(JAL-842) ensure deletions are accounted for when highlighting mouseover in alignment...

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 9054298..daa0bea 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -35,18 +35,23 @@ import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.structure.*;
 import jalview.io.*;
 import jalview.schemes.*;
+import jalview.util.ShiftList;
 import fr.orsay.lri.varna.VARNAPanel;
 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
+import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener;
+import fr.orsay.lri.varna.models.BaseList;
 import fr.orsay.lri.varna.models.VARNAConfig;
 import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
+import fr.orsay.lri.varna.models.rna.ModeleBase;
 import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
 import fr.orsay.lri.varna.models.rna.RNA;
 
 
-public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
+public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SelectionListener, SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
+, InterfaceVARNASelectionListener, VamsasSource
 
 {
   AppVarnaBinding vab;
@@ -63,30 +68,34 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,S
   }*/
   
  
-  
-  public AppVarna(String seq,String struc,String name,AlignmentPanel ap){
-         ArrayList<RNA> rnaList = new ArrayList<RNA>();
-         RNA rna1 = new RNA(name);
-         try {
-                 rna1.setRNA(seq,replaceOddGaps(struc));
-         } catch (ExceptionUnmatchedClosingParentheses e2) {
-               e2.printStackTrace();
-         } catch (ExceptionFileFormatOrSyntax e3) {
-               e3.printStackTrace();
-         }
-         rnaList.add(trimRNA(rna1));     
-         rnaList.add(rna1);
-         rna1.setName("consenus_"+rna1.getName());
-         
-         
-         vab = new AppVarnaBinding(rnaList);
-         //vab = new AppVarnaBinding(seq,struc);
-         //System.out.println("Hallo: "+name);
-         this.name=name;
-         initVarna();
-      ssm = ap.getStructureSelectionManager();
-         ssm.addStructureViewerListener(this);
-  }
+  public AppVarna(SequenceI seq,String strucseq, String struc,String name,AlignmentPanel ap){
+    ArrayList<RNA> rnaList = new ArrayList<RNA>();
+    RNA rna1 = new RNA(name);
+    try {
+      rna1.setRNA(strucseq,replaceOddGaps(struc));
+    } catch (ExceptionUnmatchedClosingParentheses e2) {
+      e2.printStackTrace();
+    } catch (ExceptionFileFormatOrSyntax e3) {
+      e3.printStackTrace();
+    }
+    RNA trim=trimRNA(rna1);
+    rnaList.add(trim);   
+    rnaList.add(rna1);
+    rna1.setName("consensus_"+rna1.getName());
+    
+    {
+      this.seqs.put(trim, seq);
+      this.seqs.put(rna1, seq);
+    }
+    vab = new AppVarnaBinding(rnaList);
+    //vab = new AppVarnaBinding(seq,struc);
+    //System.out.println("Hallo: "+name);
+    this.name=name;
+    initVarna();
+    ssm = ap.getStructureSelectionManager();
+    ssm.addStructureViewerListener(this);
+    ssm.addSelectionListener(this);
+  }     
   
   public void initVarna(){
          //vab.setFinishedInit(false);
@@ -97,6 +106,7 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,S
          getContentPane().add(split, BorderLayout.CENTER);
          //getContentPane().add(vab.getTools(), BorderLayout.NORTH);   
          varnaPanel.addVARNAListener(this);
+         varnaPanel.addSelectionListener(this);
          jalview.gui.Desktop.addInternalFrame(this,"VARNA -"+name,getBounds().width, getBounds().height);
          this.pack();
          showPanel(true);
@@ -112,6 +122,7 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,S
   }
   
   public RNA trimRNA(RNA rna){
+    ShiftList offset=new ShiftList();
          RNA rnaTrim = new RNA("trim_"+rna.getName());
          try {
                  rnaTrim.setRNA(rna.getSeq(),replaceOddGaps(rna.getStructDBN()));
@@ -123,10 +134,15 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,S
 
          StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
          StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
-         for(int i=0;i<rnaTrim.getSeq().length();i++){
+         int ofstart=-1,sleng=rnaTrim.getSeq().length();
+         for(int i=0;i<sleng;i++){
                  //TODO: Jalview utility for gap detection java.utils.isGap()
                  //TODO: Switch to jalview rna datamodel
-                 if(seq.substring(i, i+1).compareTo("-")==0 || seq.substring(i, i+1).compareTo(".")==0){
+                 if(jalview.util.Comparison.isGap(seq.charAt(i))){
+                   if (ofstart==-1)
+                   {
+                     ofstart=i;
+                   }
                          if(!rnaTrim.findPair(i).isEmpty()){
                                  int m=rnaTrim.findPair(i).get(1);
                                  int l=rnaTrim.findPair(i).get(0);
@@ -136,15 +152,27 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,S
                          }else{
                                  struc.replace(i, i+1, "*");
                          }
+                 } else {
+                   if (ofstart>-1)
+                   {
+                     offset.addShift(ofstart, ofstart-i);
+                     ofstart=-1;
+                   }
                  }
-         }
-        
-         String newSeq=rnaTrim.getSeq().replace("-", "");
+           }
+         // final gap
+          if (ofstart>-1)
+          {
+            offset.addShift(ofstart, ofstart-sleng);
+            ofstart=-1;
+          }
+         String newSeq=rnaTrim.getSeq().replace("-", "");
          rnaTrim.getSeq().replace(".", "");
          String newStruc=struc.toString().replace("*", "");
 
