last version stay many bugs ..

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 255eee0..fe2851a 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -22,8 +22,19 @@ import java.util.*;
 
 import java.awt.*;
 
+import javax.xml.parsers.ParserConfigurationException;
+
+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;
+import jalview.io.RnamlFile;
+import jalview.ws.jws1.Annotate3D;
 
 public class PDBfile extends jalview.io.AlignFile
 {
@@ -36,12 +47,12 @@ public class PDBfile extends jalview.io.AlignFile
    */
   boolean VisibleChainAnnotation = false;
 
-  public PDBfile(String inFile, String inType) throws IOException
+  public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(inFile, inType);
   }
 
-  public PDBfile(FileParse source) throws IOException
+  public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(source);
   }
@@ -51,23 +62,23 @@ 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());
-
-    try
-    {
+  
       chains = new Vector();
 
       PDBChain tmpchain;
-      String line;
+      String line=null;
       boolean modelFlag = false;
       boolean terFlag = false;
       String lastID = "";
 
       int index = 0;
       String atomnam = null;
+      try
+      {
       while ((line = nextLine()) != null)
       {
         if (line.indexOf("HEADER") == 0)
@@ -170,11 +181,37 @@ public class PDBfile extends jalview.io.AlignFile
         // maintain reference to
         // dataset
         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(path);
+          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();
+        
         if (chainannot != null)
         {
           for (int ai = 0; ai < chainannot.length; ai++)
           {
+        
             chainannot[ai].visible = VisibleChainAnnotation;
             annotations.addElement(chainannot[ai]);
           }
@@ -185,6 +222,13 @@ public class PDBfile extends jalview.io.AlignFile
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
       throw new IOException("Out of memory loading PDB File");
     }
+    catch (NumberFormatException ex)
+    {
+      if (line!=null) {
+        System.err.println("Couldn't read number from line:");
+        System.err.println(line);
+      }
+    }
   }
 
   /**
@@ -256,4 +300,17 @@ public class PDBfile extends jalview.io.AlignFile
               1.0f / (float) i, .4f, 1.0f));
     }
   }
+  public boolean isRNA(SequenceI seqs)
+  {
+         for (int i=0;i<seqs.getLength();i++){
+                 if((seqs.getCharAt(i)!='A') &&(seqs.getCharAt(i)!='C')&&(seqs.getCharAt(i)!='G')&&(seqs.getCharAt(i)!='U'))
+                 {
+                         return false;
+                 }
+         }
+        
+                 return true;
+         
+         
+  }
 }