refactored VamsasListener to allow the source of the event to be passed to handlers

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index f3502a6..fdcfaca 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -198,8 +198,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       y -= hgap;
 
-      seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment
-              .getHeight() - 1);
+      seq = Math.min((y % cHeight) / av.getCharHeight(),
+              av.alignment.getHeight() - 1);
     }
     else
     {
@@ -601,7 +601,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     if (lastMessage == null || !lastMessage.equals(tmp))
     {
       // System.err.println("mouseOver Sequence: "+tmp);
-      ssm.mouseOverSequence(sequence, index, pos);
+      ssm.mouseOverSequence(sequence, index, pos, av);
     }
     lastMessage = tmp;
   }
@@ -688,8 +688,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     if (av.showSequenceFeatures)
     {
       int rpos;
-      SequenceFeature[] features = findFeaturesAtRes(sequence
-              .getDatasetSequence(), rpos = sequence.findPosition(res));
+      SequenceFeature[] features = findFeaturesAtRes(
+              sequence.getDatasetSequence(),
+              rpos = sequence.findPosition(res));
       appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,
               this.ap.seqPanel.seqCanvas.fr.minmax);
     }
@@ -937,8 +938,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       // Which is bigger, left-right or up-down?
       if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
-              .getX()
-              - lastMousePress.getX()))
+              .getX() - lastMousePress.getX()))
       {
         int fontSize = av.font.getSize();
 
@@ -956,9 +956,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           fontSize = 1;
         }
 
-        av
-                .setFont(new Font(av.font.getName(), av.font.getStyle(),
-                        fontSize));
+        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
         av.charWidth = oldWidth;
         ap.fontChanged();
       }
@@ -1443,14 +1441,15 @@ public class SeqPanel extends JPanel implements MouseListener,
         av.setSelectionGroup(null);
       }
 
-      SequenceFeature[] features = findFeaturesAtRes(sequence
-              .getDatasetSequence(), sequence.findPosition(findRes(evt)));
+      SequenceFeature[] features = findFeaturesAtRes(
+              sequence.getDatasetSequence(),
+              sequence.findPosition(findRes(evt)));
 
       if (features != null && features.length > 0)
       {
         SearchResults highlight = new SearchResults();
-        highlight.addResult(sequence, features[0].getBegin(), features[0]
-                .getEnd());
+        highlight.addResult(sequence, features[0].getBegin(),
+                features[0].getEnd());
         seqCanvas.highlightSearchResults(highlight);
       }
       if (features != null && features.length > 0)
@@ -1554,8 +1553,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-      SequenceFeature[] allFeatures = findFeaturesAtRes(sequence
-              .getDatasetSequence(), sequence.findPosition(res));
+      SequenceFeature[] allFeatures = findFeaturesAtRes(
+              sequence.getDatasetSequence(), sequence.findPosition(res));
       Vector links = new Vector();
       for (int i = 0; i < allFeatures.length; i++)
       {
@@ -1641,20 +1640,20 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup
-                .getSequences(av.hiddenRepSequences), stretchGroup
-                .getWidth());
+        ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+                stretchGroup.getSequences(av.hiddenRepSequences),
+                stretchGroup.getWidth());
       }
 
       if (stretchGroup.cs.conservationApplied())
       {
-        SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup
-                .getName());
+        SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+                stretchGroup.getName());
       }
       else
       {
-        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup
-                .getName());
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+                stretchGroup.getName());
       }
     }
     PaintRefresher.Refresh(this, av.getSequenceSetId());
@@ -1883,7 +1882,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     // do we want to thread this ? (contention with seqsel and colsel locks, I
     // suspect)
-    boolean repaint = false;
+    // rules are: colsel is copied if there is a real intersection between
+    // sequence selection
+    boolean repaint = false, copycolsel = true;
     if (av.selectionGroup == null || !av.isSelectionGroupChanged())
     {
       SequenceGroup sgroup = null;
@@ -1898,6 +1899,12 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         sgroup = seqsel.intersect(av.alignment,
                 (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+        if ((sgroup == null || sgroup.getSize() == 0)
+                && (colsel == null || colsel.size() == 0))
+        {
+          // don't copy columns if the region didn't intersect.
+          copycolsel = false;
+        }
       }
       if (sgroup != null && sgroup.getSize() > 0)
       {
@@ -1909,7 +1916,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
       repaint = av.isSelectionGroupChanged();
     }
-    if (av.colSel == null || !av.isColSelChanged())
+    if (copycolsel && (av.colSel == null || !av.isColSelChanged()))
     {
       // the current selection is unset or from a previous message
       // so import the new colsel.
@@ -1922,6 +1929,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
       else
       {
+        // TODO: shift colSel according to the intersecting sequences
         if (av.colSel == null)
         {
           av.colSel = new ColumnSelection(colsel);
@@ -1933,7 +1941,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
       repaint |= av.isColSelChanged();
     }
-    if (av.hasHiddenColumns
+    if (copycolsel && av.hasHiddenColumns
             && (av.colSel == null || av.colSel.getHiddenColumns() == null))
     {
       System.err.println("Bad things");