last version stay many bugs ..

[jalview.git] / src / MCview / PDBfile.java

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index dede37e..fe2851a 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -29,6 +29,7 @@ import org.xml.sax.SAXException;
 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.exceptions.ExceptionUnmatchedClosingParentheses;
 
 import jalview.datamodel.*;
 import jalview.io.FileParse;
@@ -46,12 +47,12 @@ public class PDBfile extends jalview.io.AlignFile
    */
   boolean VisibleChainAnnotation = false;
 
-  public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(inFile, inType);
   }
 
-  public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(source);
   }
@@ -182,24 +183,25 @@ public class PDBfile extends jalview.io.AlignFile
         seqs.addElement(chainseq);
        if(isRNA(chainseq)==true)
        {
+          String path =inFile.getPath();
           System.out.println("this is a PDB format and RNA sequence");
-          Annotate3D an3d = new Annotate3D(id);
+          Annotate3D an3d = new Annotate3D(path);
           System.out.println(id);
           //BufferedWriter r = an3d.getReader();
           
-          BufferedReader in = new BufferedReader(new FileReader("temp.rnaml"));
+         // BufferedReader in = new BufferedReader(new FileReader("temp.rnaml"));
           
-          String str;
-          while ((str = in.readLine()) != null) {
-                    System.out.println(str);
-                    System.out.println("toto");
+          //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);
+                   // }
+          //String type = "File";
+          //RnamlFile rnaml =new RnamlFile("temp.rnaml",type);
           System.out.println("Create rnamfile object");
           //rnaml.parse("temp");
-          this.annotations =rnaml.getAnnot();
+          //this.annotations =rnaml.getAnnot();
           
        }