X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=e29f4e15e4c22cf389f97f2a1b3ec8ffc959ae30;hb=9a23ee1cee6a2ef0f797fd8e1a6a950e66ef6e72;hp=9c3a1e8304163cf92736e53c9a69afdfd449dda1;hpb=bf22060aa91d40c9d6f7e3c7f518b6bd0457921e;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 9c3a1e8..e29f4e1 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);
-      }
+    seqCanvas.addMouseMotionListener(this);
+    seqCanvas.addMouseListener(this);
 
-      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);
-        }
-
-      }
-
-      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 +248,66 @@ public class SeqPanel
       }
     }
 
-    ap.alignFrame.statusBar.setText(text.toString());
-
-    // use aa to see if the mouse pointer is on a
-    if (av.showSequenceFeatures)
+    if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
     {
-      Vector features = sequence.getSequenceFeatures();
-      Enumeration e = features.elements();
-      StringBuffer sbuffer = new StringBuffer();
+      seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+    }
 
-      while (e.hasMoreElements())
+
+    // use aa to see if the mouse pointer is on a
+    if (av.showSequenceFeatures
+        && sequence.getSequenceFeatures()!=null
+        && av.featuresDisplayed!=null)
+    {
+      int index = 0;
+      sequence.getSequenceFeatures();
+      boolean first = true;
+      while (index < sequence.getSequenceFeatures().length)
       {
-        SequenceFeature sf = (SequenceFeature) e.nextElement();
-        if (sf.getStart() <= sequence.findPosition(res) &&
+        SequenceFeature sf = sequence.getSequenceFeatures()[index];
+        if (sf.getBegin() <= sequence.findPosition(res) &&
             sf.getEnd() >= sequence.findPosition(res))
         {
-          if (sbuffer.length() > 0)
+          if(!av.featuresDisplayed.containsKey(sf.getType()))
+           {
+             index++;
+             continue;
+           }
+
+          if(first)
           {
-            sbuffer.append("; ");
+            text.append(" Sequence Feature:");
+            first = false;
           }
-          sbuffer.append(sf.getType() + " " + sf.getDescription());
-          if (sf.getStatus().length() > 0)
+
+          text.append(" "+sf.getType());
+
+          if(sf.getDescription()!=null)
+            text.append(" "+sf.getDescription());
+
+          if (sf.getStatus()!=null && sf.getStatus().length() > 0)
           {
-            sbuffer.append(" (" + sf.getStatus() + ")");
+            text.append(" (" + sf.getStatus() + ")");
           }
+          text.append("; ");
         }
 
+        index++;
+
       }
     }
 
+     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);
@@ -428,7 +431,11 @@ public class SeqPanel
             }
             else
             {
-
+              if(scrollThread!=null)
+              {
+                scrollThread.running = false;
+                scrollThread = null;
+              }
               break;
             }
           }
@@ -437,18 +444,21 @@ public class SeqPanel
       }
     }
 
+    mouseDragging = true;
+    if (res > av.endRes || res < av.startRes)
+    {
+      mouseExited(evt);
+    }
+
+    if (scrollThread != null)
+      scrollThread.setEvent(evt);
+
+
     endEdit = res;
     lastres = res;
     seqCanvas.repaint();
   }
 
-  public void drawChars(int seqstart, int seqend, int start)
-  {
-    seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,
-                        av.getStartRes(), av.getStartSeq(), 0);
-    seqCanvas.repaint();
-  }
-
   public void insertChar(int j, int seq)
   {
     av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
@@ -481,11 +491,20 @@ public class SeqPanel
   int oldSeq = -1;
   public void doMousePressedDefineMode(MouseEvent evt)
   {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+      scrollThread = null;
+    }
+
     int res = findRes(evt);
     int seq = findSeq(evt);
     oldSeq = seq;
     startWrapBlock=wrappedBlock;
 
+    if(seq==-1)
+      return;
+
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
     if (sequence == null || res > sequence.getLength())
@@ -586,23 +605,25 @@ public class SeqPanel
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
-    if(mouseDragging)
-     {
-       stretchGroup.recalcConservation();
-       mouseDragging = false;
-     }
-
     if (stretchGroup == null)
     {
-      return;
+        return;
     }
 
     if(stretchGroup.cs!=null)
     {
+      if (stretchGroup.cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
+            sequences,
+            stretchGroup.getWidth());
+      }
+
       if (stretchGroup.cs.conservationApplied())
       {
         SliderPanel.setConservationSlider(ap, stretchGroup.cs,
                                           stretchGroup.getName());
+        stretchGroup.recalcConservation();
       }
       else
       {
@@ -613,121 +634,143 @@ public class SeqPanel
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
-    seqCanvas.repaint();
+    PaintRefresher.Refresh(av.alignment);
     ap.repaint();
   }
 
-  boolean remove = false;
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
     int res = findRes(evt);
     int y = findSeq(evt);
 
     if(wrappedBlock!=startWrapBlock)
-        return;
+      return;
 
