selection sending and receiving, autoscrolling to highlighted position

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index c8fcd39..eaa685d 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -29,6 +29,7 @@ import javax.swing.*;
 import jalview.datamodel.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
+import jalview.structure.SelectionSource;
 
 /**
  * DOCUMENT ME!
@@ -114,7 +115,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
         }
       }
     });
-
     fontChanged();
     adjustAnnotationHeight();
 
@@ -228,23 +228,57 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void highlightSearchResults(SearchResults results)
   {
+    scrollToPosition(results);
     seqPanel.seqCanvas.highlightSearchResults(results);
-
+  }
+  /**
+   * scroll the view to show the position of the highlighted
+   * region in results (if any) and redraw the overview
+   * @param results
+   */
+  public void scrollToPosition(SearchResults results) {
+    scrollToPosition(results, true);
+  }
+  /**
+   * scroll the view to show the position of the highlighted
+   * region in results (if any)
+   * @param results
+   * @param redrawOverview - when set, the overview will be recalculated (takes longer)
+   */
+  public void scrollToPosition(SearchResults results, boolean redrawOverview) {
     // do we need to scroll the panel?
-    if (results != null)
+    if (results != null && results.getSize()>0)
     {
-      SequenceI seq = results.getResultSequence(0);
-      int seqIndex = av.alignment.findIndex(seq);
-      int start = seq.findIndex(results.getResultStart(0)) - 1;
-      int end = seq.findIndex(results.getResultEnd(0)) - 1;
-
+      int seqIndex = av.alignment.findIndex(results);
+      if (seqIndex==-1)
+      {
+        return;
+      }
+      SequenceI seq = av.alignment.getSequenceAt(seqIndex);
+      int [] r = results.getResults(seq, seq.getStart(), seq.getEnd());
+      if (r==null)
+      {
+        return;
+      }
+      int start = r[0];
+      int end = r[1];
+      if (start<0)
+      {
+        return;
+      }
+      if (end==seq.getEnd())
+      {
+        return;
+      }
       if (!av.wrapAlignment)
       {
-        if ((av.getStartRes() > end)
-                || (av.getEndRes() < start)
-                || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+        if ((av.getStartRes() >= start)
+                || (av.getEndRes() <= end))
+        {
+          setScrollValues(start-1, seqIndex);
+        } else if ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))
         {
-          setScrollValues(start, seqIndex);
+          setScrollValues(av.getStartRes(), seqIndex);
         }
       }
       else
@@ -252,19 +286,23 @@ public class AlignmentPanel extends GAlignmentPanel implements
         scrollToWrappedVisible(start);
       }
     }
-
-    paintAlignment(true);
+    if (!redrawOverview && overviewPanel!=null)
+    {
+      overviewPanel.setBoxPosition();
+    } 
+    paintAlignment(!redrawOverview);
   }
 
   void scrollToWrappedVisible(int res)
   {
     int cwidth = seqPanel.seqCanvas
             .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-    if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+    if (res < av.getStartRes() || res >= (av.getStartRes()+cwidth))
     {
-      vscroll.setValue(res / cwidth);
+      vscroll.setValue((res / cwidth));
       av.startRes = vscroll.getValue() * cwidth;
     }
+
   }
 
   /**
@@ -439,7 +477,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void setScrollValues(int x, int y)
   {
-
+    if (av==null || av.alignment==null)
+    {
+      return;
+    }
     int width = av.alignment.getWidth();
     int height = av.alignment.getHeight();
 

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 63a57f8..939ba45 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -36,7 +36,7 @@ import jalview.structure.*;
  * @version $Revision$
  */
 public class SeqPanel extends JPanel implements MouseListener,
-        MouseMotionListener, MouseWheelListener, SequenceListener
+        MouseMotionListener, MouseWheelListener, SequenceListener, SelectionListener
 
 {
   /** DOCUMENT ME!! */
@@ -124,6 +124,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       addMouseWheelListener(this);
       ssm = StructureSelectionManager.getStructureSelectionManager();
       ssm.addStructureViewerListener(this);
+      ssm.addSelectionListener(this);
     }
   }
 
@@ -455,6 +456,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     ap.paintAlignment(false);
+    av.sendSelection();
   }
 
   void insertGapAtCursor(boolean group)
@@ -605,6 +607,10 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   public void highlightSequence(SearchResults results)
   {
+    if (av.followHighlight)
+    {
+      ap.scrollToPosition(results, false);
+    }
     seqCanvas.highlightSearchResults(results);
   }
 
@@ -1531,6 +1537,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       sg.setEndRes(res);
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
+      
       stretchGroup = sg;
 
       if (av.getConservationSelected())
@@ -1608,7 +1615,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
-
+    av.sendSelection();
   }
 
   /**
@@ -1808,4 +1815,50 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
   }
+  /**
+   * modify current selection according to a received message.
+   */
+  public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+          SelectionSource source)
+  {
+    // TODO: fix this hack - source of messages is align viewport, but SeqPanel handles selection messages...
+    if (av==source)
+    {
+      return;
+    }
+    // do we want to thread this ? (contention with seqsel and colsel locks, I suspect)
+    boolean repaint=false;
+    if (av.followSelection)
+    {
+      if (av.selectionGroup==null || !av.isSelectionGroupChanged())
+      {
+        SequenceGroup sgroup = (seqsel!=null) ? seqsel.intersect(av.alignment, (av.hasHiddenRows) ? av.hiddenRepSequences : null)
+                  : null;
+        if (sgroup!=null && sgroup.getSize()>0)
+        {
+          av.setSelectionGroup(sgroup);
+        } else {
+          av.setSelectionGroup(null);
+        }
+        repaint = av.isSelectionGroupChanged();
+      }
+      if (av.colSel==null || !av.isColSelChanged())
+      {
+        // Check to see if the current selection is from a previous message
+        if (colsel==null || colsel.size()==0)
+        {
+          av.colSel.clear();
+        } else {
+          av.colSel = new ColumnSelection(colsel);
+        } 
+        repaint |= av.isColSelChanged();
+      }
+    }
+    if (repaint)
+    {
+      // probably finessing with multiple redraws here
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
+      // ap.paintAlignment(false);
+    }
+  }
 }