X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=daff328cc57240ad7e34403a2af103c31f561c70;hb=1858fc1b685034eb94cf3793ad9a4203816134d6;hp=1720edc66d3a989120e2d1b052ea0ff31aac0006;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 1720edc..daff328 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;
@@ -60,100 +60,42 @@ public class SeqPanel
 
     ap = p;
 
-    seqCanvas.addMouseMotionListener(new MouseMotionAdapter()
-    {
-      public void mouseMoved(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
-        doMouseMoved(evt);
-      }
+    seqCanvas.addMouseMotionListener(this);
+    seqCanvas.addMouseListener(this);
 
-      public void mouseDragged(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
-        if (editingSeqs)
-        {
-          doMouseDragged(evt);
-        }
-        else
-        {
-          doMouseDraggedDefineMode(evt);
-        }
-      }
-    });
-
-    seqCanvas.addMouseListener(new MouseAdapter()
-    {
-      public void mouseReleased(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
-        if (editingSeqs)
-        {
-          doMouseReleased(evt);
-        }
-        else
-        {
-          doMouseReleasedDefineMode(evt);
-        }
-
-      }
-
-      public void mousePressed(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
-        if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
-        {
-          if (evt.isAltDown() || evt.isControlDown())
-          {
-            groupEditing = true;
-          }
+    seqCanvas.repaint();
+  }
 
-          editingSeqs = true;
-          doMousePressed(evt);
-        }
-        else
-        {
-          doMousePressedDefineMode(evt);
-        }
-      }
 
-      public void mouseExited(MouseEvent evt)
-      {
-        if (av.getWrapAlignment() || 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 (av.getWrapAlignment() || 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)
     {
@@ -168,18 +110,80 @@ public class SeqPanel
     ap.repaint();
   }
 
+  int startWrapBlock=-1;
+  int wrappedBlock=-1;
+  int findRes(MouseEvent evt)
+ {
+   int res = 0;
+   int x = evt.getX();
+
+  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 -= hgap;
+      x -= seqCanvas.LABEL_WEST;
+
+
+      int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
+
+      wrappedBlock = y / cHeight;
+      wrappedBlock += av.getStartRes() / cwidth;
+
+      res = wrappedBlock * cwidth + x / av.getCharWidth();
+
+  }
+  else
+  {
+      res = (x / av.getCharWidth()) + av.getStartRes();
+  }
+
+  return res;
+
+ }
+
+ int findSeq(MouseEvent evt)
+ {
+
+   int seq = 0;
+   int y = evt.getY();
+
+   if (av.wrapAlignment)
+   {
+     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
+   {
+     seq = (y / av.getCharHeight()) + av.getStartSeq();
+   }
+
+   return seq;
+ }
+
+
   public void doMousePressed(MouseEvent evt)
   {
     ap.alignFrame.addHistoryItem(new HistoryItem(
         "Edit Sequence", av.alignment, HistoryItem.EDIT));
-    int seq;
-    int res;
 
-    int x = evt.getX();
-    int y = evt.getY();
-
-    res = x / av.getCharWidth() + av.getStartRes();
-    seq = y / av.getCharHeight() + av.getStartSeq();
+    int seq = findSeq(evt);
+    int res = findRes(evt);
 
     if (seq < av.getAlignment().getHeight() &&
         res < av.getAlignment().getSequenceAt(seq).getLength())
@@ -200,30 +204,12 @@ public class SeqPanel
     return;
   }
 
-  public void doMouseMoved(MouseEvent evt)
+  public void mouseMoved(MouseEvent evt)
   {
-    int res = 0, seq = 0;
-    int x = evt.getX();
-    int y = evt.getY();
-    if (av.wrapAlignment)
-    {
-      y -= 2 * av.charHeight;
-      int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
-
-      res = (int) ( (y / chunkHeight) * (getSize().width / av.charWidth)) +
-          x / av.getCharWidth() + av.getStartRes();
-
-      y %= chunkHeight;
-      seq = y / av.getCharHeight() + av.getStartSeq();
-
-    }
-    else
-    {
-      res = x / av.getCharWidth() + av.getStartRes();
-      seq = y / av.getCharHeight() + av.getStartSeq();
-    }
+    int res = findRes(evt);
+    int seq = findSeq(evt);
 
-    if (seq >= av.getAlignment().getHeight())
+    if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
     {
       return;
     }
@@ -234,57 +220,95 @@ public class SeqPanel
       return;
     }
 
-    Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-    String aa = "";
+    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+            sequence.getName());
+
+    Object obj = null;
+    if (av.alignment.isNucleotide())
+    {
+      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+          "");
+      if(obj!=null)
+        text.append(" Nucleotide: ");
+    }
+    else
+    {
+      obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+      if(obj!=null)
+        text.append("  Residue: ");
+    }
+
     if (obj != null)
     {
-      aa = obj.toString();
+
+      if (obj != "")
+      {
+        text.append(obj + " (" +
+                    av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+      }
     }
 
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                         sequence.getName());
-    if (aa != "")
+    if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
     {
-      text.append("  Residue: " + aa + " (" +
-                  av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+      seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
     }
 
-    ap.alignFrame.statusBar.setText(text.toString());
 
     // 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();
-
-      while (e.hasMoreElements())
+      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 = evt.getX() / av.getCharWidth() + av.getStartRes();
+    int res = findRes(evt);
     if (res < 0)
     {
       res = 0;
@@ -421,8 +445,7 @@ public class SeqPanel
 
   public void drawChars(int seqstart, int seqend, int start)
   {
-    seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,
-                        av.getStartRes(), av.getStartSeq(), 0);
+    seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,  0);
     seqCanvas.repaint();
   }
 
