X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=2f06d64b83a33d1e7b4f5b4441c526e2a68035dc;hb=de468b0bf50850a89c6a8a7acfa4ff5b689ffed1;hp=9c3a1e8304163cf92736e53c9a69afdfd449dda1;hpb=bf22060aa91d40c9d6f7e3c7f518b6bd0457921e;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 9c3a1e8..2f06d64 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -28,7 +28,7 @@ import jalview.datamodel.*;
 import jalview.schemes.*;
 
 public class SeqPanel
-    extends Panel
+    extends Panel implements MouseMotionListener, MouseListener
 {
 
   public SeqCanvas seqCanvas;
@@ -60,84 +60,42 @@ public class SeqPanel
 
     ap = p;
 
-    seqCanvas.addMouseMotionListener(new MouseMotionAdapter()
-    {
-      public void mouseMoved(MouseEvent evt)
-      {
-        doMouseMoved(evt);
-      }
-
-      public void mouseDragged(MouseEvent evt)
-      {
-        if (editingSeqs)
-        {
-          doMouseDragged(evt);
-        }
-        else
-        {
-          doMouseDraggedDefineMode(evt);
-        }
-      }
-    });
-
-    seqCanvas.addMouseListener(new MouseAdapter()
-    {
-      public void mouseReleased(MouseEvent evt)
-      {
-        if (editingSeqs)
-        {
-          doMouseReleased(evt);
-        }
-        else
-        {
-          doMouseReleasedDefineMode(evt);
-        }
+    seqCanvas.addMouseMotionListener(this);
+    seqCanvas.addMouseListener(this);
 
-      }
-
-      public void mousePressed(MouseEvent evt)
-      {
-        if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
-        {
-          if (evt.isAltDown() || evt.isControlDown())
-          {
-            groupEditing = true;
-          }
-
-          editingSeqs = true;
-          doMousePressed(evt);
-        }
-        else
-        {
-          doMousePressedDefineMode(evt);
-        }
-      }
+    seqCanvas.repaint();
+  }
 
-      public void mouseExited(MouseEvent evt)
-      {
-        if (editingSeqs)
-        {
-          return;
-        }
-        doMouseExitedDefineMode(evt);
 
-      }
+     public void mousePressed(MouseEvent evt)
+     {
+       if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+       {
+         if (evt.isAltDown() || evt.isControlDown())
+         {
+           groupEditing = true;
+         }
+
+         editingSeqs = true;
+         doMousePressed(evt);
+       }
+       else
+       {
+         doMousePressedDefineMode(evt);
+       }
+     }
 
-      public void mouseEntered(MouseEvent evt)
-      {
-        if (editingSeqs)
-        {
-          return;
-        }
-        doMouseEnteredDefineMode(evt);
-      }
+     public void mouseClicked(MouseEvent evt){}
 
-    });
-    seqCanvas.repaint();
-  }
 
-  public void doMouseReleased(MouseEvent evt)
+  public void mouseReleased(MouseEvent evt)
   {
+    if (!editingSeqs)
+    {
+      doMouseReleasedDefineMode(evt);
+      return;
+    }
+
 
     if (seqEditOccurred > -1)
     {
@@ -161,16 +119,26 @@ public class SeqPanel
 
   if (av.wrapAlignment)
   {
+
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+      hgap += av.charHeight;
+
+    int cHeight = av.getAlignment().getHeight() * av.charHeight
+        + hgap + seqCanvas.getAnnotationHeight();
+
       int y = evt.getY();
-      y -= (2 * av.charHeight);
+      y -= hgap;
       x -= seqCanvas.LABEL_WEST;
 
-      int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
-      int cwidth = seqCanvas.getWrappedCanvasWidth(this.getSize().width);
-      wrappedBlock = y/chunkHeight;
-      wrappedBlock += av.getStartRes()/cwidth;
 
-      res = wrappedBlock*cwidth   +   x / av.getCharWidth();
+      int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
+
+      wrappedBlock = y / cHeight;
+      wrappedBlock += av.getStartRes() / cwidth;
+
+      res = wrappedBlock * cwidth + x / av.getCharWidth();
+
   }
   else
   {
@@ -183,14 +151,22 @@ public class SeqPanel
 
  int findSeq(MouseEvent evt)
  {
+
    int seq = 0;
    int y = evt.getY();
 
    if (av.wrapAlignment)
    {
-     y -= (2 * av.charHeight);
-     int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
-     seq = ( (y % chunkHeight) / av.getCharHeight());
+     int hgap = av.charHeight;
+     if (av.scaleAboveWrapped)
+       hgap += av.charHeight;
+
+     int cHeight = av.getAlignment().getHeight() * av.charHeight
+         + hgap + seqCanvas.getAnnotationHeight();
+
+       y -= hgap;
+
+     seq = ( (y % cHeight) / av.getCharHeight());
    }
    else
    {
@@ -228,7 +204,7 @@ public class SeqPanel
     return;
   }
 
-  public void doMouseMoved(MouseEvent evt)
+  public void mouseMoved(MouseEvent evt)
   {
     int res = findRes(evt);
     int seq = findSeq(evt);
@@ -272,39 +248,52 @@ public class SeqPanel
       }
     }
 
-    ap.alignFrame.statusBar.setText(text.toString());
+    if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+    {
+      seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+    }
+
 
     // use aa to see if the mouse pointer is on a
-    if (av.showSequenceFeatures)
+    if (av.showSequenceFeatures && sequence.getSequenceFeatures()!=null)
     {
       Vector features = sequence.getSequenceFeatures();
       Enumeration e = features.elements();
-      StringBuffer sbuffer = new StringBuffer();
-
+      boolean first = true;
       while (e.hasMoreElements())
       {
         SequenceFeature sf = (SequenceFeature) e.nextElement();
-        if (sf.getStart() <= sequence.findPosition(res) &&
+        if (sf.getBegin() <= sequence.findPosition(res) &&
             sf.getEnd() >= sequence.findPosition(res))
         {
-          if (sbuffer.length() > 0)
+          if(first)
           {
-            sbuffer.append("; ");
+            text.append(" Sequence Feature: ");
+            first = false;
           }
-          sbuffer.append(sf.getType() + " " + sf.getDescription());
+
+          text.append(sf.getDescription());
           if (sf.getStatus().length() > 0)
           {
-            sbuffer.append(" (" + sf.getStatus() + ")");
+            text.append(" (" + sf.getStatus() + ")");
           }
+          text.append("; ");
         }
 
       }
     }
 
+     ap.alignFrame.statusBar.setText(text.toString());
+
   }
 
-  public void doMouseDragged(MouseEvent evt)
+  public void mouseDragged(MouseEvent evt)
   {
+    if (!editingSeqs)
+    {
+      doMouseDraggedDefineMode(evt);
+      return;
+    }
 
     // If we're dragging we're editing
     int res = findRes(evt);
@@ -486,6 +475,9 @@ public class SeqPanel
     oldSeq = seq;
     startWrapBlock=wrappedBlock;
 
+    if(seq==-1)
+      return;
+
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
     if (sequence == null || res > sequence.getLength())
@@ -717,15 +709,15 @@ public class SeqPanel
     seqCanvas.repaint();
   }
 
-  public void doMouseEnteredDefineMode(MouseEvent e)
+  public void mouseEntered(MouseEvent e)
   {
-    if (scrollThread != null)
+    if (editingSeqs && scrollThread != null)
     {
       scrollThread.running = false;
     }
   }
 
-  public void doMouseExitedDefineMode(MouseEvent e)
+  public void mouseExited(MouseEvent e)
   {
     if (mouseDragging)
     {