X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=90542981d0351b1389a21b2019b0dfb6632a7e2d;hb=57c960648b550f10c7db40e39c7bb6a761d732b1;hp=7a1e206fa4b060bca27653124e8f78b20b4eb97b;hpb=f2469e3ede414575d5e8cd510ed5c916095b55bf;p=jalview.git

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 7a1e206..9054298 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.*;
 
@@ -38,58 +41,123 @@ 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.models.VARNAConfig;
+import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
+import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
 import fr.orsay.lri.varna.models.rna.RNA;
 
 
-public class AppVarna extends JInternalFrame implements InterfaceVARNAListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
+public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
 
 {
   AppVarnaBinding vab;
 
   VARNAPanel varnaPanel;
   
-  String name;
+  public String name;
+  
+  public StructureSelectionManager ssm;
   
   /*public AppVarna(){
 	  vab = new AppVarnaBinding(); 
 	  initVarna();
   }*/
   
-  public AppVarna(String seq,String struc,String name){
+ 
+  
+  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,struc);
-	 } catch (ExceptionUnmatchedClosingParentheses e2) {
+		  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);
-	  name=this.name;
-	  initVarna();	  
+	  //System.out.println("Hallo: "+name);
+	  this.name=name;
+	  initVarna();
+      ssm = ap.getStructureSelectionManager();
+	  ssm.addStructureViewerListener(this);
   }
   
   public void initVarna(){
-	  //TODO: Why is it not possible to include varnaPanel in the AppVarna-Jframe?
 	  //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(varnaPanel, BorderLayout.CENTER);
-	  
+	  getContentPane().add(split, BorderLayout.CENTER);
+	  //getContentPane().add(vab.getTools(), BorderLayout.NORTH);	
 	  varnaPanel.addVARNAListener(this);
-	  jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height);
+	  jalview.gui.Desktop.addInternalFrame(this,"VARNA -"+name,getBounds().width, getBounds().height);
 	  this.pack();
-	  this.setVisible(true);
-	  //showPanel(true);
+	  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){
+	  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();
+	  }
+
+	  StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
+	  StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
+	  for(int i=0;i<rnaTrim.getSeq().length();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(!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, "*");
+			  }
+		  }
+	  }
+	 
+	  String newSeq=rnaTrim.getSeq().replace("-", "");
+	  rnaTrim.getSeq().replace(".", "");
+	  String newStruc=struc.toString().replace("*", "");
+
+	  try {
+		rnaTrim.setRNA(newSeq,newStruc);
+	  } catch (ExceptionUnmatchedClosingParentheses e) {
+		// TODO Auto-generated catch block
+		e.printStackTrace();
+	  } catch (ExceptionFileFormatOrSyntax e) {
+		// TODO Auto-generated catch block
+		e.printStackTrace();
+	  }
+	  
+	  return rnaTrim;
+  }
+
   public void showPanel(boolean show){
-	  varnaPanel.setVisible(show);
+	  this.setVisible(show);
   }
   
   private boolean _started = false;
@@ -110,23 +178,48 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
   }
 
 @Override
-public void onLayoutChanged() {
+public void onUINewStructure(VARNAConfig v, RNA r) {
 	// TODO Auto-generated method stub
 	
 }
 
 @Override
-public void onUINewStructure(VARNAConfig v, RNA r) {
-	//TODO _rnaList.add(v, r,"",true);
+public void onWarningEmitted(String s) {
 	// TODO Auto-generated method stub
 	
 }
+/**
+ * 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
+ */
+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;
+	vab.updateSelectedRNA(rna);
+}
 
 @Override
-public void onWarningEmitted(String s) {
+public void mouseOverStructure(int atomIndex, String strInfo) {
 	// TODO Auto-generated method stub
 	
 }
+
+@Override
+public void onStructureRedrawn()
+{
+  // TODO Auto-generated method stub
   
+}
+
 
 }