From: janengelhardt <engelhardt87@googlemail.com>
Date: Mon, 11 Jul 2011 01:20:30 +0000 (+0200)
Subject: JAL-842; trimming single structures for single sequences added;
X-Git-Tag: Jalview_2_9~576^2~27
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d6f9234284710c0f6eaa1c51626dde81c4db103a;p=jalview.git

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

Change-Id: I041c71aafd0081875b948b9978c2411154033408
---

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 012d0d1..5dd65c4 100644
--- 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;
 
 
@@ -65,8 +67,10 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
 	  } 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);
@@ -90,28 +94,47 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
   }
   
   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(),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) {
+	  } 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){
diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 092e850..1d2d8fd 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -234,9 +234,9 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 		vp.setPreferredSize(new Dimension(400, 400));
 		for(int i=0;i<rnaInList.size();i++){
 			if(i<rnaInList.size()-1){
-				_rnaList.add(vp.getConfig().clone(),rnaInList.get(i),generateDefaultName());
+				_rnaList.add(vp.getConfig().clone(),rnaInList.get(i),rnaInList.get(i).getName());
 			}else{
-				_rnaList.add(vp.getConfig().clone(),rnaInList.get(i),generateDefaultName(),true);
+				_rnaList.add(vp.getConfig().clone(),rnaInList.get(i),rnaInList.get(i).getName(),true);
 			}
 		}