X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=3209960d6f183e9a9901884df259378a40a9f61a;hb=6efabb12ac7f2ed3bb6bb9e47505cf0112784837;hp=444b6bbb0f4bc6cf0104a468ec2add8689984497;hpb=019042a9f87d94260b3060cdf45ab93ca714a46d;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 444b6bb..3209960 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -18,8 +18,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
-
 import jalview.datamodel.*;
 
 import jalview.schemes.*;
@@ -91,21 +89,31 @@ public class SeqPanel extends JPanel
 
         ap = p;
 
+
         addMouseMotionListener(new MouseMotionAdapter()
             {
                 public void mouseMoved(MouseEvent evt)
                 {
                     doMouseMoved(evt);
+                    if (editingSeqs)
+                    {
+                      // This is because MacOSX creates a mouseMoved
+                      // If control is down
+                      if(!av.isDataset())
+                        doMouseDragged(evt);
+                    }
                 }
 
                 public void mouseDragged(MouseEvent evt)
                 {
                     if (editingSeqs)
                     {
+                      if(!av.isDataset())
                         doMouseDragged(evt);
                     }
                     else
                     {
+                      if(!av.isDataset())
                         doMouseDraggedDefineMode(evt);
                     }
                 }
@@ -120,7 +128,7 @@ public class SeqPanel extends JPanel
            {
              Font font = av.getFont();
              int fontSize = font.getSize();
-             if (e.getWheelRotation() > 0 && fontSize < 30)
+             if (e.getWheelRotation() > 0 && fontSize < 51)
                fontSize++;
              else if (fontSize > 1)
                fontSize--;
@@ -140,69 +148,75 @@ public class SeqPanel extends JPanel
        });
 
 
-        addMouseListener(new MouseAdapter()
-            {
-                public void mouseReleased(MouseEvent evt)
-                {
-                    mouseWheelPressed = false;
-
-                    if (editingSeqs)
-                    {
-                        doMouseReleased(evt);
-                    }
-                    else
-                    {
-                        doMouseReleasedDefineMode(evt);
-                    }
-                }
-
-                public void mousePressed(MouseEvent evt)
-                {
-                  if( javax.swing.SwingUtilities.isMiddleMouseButton(evt))
-                  {
-                    mouseWheelPressed = true;
-                    return;
-                  }
+       if(!av.isDataset())
+       {
+         addMouseListener(new MouseAdapter()
+         {
+           public void mouseReleased(MouseEvent evt)
+           {
+             mouseWheelPressed = false;
 
-                    if (evt.isShiftDown() || evt.isAltDown() ||
-                            evt.isControlDown())
-                    {
-                        if (evt.isAltDown() || evt.isControlDown())
-                        {
-                            groupEditing = true;
-                        }
+             if (editingSeqs)
+             {
+               doMouseReleased(evt);
+             }
+             else
+             {
+               doMouseReleasedDefineMode(evt);
+             }
+           }
 
-                        editingSeqs = true;
-                        doMousePressed(evt);
-                    }
-                    else
-                    {
-                        doMousePressedDefineMode(evt);
-                    }
-                }
+           public void mousePressed(MouseEvent evt)
+           {
+             if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+             {
+               mouseWheelPressed = true;
+               return;
+             }
+
+             if (evt.isShiftDown() || evt.isAltDown() ||
+                 evt.isControlDown())
+             {
+               if (evt.isAltDown() || evt.isControlDown())
+               {
+                 groupEditing = true;
+
+               }
+
+               editingSeqs = true;
+               doMousePressed(evt);
+             }
+             else
+             {
+               doMousePressedDefineMode(evt);
+             }
+           }
 
-                public void mouseExited(MouseEvent evt)
-                {
-                  if (editingSeqs)
-                  {
-                    return;
-                  }
+           public void mouseExited(MouseEvent evt)
+           {
+             if (editingSeqs)
+             {
+               return;
+             }
 
-                  doMouseExitedDefineMode(evt);
-                }
+             doMouseExitedDefineMode(evt);
+           }
 
-                public void mouseEntered(MouseEvent evt)
-                {
-                  if (editingSeqs)
-                  {
-                    return;
-                  }
+           public void mouseEntered(MouseEvent evt)
+           {
+             if (editingSeqs)
+             {
+               return;
+             }
 
