X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=7c524ad3fcc6feaa8101f4ecfd9d5e9c35486859;hb=dea32f71ff7f8a80cc8494864b6605921d81fafa;hp=ee7676ce79e749da0ef7467b38a8e816d9053c91;hpb=da18eb63c94018e134fb60d70e6de43e99bbff50;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index ee7676c..7c524ad 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -152,6 +152,8 @@ public class SeqPanel
     ap.repaint();
   }
 
+  int startWrapBlock=-1;
+  int wrappedBlock=-1;
   int findRes(MouseEvent evt)
  {
    int res = 0;
@@ -159,16 +161,26 @@ 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);
-      int block = y/chunkHeight;
-      block += av.getStartRes()/cwidth;
 
-      res = block*cwidth   +   x / av.getCharWidth();
+      int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
+
+      wrappedBlock = y / cHeight;
+      wrappedBlock += av.getStartRes() / cwidth;
+
+      res = wrappedBlock * cwidth + x / av.getCharWidth();
+
   }
   else
   {
@@ -181,14 +193,22 @@ 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
    {
@@ -231,7 +251,7 @@ public class SeqPanel
     int res = findRes(evt);
     int seq = findSeq(evt);
 
-    if (seq >= av.getAlignment().getHeight() || seq<0)
+    if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
     {
       return;
     }
@@ -242,19 +262,37 @@ 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());
@@ -269,7 +307,7 @@ public class SeqPanel
       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)
@@ -457,105 +495,7 @@ public class SeqPanel
         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 (av.getSelectionGroup() != null)
-    {
-        av.getSelectionGroup().recalcConservation();
-    }
-
-    if(cs!=null)
-    {
-      if (cs.conservationApplied())
-      {
-        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);
-
-        if (cs instanceof ClustalxColourScheme)
-        {
-          ((ClustalxColourScheme)cs).
-              resetClustalX(av.alignment.getSequences(),
-                                av.alignment.getWidth());
-          cs.setConservation(c);
-          av.setGlobalColourScheme(cs);
-        }
-        else
-        {
-          cs.setConservation(c);
-          av.setGlobalColourScheme(cs);
-        }
-
-      }
-
-      if (cs instanceof ClustalxColourScheme)
-      {
-        ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
-                                                   av.alignment.getWidth());
-        av.setGlobalColourScheme(cs);
-      }
-        }
+    av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
   }
 
 //////////////////////////////////////////
@@ -567,6 +507,7 @@ public class SeqPanel
     int res = findRes(evt);
     int seq = findSeq(evt);
     oldSeq = seq;
+    startWrapBlock=wrappedBlock;
 
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
@@ -705,6 +646,9 @@ public class SeqPanel
     int res = findRes(evt);
     int y = findSeq(evt);
 
+    if(wrappedBlock!=startWrapBlock)
+        return;
+
     if(y>=av.alignment.getHeight())
       y = av.alignment.getHeight()-1;
 
@@ -713,7 +657,7 @@ public class SeqPanel
       return;
     }
 
-    if (res > av.alignment.getWidth() && !av.getWrapAlignment())
+    if (res > av.alignment.getWidth())
     {
       res = av.alignment.getWidth() - 1;
     }