          try {
                rnaTrim.setRNA(newSeq,newStruc);
+               registerOffset(rnaTrim,offset);
          } catch (ExceptionUnmatchedClosingParentheses e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
@@ -152,9 +180,16 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,S
                // TODO Auto-generated catch block
                e.printStackTrace();
          }
-         
          return rnaTrim;
   }
+  Map<RNA,SequenceI> seqs=new Hashtable<RNA,SequenceI>();
+  Map<RNA,ShiftList> offsets=new Hashtable<RNA,ShiftList>();
+  Map<RNA,ShiftList> offsetsInv=new Hashtable<RNA,ShiftList>();
+  private void registerOffset(RNA rnaTrim, ShiftList offset)
+  {
+    offsets.put(rnaTrim, offset);
+    offsetsInv.put(rnaTrim,offset.getInverse());
+  }
 
   public void showPanel(boolean show){
          this.setVisible(show);
@@ -179,8 +214,7 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,S
 
 @Override
 public void onUINewStructure(VARNAConfig v, RNA r) {
-       // TODO Auto-generated method stub
-       
+  
 }
 
 @Override
@@ -188,6 +222,31 @@ public void onWarningEmitted(String s) {
        // TODO Auto-generated method stub
        
 }
+private class VarnaHighlighter {
+  private  HighlightRegionAnnotation _lastHighlight;
+  private RNA _lastRNAhighlighted=null;
+  public void highlightRegion(RNA rna, int start,int end)
+  {
+  if (_lastRNAhighlighted!=null)
+  {
+    _lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
+  }
+  HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(rna.getBasesBetween(start,end));
+  rna.addHighlightRegion(highlight);
+  _lastHighlight=highlight;
+  _lastRNAhighlighted=rna;
+
+  }
+  public HighlightRegionAnnotation getLastHighlight() {
+    return _lastHighlight;
+  }
+  public RNA getLastRNA()
+  {
+    return _lastRNAhighlighted;
+  }
+}
+VarnaHighlighter mouseOverHighlighter=new VarnaHighlighter(),
+selectionHighlighter=new VarnaHighlighter();
 /**
  * If a mouseOver event from the AlignmentPanel 
  * is noticed the currently selected RNA in the 
@@ -195,16 +254,15 @@ public void onWarningEmitted(String s) {
  * To be able to remove it before the next highlight
  * it is saved in _lastHighlight
  */
-private  HighlightRegionAnnotation _lastHighlight;
 @Override
 public void mouseOverSequence(SequenceI sequence, int index) {
-       // TODO Auto-generated method stub
-       RNA rna=vab.getSelectedRNA();
-       rna.removeHighlightRegion(_lastHighlight);
-       
-       HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(rna.getBasesBetween(index,index));
-       rna.addHighlightRegion(highlight);
-       _lastHighlight=highlight;
+        RNA rna=vab.getSelectedRNA();
+       ShiftList shift=offsets.get(rna);
+       if (shift!=null)
+       {
+         index=shift.shift(index);
+       }
+       mouseOverHighlighter.highlightRegion(rna, index, index);
        vab.updateSelectedRNA(rna);
 }
 
@@ -221,5 +279,46 @@ public void onStructureRedrawn()
   
 }
 
+@Override
+public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+        SelectionSource source)
+{
+  int start=seqsel.getStartRes(),end=seqsel.getEndRes();
+  RNA rna=vab.getSelectedRNA();
+  ShiftList shift=offsets.get(rna);
+  if (shift!=null)
+  {
+    start=shift.shift(start);
+    end=shift.shift(end);
+  }
+  selectionHighlighter.highlightRegion(rna, start, end);
+  selectionHighlighter.getLastHighlight().setOutlineColor(seqsel.getOutlineColour());
+  vab.updateSelectedRNA(rna);
+}
+
+@Override
+public void onHoverChanged(ModeleBase arg0, ModeleBase arg1)
+{
+  RNA rna=vab.getSelectedRNA();
+  ShiftList shift=offsetsInv.get(rna);
+  SequenceI seq=seqs.get(rna);
+  if (arg1!=null && seq!=null)
+  {
+    if (shift!=null)
+    {
+      ssm.mouseOverVamsasSequence(seq, seq.findIndex(arg1.getIndex()), this);
+    } else {
+      ssm.mouseOverVamsasSequence(seq, arg1.getIndex(),  this);
+    }
+  }
+}
+
+@Override
+public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
+{
+  // TODO Auto-generated method stub
+  
+}
+
 
 }

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 23a5008..6139764 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -277,7 +277,7 @@ public class PopupMenu extends JPopupMenu
             {
               public void actionPerformed(ActionEvent e)
               {
-                new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+                new AppVarna(seq, seq.getSequenceAsString(), rnastruc, seq
                         .getName(), ap);
               }
             });
@@ -304,7 +304,7 @@ public class PopupMenu extends JPopupMenu
                 public void actionPerformed(ActionEvent e)
                 {
                   // TODO: VARNA does'nt print gaps in the sequence
-                  new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+                  new AppVarna(seq,seq.getSequenceAsString(), rnastruc, seq
                           .getName(), ap);
                 }
               });