@@ -445,42 +468,11 @@ public class SeqPanel
   {
     if (endEdit == startEdit)
     {
-      ap.alignFrame.historyList.pop();
-      ap.alignFrame.updateEditMenuBar();
-    }
-
-    av.updateConservation();
-    av.updateConsensus();
-
-    // Y O Y CLUSTALX
-    ColourSchemeI cs = av.getGlobalColourScheme();
-    if (cs instanceof ConservationColourScheme)
-    {
-      ConservationColourScheme ccs = (ConservationColourScheme) cs;
-      if (ccs.cs instanceof ClustalxColourScheme)
-      {
-        jalview.analysis.Conservation c = new jalview.analysis.Conservation
-            ("All",
-             ResidueProperties.propHash, 3,
-             av.alignment.getSequences(), 0,
-             av.alignment.getWidth() - 1);
-        c.calculate();
-        c.verdict(false, av.ConsPercGaps);
-
-        ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
-        cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());
-        ccs = new ConservationColourScheme(c, cxs);
-        av.setGlobalColourScheme(ccs);
-      }
-    }
-
-    if (cs instanceof ClustalxColourScheme)
-    {
-      ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
-                                                 av.alignment.getWidth());
-      av.setGlobalColourScheme(cs);
+        ap.alignFrame.historyList.pop();
+        ap.alignFrame.updateEditMenuBar();
     }
 
+    av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
   }
 
 //////////////////////////////////////////
@@ -489,9 +481,13 @@ public class SeqPanel
   int oldSeq = -1;
   public void doMousePressedDefineMode(MouseEvent evt)
   {
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-    int seq = evt.getY() / av.getCharHeight() + av.getStartSeq();
+    int res = findRes(evt);
+    int seq = findSeq(evt);
     oldSeq = seq;
+    startWrapBlock=wrappedBlock;
+
+    if(seq==-1)
+      return;
 
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
@@ -545,7 +541,7 @@ public class SeqPanel
       SequenceGroup sg = new SequenceGroup();
       sg.setStartRes(res);
       sg.setEndRes(res);
-      sg.addSequence(sequence);
+      sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
       stretchGroup = sg;
 
@@ -566,7 +562,7 @@ public class SeqPanel
     else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
              InputEvent.BUTTON3_MASK)
     {
-      APopupMenu popup = new APopupMenu(ap, null);
+      APopupMenu popup = new APopupMenu(ap, null, null);
       this.add(popup);
       popup.show(this, evt.getX(), evt.getY());
     }
@@ -593,50 +589,48 @@ public class SeqPanel
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
-    mouseDragging = false;
+    if(mouseDragging)
+     {
+       stretchGroup.recalcConservation();
+       mouseDragging = false;
+     }
 
     if (stretchGroup == null)
     {
       return;
     }
 
-    if (stretchGroup.cs instanceof ClustalxColourScheme)
-    {
-      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences,
-                                                 av.alignment.getWidth());
-      seqCanvas.repaint();
-    }
-
-    else if (stretchGroup.cs instanceof ConservationColourScheme)
+    if(stretchGroup.cs!=null)
     {
-      ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
-      stretchGroup.cs = ccs;
-      SliderPanel.setConservationSlider(ap, stretchGroup.cs,
-                                        stretchGroup.getName());
-
-      seqCanvas.repaint();
-    }
-    else
-    {
-      if (stretchGroup.cs != null)
+      if (stretchGroup.cs.conservationApplied())
+      {
+        SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+                                          stretchGroup.getName());
+      }
+      else
       {
         SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
                                        stretchGroup.getName());
       }
-
     }
-
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
+    seqCanvas.repaint();
     ap.repaint();
   }
 
   boolean remove = false;
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-    int y = evt.getY() / av.getCharHeight() + av.getStartSeq();
+    int res = findRes(evt);
+    int y = findSeq(evt);
+
+    if(wrappedBlock!=startWrapBlock)
+        return;
+
+    if(y>=av.alignment.getHeight())
+      y = av.alignment.getHeight()-1;
 
     if (stretchGroup == null)
     {
@@ -664,7 +658,7 @@ public class SeqPanel
     {
       res = av.getStartRes();
     }
-    else if (res > av.getEndRes())
+    else if (res > av.getEndRes() && !av.getWrapAlignment())
     {
       res = av.getEndRes();
     }
@@ -705,16 +699,15 @@ public class SeqPanel
 
       if (stretchGroup.sequences.contains(nextSeq))
       {
-        stretchGroup.deleteSequence(seq);
-        stretchGroup.deleteSequence(nextSeq);
+        stretchGroup.deleteSequence(seq, false);
       }
       else
       {
         if (seq != null)
         {
-          stretchGroup.addSequence(seq);
+          stretchGroup.addSequence(seq, false);
         }
-        stretchGroup.addSequence(nextSeq);
+        stretchGroup.addSequence(nextSeq, false);
       }
     }
     oldSeq = y;
@@ -727,26 +720,20 @@ 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 (av.getWrapAlignment())
-    {
-      return;
-    }
-
     if (mouseDragging)
     {
       scrollThread = new ScrollThread();
     }
-
   }
 
   // this class allows scrolling off the bottom of the visible alignment