X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=daa0beae83ad0ce9234a17f1531d9284e5b672c1;hb=8f3cf5f09e970ac6e5d9032c03ec29f69fb4b356;hp=3a67e10f469e04dc8e9a6af9a236f5bb18ba6ba3;hpb=1b277fdca45c13f59c3887780f14a37bb1beeb60;p=jalview.git

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 3a67e10..daa0bea 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -18,7 +18,10 @@
 package jalview.gui;
 
 import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import java.awt.*;
+
 import javax.swing.*;
 import javax.swing.event.*;
 
@@ -32,29 +35,164 @@ 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 Runnable,SequenceStructureBinding, ViewSetProvider
+public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SelectionListener, SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
+, InterfaceVARNASelectionListener, VamsasSource
 
 {
   AppVarnaBinding vab;
 
-  JPanel scriptWindow;
-
-  JSplitPane splitPane;
+  VARNAPanel varnaPanel;
+  
+  public String name;
+  
+  public StructureSelectionManager ssm;
+  
+  /*public AppVarna(){
+	  vab = new AppVarnaBinding(); 
+	  initVarna();
+  }*/
+  
+ 
+  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);
+	  varnaPanel=vab.get_varnaPanel();
+	  setBackground(Color.white);
+	  JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,vab.getListPanel(),varnaPanel);
+	  getContentPane().setLayout(new BorderLayout());
+	  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);
+  }
+  
+  public String replaceOddGaps(String oldStr){
+	  String patternStr = "[^([{<>}])]";
+      String replacementStr = ".";
+      Pattern pattern = Pattern.compile(patternStr);
+      Matcher matcher = pattern.matcher(oldStr);
+      String newStr=matcher.replaceAll(replacementStr);
+	  return newStr;
+  }
+  
+  public RNA trimRNA(RNA rna){
+    ShiftList offset=new ShiftList();
+	  RNA rnaTrim = new RNA("trim_"+rna.getName());
+	  try {
+		  rnaTrim.setRNA(rna.getSeq(),replaceOddGaps(rna.getStructDBN()));
+	  } catch (ExceptionUnmatchedClosingParentheses e2) {
+		e2.printStackTrace();
+	  } catch (ExceptionFileFormatOrSyntax e3) {
+		e3.printStackTrace();
+	  }
 
-  //RenderPanel renderPanel;
+	  StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
+	  StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
+	  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(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);
+				  
+				  struc.replace(m, m+1, "*");
+				  struc.replace(l, l+1, "*");
+			  }else{
+				  struc.replace(i, i+1, "*");
+			  }
+		  } else {
+		    if (ofstart>-1)
+		    {
+		      offset.addShift(ofstart, ofstart-i);
+		      ofstart=-1;
+		    }
+		  }
+	    }
+	  // 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("*", "");
 
-  AlignmentPanel ap;
+	  try {
+		rnaTrim.setRNA(newSeq,newStruc);
+		registerOffset(rnaTrim,offset);
+	  } catch (ExceptionUnmatchedClosingParentheses e) {
+		// TODO Auto-generated catch block
+		e.printStackTrace();
+	  } catch (ExceptionFileFormatOrSyntax e) {
+		// 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());
+  }
 
-  Vector atomsPicked = new Vector();
-  
-  void initVarna(){
-	  //vab.setFinishedInit(false);
-	  //renderPanel = new RenderPanel();
-	  // TODO: consider waiting until the structure/view is fully loaded before
-	  // displaying
-	  //this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
-	  jalview.gui.Desktop.addInternalFrame(this,"test",300,300);
+  public void showPanel(boolean show){
+	  this.setVisible(show);
   }
   
   private boolean _started = false;
@@ -73,6 +211,114 @@ public class AppVarna extends JInternalFrame // implements Runnable,SequenceStru
         Cache.log.error("Couldn't open Varna viewer!", ex);
       }
   }
+
+@Override
+public void onUINewStructure(VARNAConfig v, RNA r) {
+  
+}
+
+@Override
+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 
+ * VARNA window is highlighted at the specific position. 
+ * To be able to remove it before the next highlight
+ * it is saved in _lastHighlight
+ */
+@Override
+public void mouseOverSequence(SequenceI sequence, int index) {
+        RNA rna=vab.getSelectedRNA();
+	ShiftList shift=offsets.get(rna);
+	if (shift!=null)
+	{
+	  index=shift.shift(index);
+	}
+	mouseOverHighlighter.highlightRegion(rna, index, index);
+	vab.updateSelectedRNA(rna);
+}
+
+@Override
+public void mouseOverStructure(int atomIndex, String strInfo) {
+	// TODO Auto-generated method stub
+	
+}
+
+@Override
+public void onStructureRedrawn()
+{
+  // TODO Auto-generated method stub
+  
+}
+
+@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
   
+}
+
 
 }