JAL-842; Text element containing the structure is not visible anymore

[jalview.git] / src / jalview / gui / AppVarna.java

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 012d0d1..35e9d35 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -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.*;
 
@@ -38,10 +41,13 @@ 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.ModeleStyleBP;
 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;
@@ -50,29 +56,37 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
   
   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);
+                 rna1.setRNA(seq,replaceOddGaps(struc));
          } catch (ExceptionUnmatchedClosingParentheses e2) {
                e2.printStackTrace();
          } catch (ExceptionFileFormatOrSyntax e3) {
                e3.printStackTrace();
          }
+         rnaList.add(trimRNA(rna1));     
          rnaList.add(rna1);
-         rnaList.add(trimRNA(rna1));
+         rna1.setName("consenus_"+rna1.getName());
+         
          
          vab = new AppVarnaBinding(rnaList);
          //vab = new AppVarnaBinding(seq,struc);
          //System.out.println("Hallo: "+name);
          this.name=name;
-         initVarna();    
+         initVarna();
+      ssm = ap.getStructureSelectionManager();
+         ssm.addStructureViewerListener(this);
   }
   
   public void initVarna(){
@@ -89,29 +103,58 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
          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(rna.getName()+"_trim");
-         String seq=rna.getSeq();
-         String struc=rna.getStructDBN();
-         String newSeq="";
-         String newStruc="";
-         for(int i=0;i<seq.length();i++){
-                 if(seq.substring(i, i+1).compareTo("-")!=0){
-                         newSeq=newSeq+seq.substring(i, i+1);
-                         newStruc=newStruc+struc.substring(i,i+1);
+         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) {
+         } catch (ExceptionUnmatchedClosingParentheses e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
-       } catch (ExceptionFileFormatOrSyntax e) {
+         } catch (ExceptionFileFormatOrSyntax e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
-       }
-       //System.out.println(newSeq+"\t"+newStruc);
-       return rnaTrim;
+         }
+         
+         return rnaTrim;
   }
 
   public void showPanel(boolean show){
@@ -143,7 +186,6 @@ public void onLayoutChanged() {
 
 @Override
 public void onUINewStructure(VARNAConfig v, RNA r) {
-       //TODO _rnaList.add(v, r,"",true);
        // TODO Auto-generated method stub
        
 }
@@ -153,6 +195,30 @@ 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 mouseOverStructure(int atomIndex, String strInfo) {
+       // TODO Auto-generated method stub
+       
+}
 
 }