Merge branch 'develop' into menard

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index a6ad951..2005886 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -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);
   }
@@ -51,7 +62,7 @@ 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());
@@ -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]);
           }
@@ -263,4 +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;
+         
+         
+  }
 }