JAL-842; trimming single structures for single sequences added;

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 524ac82..5dd65c4 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -38,6 +38,8 @@ 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.rna.ModeleBaseNucleotide;
+import fr.orsay.lri.varna.models.rna.ModeleStyleBP;
 import fr.orsay.lri.varna.models.rna.RNA;
 
 
@@ -48,15 +50,7 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
 
   VARNAPanel varnaPanel;
   
-  String name;
-
-  //JSplitPane splitPane;
-
-  //RenderPanel renderPanel;
-
-  //AlignmentPanel ap;
-
-  //Vector atomsPicked = new Vector();
+  public String name;
   
   /*public AppVarna(){
          vab = new AppVarnaBinding(); 
@@ -68,40 +62,83 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
          RNA rna1 = new RNA(name);
          try {
                  rna1.setRNA(seq,struc);
-        } catch (ExceptionUnmatchedClosingParentheses e2) {
+         } 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;
+         vab = new AppVarnaBinding(rnaList);
+         //vab = new AppVarnaBinding(seq,struc);
+         //System.out.println("Hallo: "+name);
+         this.name=name;
          initVarna();    
   }
   
   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);
-         System.out.println("vp: "+vab.get_varnaPanel().getName());
-         //varnaPanel.setVisible(true);
+         JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,vab.getListPanel(),varnaPanel);
          getContentPane().setLayout(new BorderLayout());
-         getContentPane().add(varnaPanel, BorderLayout.CENTER);
-         setVisible(true);
+         getContentPane().add(split, BorderLayout.CENTER);
+         //getContentPane().add(vab.getTools(), BorderLayout.NORTH);   
          varnaPanel.addVARNAListener(this);
-         jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height);  
-         //showPanel(true);
+         jalview.gui.Desktop.addInternalFrame(this,"VARNA -"+name,getBounds().width, getBounds().height);
+         this.pack();
+         showPanel(true);
   }
   
+  public RNA trimRNA(RNA rna){
+         RNA rnaTrim = new RNA("trim_"+rna.getName());
+         try {
+                 rnaTrim.setRNA(rna.getSeq(),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++){
+                 if(seq.substring(i, i+1).compareTo("-")==0 || seq.substring(i, i+1).compareTo(".")==0){
+                         if(!rnaTrim.findPair(i).isEmpty()){
+                                 System.out.println(rnaTrim.findPair(i));
+                                 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){
-         //vab.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-         //vab.pack();
-         //vab.setVisible(show);
-           
-         varnaPanel.setVisible(show);
+         this.setVisible(show);
   }
   
   private boolean _started = false;