-                    doMouseEnteredDefineMode(evt);
-                }
-            });
+             doMouseEnteredDefineMode(evt);
+           }
+         });
+       }
     }
 
+    int startWrapBlock=-1;
+    int wrappedBlock=-1;
     int findRes(MouseEvent evt)
    {
      int res = 0;
@@ -210,16 +224,26 @@ public class SeqPanel extends JPanel
 
     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.getWidth());
-        int block = y/chunkHeight;
-        block += av.getStartRes()/cwidth;
 
-        res = block*cwidth   +   x / av.getCharWidth();
+        wrappedBlock = y / cHeight;
+        wrappedBlock += av.getStartRes() / cwidth;
+
+        res = wrappedBlock * cwidth + x / av.getCharWidth();
+
     }
     else
     {
@@ -232,14 +256,22 @@ public class SeqPanel extends JPanel
 
    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
      {
@@ -284,6 +316,9 @@ public class SeqPanel extends JPanel
       int seq = findSeq(evt);
       int res = findRes(evt);
 
+      if(seq<0 || res<0)
+        return;
+
         if ((seq < av.getAlignment().getHeight()) &&
                 (res < av.getAlignment().getSequenceAt(seq).getLength()))
         {
@@ -319,25 +354,41 @@ public class SeqPanel extends JPanel
 
       if (res > sequence.getLength())
       {
-          return;
-        }
+        return;
+      }
 
-        Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
-                "");
-        String aa = "";
+      if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+      {
+        seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+      }
 
-        if (obj != null)
-        {
-            aa = obj.toString();
-        }
 
         StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
                 sequence.getName());
 
-        if (aa != "")
+        Object obj = null;
+        if (av.alignment.isNucleotide())
         {
-            text.append("  Residue: " + aa + " (" +
-                av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+          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)
+        {
+
+          if (obj != "")
+          {
+            text.append( obj + " (" +
+                        av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+          }
         }
 
         ap.alignFrame.statusBar.setText(text.toString());
@@ -345,32 +396,54 @@ public class SeqPanel extends JPanel
         // use aa to see if the mouse pointer is on a
         if (av.showSequenceFeatures)
         {
-            Vector features = sequence.getSequenceFeatures();
-            Enumeration e = features.elements();
-            StringBuffer sbuffer = new StringBuffer();
-
-            while (e.hasMoreElements())
+            Vector features = sequence.getDatasetSequence().getSequenceFeatures();
+            if(features!=null)
             {
-                SequenceFeature sf = (SequenceFeature) e.nextElement();
+              StringBuffer sbuffer = new StringBuffer("<html>");
 
-                if ((sf.getStart() <= sequence.findPosition(res)) &&
-                        (sf.getEnd() >= sequence.findPosition(res)))
+              for (int i = 0; i < features.size(); i++)
+              {
+                SequenceFeature sf = (SequenceFeature) features.elementAt(i);
+
+                if ( (sf.getBegin() <= sequence.findPosition(res)) &&
+                    (sf.getEnd() >= sequence.findPosition(res)))
                 {
-                    if (sbuffer.length() > 0)
+                  if (sf.getType().equals("disulfide bond"))
+                  {
+                    if (sf.getBegin() == sequence.findPosition(res)
+                        || sf.getEnd() == sequence.findPosition(res))
                     {
-                        sbuffer.append("; ");
+                      if (sbuffer.length() > 6)
+                        sbuffer.append("<br>");
+                      sbuffer.append("disulfide bond " + sf.getBegin() + ":" +
+                                     sf.getEnd());
                     }
+                  }
+                  else
+                  {
+                    if (sbuffer.length() > 6)
+                      sbuffer.append("<br>");
+                    sbuffer.append(sf.getType());
+                    if (sf.getDescription() != null)
+                      sbuffer.append(" " + sf.getDescription());
 
-                    sbuffer.append(sf.getType() + " " + sf.getDescription());
-
-                    if (sf.getStatus().length() > 0)
+                    if (sf.getStatus() != null)
                     {
-                        sbuffer.append(" (" + sf.getStatus() + ")");
+                      sbuffer.append(" (" + sf.getStatus() + ")");
                     }
+                  }
                 }
-            }
 
