X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=dede37e6c7ba96fc4da3c8e89c57a09bce84de97;hb=c5677e9860106a821a3e6e0429b20ede7b9a732a;hp=bb4817420c4f2d01905aa423c4d40d5193c2ff05;hpb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index bb48174..dede37e 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -32,6 +32,8 @@ import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
 
 import jalview.datamodel.*;
 import jalview.io.FileParse;
+import jalview.io.RnamlFile;
+import jalview.ws.jws1.Annotate3D;
 
 public class PDBfile extends jalview.io.AlignFile
 {
@@ -44,12 +46,12 @@ public class PDBfile extends jalview.io.AlignFile
    */
   boolean VisibleChainAnnotation = false;
 
-  public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+  public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
   {
     super(inFile, inType);
   }
 
-  public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+  public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
   {
     super(source);
   }
@@ -59,7 +61,7 @@ public class PDBfile extends jalview.io.AlignFile
     return null;
   }
 
-  public void parse() throws IOException
+  public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
   {
     // TODO set the filename sensibly - try using data source name.
     id = safeName(getDataName());
@@ -181,6 +183,24 @@ public class PDBfile extends jalview.io.AlignFile
        if(isRNA(chainseq)==true)
        {
     	   System.out.println("this is a PDB format and RNA sequence");
+    	   Annotate3D an3d = new Annotate3D(id);
+    	   System.out.println(id);
+    	   //BufferedWriter r = an3d.getReader();
+    	   
+    	   BufferedReader in = new BufferedReader(new FileReader("temp.rnaml"));
+    	   
+    	   String str;
+    	   while ((str = in.readLine()) != null) {
+  		     System.out.println(str);
+  		     System.out.println("toto");
+
+  		     }
+    	   String type = "File";
+    	   RnamlFile rnaml =new RnamlFile("temp.rnaml",type);
+    	   System.out.println("Create rnamfile object");
+    	   //rnaml.parse("temp");
+    	   this.annotations =rnaml.getAnnot();
+    	   
        }
         
         AlignmentAnnotation[] chainannot = chainseq.getAnnotation();