-    if(y>=av.alignment.getHeight())
-      y = av.alignment.getHeight()-1;
+     if (stretchGroup == null)
+     {
+          return;
+     }
 
-    if (stretchGroup == null)
-    {
-      return;
-    }
+     mouseDragging = true;
 
-    if (res > av.alignment.getWidth())
-    {
-      res = av.alignment.getWidth() - 1;
-    }
 
-    if (stretchGroup.getEndRes() == res)
-    {
-      // Edit end res position of selected group
-      changeEndRes = true;
-    }
+      if(y > av.alignment.getHeight())
+      {
+        y = av.alignment.getHeight() -1;
+      }
 
-    else if (stretchGroup.getStartRes() == res)
-    {
-      // Edit start res position of selected group
-      changeStartRes = true;
-    }
+      if(res>av.alignment.getWidth())
+        res = av.alignment.getWidth()-1;
 
-    if (res < av.getStartRes())
-    {
-      res = av.getStartRes();
-    }
-    else if (res > av.getEndRes() && !av.getWrapAlignment())
-    {
-      res = av.getEndRes();
-    }
+      if (stretchGroup.getEndRes() == res)
+      {
+          // Edit end res position of selected group
+          changeEndRes = true;
+      }
+      else if (stretchGroup.getStartRes() == res)
+      {
+          // Edit start res position of selected group
+          changeStartRes = true;
+      }
 
-    if (changeEndRes)
-    {
-      if (res > stretchGroup.getStartRes() - 1)
+      if (res < 0)
       {
-        stretchGroup.setEndRes(res);
+          res = 0;
       }
-    }
-    else if (changeStartRes)
-    {
-      if (res < stretchGroup.getEndRes() + 1)
+
+      if (changeEndRes)
+      {
+          if (res > (stretchGroup.getStartRes() - 1))
+          {
+              stretchGroup.setEndRes(res);
+          }
+      }
+      else if (changeStartRes)
       {
-        stretchGroup.setStartRes(res);
+          if (res < (stretchGroup.getEndRes() + 1))
+          {
+              stretchGroup.setStartRes(res);
+          }
       }
-    }
 
-    int dragDirection = 0;
-    if (y > oldSeq)
-    {
-      dragDirection = 1;
-    }
-    else if (y < oldSeq)
-    {
-      dragDirection = -1;
-    }
+      int dragDirection = 0;
 
-    while (y != oldSeq && oldSeq > 0 && y < av.alignment.getHeight())
-    {
-      // This routine ensures we don't skip any sequences, as the
-      // selection is quite slow.
-      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+      if (y > oldSeq)
+      {
+          dragDirection = 1;
+      }
+      else if (y < oldSeq)
+      {
+          dragDirection = -1;
+      }
 
-      oldSeq += dragDirection;
-      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-      if (stretchGroup.sequences.contains(nextSeq))
+      while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
       {
-        stretchGroup.deleteSequence(seq, false);
+          // This routine ensures we don't skip any sequences, as the
+          // selection is quite slow.
+          Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+          oldSeq += dragDirection;
+
+          if(oldSeq<0)
+            break;
+
+          Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+          if (stretchGroup.sequences.contains(nextSeq))
+          {
+              stretchGroup.deleteSequence(seq, false);
+          }
+          else
+          {
+              if (seq != null)
+              {
+                  stretchGroup.addSequence(seq, false);
+              }
+
+              stretchGroup.addSequence(nextSeq, false);
+          }
       }
-      else
+
+      if(oldSeq < 0)
+        oldSeq = -1;
+
+
+      if(res>av.endRes || res<av.startRes
+          || y<av.startSeq || y>av.endSeq)
       {
-        if (seq != null)
-        {
-          stretchGroup.addSequence(seq, false);
-        }
-        stretchGroup.addSequence(nextSeq, false);
+        mouseExited(evt);
+      }
+
+      if (scrollThread != null)
+      {
+        scrollThread.setEvent(evt);
       }
+
+      seqCanvas.repaint();
     }
-    oldSeq = y;
-    mouseDragging = true;
-    if (scrollThread != null)
+
+    public void mouseEntered(MouseEvent e)
     {
-      scrollThread.setEvent(evt);
-    }
+      if (oldSeq < 0)
+        oldSeq = 0;
 
-    seqCanvas.repaint();
-  }
+      if (scrollThread != null)
+      {
+        scrollThread.running = false;
+        scrollThread = null;
+      }
+    }
 
-  public void doMouseEnteredDefineMode(MouseEvent e)
+  public void mouseExited(MouseEvent e)
   {
-    if (scrollThread != null)
+    if (av.getWrapAlignment())
     {
-      scrollThread.running = false;
+      return;
     }
-  }
 
-  public void doMouseExitedDefineMode(MouseEvent e)
-  {
-    if (mouseDragging)
+    if (mouseDragging && scrollThread==null)
     {
       scrollThread = new ScrollThread();
     }
@@ -759,6 +802,7 @@ public class SeqPanel
       running = true;
       while (running)
       {
+
         if (evt != null)
         {