-            this.setToolTipText(sbuffer.toString());
+              }
+
+              sbuffer.append("</html>");
+              if(sbuffer.length()==13) // <html></html>
+                setToolTipText("");
+              else
+               setToolTipText(sbuffer.toString());
+            }
+            else
+              setToolTipText("");
         }
     }
 
@@ -580,97 +653,8 @@ public class SeqPanel extends JPanel
         ap.alignFrame.updateEditMenuBar();
       }
 
-      av.updateConservation();
-      av.updateConsensus();
-
-      //Does the edit affect any groups?
-      //////////////////////////////
-      Vector groupsToUpdate = new Vector();
-      SequenceGroup sg = av.getSelectionGroup();
-
-      int s, g, gSize = av.alignment.getGroups().size();
-      if (sg != null)
-      {
-        groupsToUpdate.addElement(av.getSelectionGroup());
-        int sSize = sg.getSize();
-        for (s = 0; s < sSize; s++)
-        {
-          SequenceI seq = sg.getSequenceAt(s);
-
-          for (g = 0; g < gSize; g++)
-          {
-            SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().
-                elementAt(
-                    g);
-            if (sg2.sequences.contains(seq))
-            {
-              if (!groupsToUpdate.contains(sg2))
-                groupsToUpdate.addElement(sg2);
-              continue;
-            }
-          }
-        }
-      }
-      else
-      {
-        SequenceI seq = av.alignment.getSequenceAt(startseq);
-        for (g = 0; g < gSize; g++)
-        {
-          SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt(
-              g);
-          if (sg2.sequences.contains(seq))
-          {
-            if (!groupsToUpdate.contains(sg2))
-              groupsToUpdate.addElement(sg2);
-            continue;
-          }
-        }
-      }
-
-      gSize = groupsToUpdate.size();
-      for (g = 0; g < gSize; g++)
-      {
-        ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation();
-      }
-      ////End of updating groups
-      //////////////////////////////////////////
-
-        // Y O Y CLUSTALX
-        ColourSchemeI cs = av.getGlobalColourScheme();
-        if(cs!=null)
-        {
-          if (cs.conservationApplied())
-          {
-            Conservation c = new Conservation("All",
-                                              ResidueProperties.propHash, 3,
-                                              av.alignment.getSequences(),
-                                              0, av.alignment.getWidth() - 1);
-            c.calculate();
-            c.verdict(false, av.ConsPercGaps);
-
-            if (cs instanceof ClustalxColourScheme)
-            {
-              ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
-              cxs.resetClustalX(av.alignment.getSequences(),
-                                av.alignment.getWidth());
-              cs.setConservation(c);
-              av.setGlobalColourScheme(cs);
-            }
-            else
-            {
-              cs.setConservation(c);
-              av.setGlobalColourScheme(cs);
-            }
-
-          }
+      av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
 
-          if (cs instanceof ClustalxColourScheme)
-          {
-            ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
-                                                       av.alignment.getWidth());
-            av.setGlobalColourScheme(cs);
-          }
-        }
     }
 
     /**
@@ -684,6 +668,21 @@ public class SeqPanel extends JPanel
       int seq = findSeq(evt);
       oldSeq = seq;
 
+      startWrapBlock=wrappedBlock;
+
+      if(av.wrapAlignment && seq>av.alignment.getHeight())
+      {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              "Cannot edit annotations in wrapped view.",
+              "Wrapped view - no edit",
+              JOptionPane.WARNING_MESSAGE);
+        return;
+      }
+
+      if(seq<0 || res<0)
+            return;
+
+
         SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
         if ((sequence == null) || (res > sequence.getLength()))
@@ -831,6 +830,9 @@ public class SeqPanel extends JPanel
       int res = findRes(evt);
       int y = findSeq(evt);
 
+      if(wrappedBlock!=startWrapBlock)
+        return;
+
       if (stretchGroup == null)
       {
             return;
@@ -1007,7 +1009,7 @@ public class SeqPanel extends JPanel
 
                 try
                 {
-                    Thread.sleep(75);
+                    Thread.sleep(20);
                 }
                 catch (Exception ex)
                 {