Color col, boolean clearSelected)
   {
     SequenceI rseq = tp.assocAnnotation.sequenceRef;
     if (av == null || av.getAlignment() == null)
@@ -1219,18 +1250,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
                 : colm;
       }
-      if (!av.hasHiddenColumns() || hc.isVisible(offp - 1))
+      if (!av.hasHiddenColumns() || hc.isVisible(offp))
       {
-        if (cs.contains(offp - 1))
+        if (clearSelected || cs.contains(offp))
         {
-          cs.removeElement(offp - 1);
+          cs.removeElement(offp);
         }
         else
         {
-          cs.addElement(offp - 1);
+          cs.addElement(offp);
         }
       }
     }
+    PaintRefresher.Refresh(tp, av.getSequenceSetId());
   }
 
   public void createSeqGroupFor(AlignmentPanel[] aps, Vector<BinaryNode> l,