X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FRnamlFile.java;h=69786fba1dad765ce09847a0244d5c21c4c930d2;hb=c5677e9860106a821a3e6e0429b20ede7b9a732a;hp=e614e6b9dd08de41ecaddc3b668983c175b8be0b;hpb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;p=jalview.git

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index e614e6b..69786fb 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -10,6 +10,7 @@ import jalview.datamodel.SecondaryStructureAnnotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.ws.jws1.Annotate3D;
 
 import java.io.BufferedReader;
 import java.io.FileNotFoundException;
@@ -36,6 +37,7 @@ import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
 import fr.orsay.lri.varna.factories.RNAFactory;
+import fr.orsay.lri.varna.factories.RNAFactory.RNAFileType;
 import fr.orsay.lri.varna.models.rna.RNA;
 import fr.orsay.lri.varna.utils.RNAMLParser;
 
@@ -45,6 +47,7 @@ import fr.orsay.lri.varna.utils.RNAMLParser;
 public class RnamlFile extends AlignFile
 {
 	 public String id;
+	 protected ArrayList<RNA> result;
 	 
 	 public RnamlFile()
 	  {
@@ -52,36 +55,114 @@ public class RnamlFile extends AlignFile
 		
 	  }
 	 
-	 public RnamlFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+	 public RnamlFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
 	  {
 	    super(inFile, type);
 	    
 	  }
 
-	  public RnamlFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+	  public RnamlFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
 	  {
 	    super(source);
 	    
 	  }
 	  
+//	  public RnamlFile(BufferedReader r) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+//	  {
+//		  	super();	    
+//		    parse(r);
+//		    // sets the index of each sequence in the alignment
+//		    for( int i=0,c=seqs.size(); i<c; i++ ) {  
+//		    	seqs.get(i).setIndex(i);  
+//		    }
+//		  
+//	    
+//	  }
 	  
+	public BufferedReader CreateReader() throws FileNotFoundException
+	{
+		 FileReader fr = null;
+		  fr = new FileReader(inFile); 
+		  
+		  BufferedReader r = new BufferedReader (fr);
+		  return r;
+	}
 	
 	
-	  public void parse() throws ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax, FileNotFoundException 
-	  {
-		  System.out.println("this is a rnaml file");
-		  
-		  
-		  FileReader fr = null;
+	public void parse() throws FileNotFoundException, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
+	{
+		 FileReader fr = null;
 		  fr = new FileReader(inFile); 
 		  
 		  BufferedReader r = new BufferedReader (fr);
-		 
+		 Hashtable seqhash = new Hashtable();
+		  Vector headers = new Vector();
+		  //ArrayList<String> seq =new ArrayList();
+		  //System.out.println(r);
+		   
+		  
+		 result = RNAFactory.loadSecStrRNAML(r);
+		  
+		 System.out.println("this is the secondary scructure:" +result.toArray());
+		  //System.out.println("this is the secondary scructure:" +result.toString());
+		  //System.out.println("this is the secondary scructure:" +result.size());
+			for(int i=0;i<result.size();i++)
+			{
+		  //System.out.println(result.get(0).getSeq());
+		  //System.out.println(result.get(0).getStructBPSEQ());
+		  //System.out.println(result.get(0).getStructDBN(true));
+		  String rna1 =result.get(0).getStructDBN(true);
+		  //System.out.println(result.get(0).getAnnotations());
+		  String seq = result.get(0).getSeq();
+		  System.out.println(type); //the type is "File"
+		  System.out.println(inFile );//inFile is the path
+		  int begin=0;
+		  int end = seq.length()-1;
+		  SequenceI[] seqs = new SequenceI[1];
+		  id = safeName(getDataName());
+		  seqs[0] = new Sequence(id, seq, begin, end);
+		  SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
+		  seqs[0].addSequenceFeature(feat);
+		  this.setSeqs(seqs);
+		  
+		  String[] annot=new String[10000] ;
+		  Annotation[] ann = new Annotation[1000];
+		  for(int j=0;j<rna1.length();j++)
+			{
+		  annot[j] =rna1.substring(j,j+1);
+		  System.out.println(annot[j]);
+			}
+		  
+		  for(int k=0;k<rna1.length();k++)
+		{
+			  ann[k] = new Annotation(annot[k], "", ' ', 0f);
+			  
+			  ann[k].secondaryStructure = jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0);
+			  
+		}
+		  AlignmentAnnotation align = new AlignmentAnnotation("Secondary structure","",ann);
+		  seqs[0].addAlignmentAnnotation(align);
+		  seqs[0].setRNA(result.get(begin));
+		  this.annotations.addElement(align);
+		  
+		  
+		}
+		
+		//Annotate3D tintin = new Annotate3D();
+		  
+		//System.out.println(tintin);  
+	}
+	  
+	
+	  public void parse(BufferedReader r) throws ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax 
+	  {
+		   System.out.println("parse with Buffer (RnamlFile");
 		  Hashtable seqhash = new Hashtable();
 		  Vector headers = new Vector();
 		  //ArrayList<String> seq =new ArrayList();
-		  System.out.println(r);
-		  ArrayList<RNA> result = RNAFactory.loadSecStrRNAML(r);
+		  //System.out.println(r);
+		  
+		  result = RNAFactory.loadSecStr(r,RNAFileType.FILE_TYPE_RNAML);
 		  
 		  System.out.println("this is the secondary scructure:" +result.toArray());
 		  System.out.println("this is the secondary scructure:" +result.toString());
@@ -110,7 +191,7 @@ public class RnamlFile extends AlignFile
 		  for(int j=0;j<rna1.length();j++)
 			{
 		  annot[j] =rna1.substring(j,j+1);
-		  System.out.println(annot[j]);
+		  //System.out.println(annot[j]);
 			}
 		  
 		  for(int k=0;k<rna1.length();k++)
@@ -124,8 +205,9 @@ public class RnamlFile extends AlignFile
 		  seqs[0].addAlignmentAnnotation(align);
 		  this.annotations.addElement(align);
 		}
+		//Annotate3D tintin = new Annotate3D();
 		  
-		  
+		//System.out.println(tintin);  
 		  
 		  
 		  
@@ -268,5 +350,14 @@ public class RnamlFile extends AlignFile
 	    return dataName;
 	  }
 	  
+	  public ArrayList getRNA()
+	  {
+		  return result;
+	  }
+	  
+	  public Vector getAnnot()
+	  {
+		  return annotations;
+	  }
 }