JAL-1028 JAL-674 hooks to call external processing for peptide and nucleic acid seque...

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 1b3aa8b..99d55b0 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -22,14 +22,6 @@ 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.analysis.AlignSeq;
 import jalview.datamodel.*;
@@ -47,12 +39,12 @@ public class PDBfile extends jalview.io.AlignFile
    */
   boolean VisibleChainAnnotation = false;
 
-  public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PDBfile(String inFile, String inType) throws Exception
   {
     super(inFile, inType);
   }
 
-  public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PDBfile(FileParse source) throws Exception
   {
     super(source);
   }
@@ -62,13 +54,13 @@ public class PDBfile extends jalview.io.AlignFile
     return null;
   }
 
-  public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public void parse() throws Exception
   {
     // TODO set the filename sensibly - try using data source name.
     id = safeName(getDataName());
 
     chains = new Vector();
-    ArrayList<SequenceI> rna=new ArrayList<SequenceI>();
+    ArrayList<SequenceI> rna=new ArrayList<SequenceI>(), prot=new ArrayList<SequenceI>();
     PDBChain tmpchain;
     String line = null;
     boolean modelFlag = false;
@@ -186,6 +178,8 @@ public class PDBfile extends jalview.io.AlignFile
        if(isRNA(chainseq)==true)
        {
          rna.add(chainseq);
+       } else {
+         prot.add(chainseq);
        }
          
         AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
@@ -209,6 +203,15 @@ public class PDBfile extends jalview.io.AlignFile
         x.printStackTrace();
         
       };
+      if (prot.size()>0)
+      try {
+        processPdbFileWithJmol(prot);
+      } catch (Exception x)
+      {
+        System.err.println("Exceptions when dealing with RNA in pdb file");
+        x.printStackTrace();
+        
+      };
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
@@ -222,7 +225,13 @@ public class PDBfile extends jalview.io.AlignFile
       }
     }
   }
-
+  private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
+  {
+//    System.out.println("this is a PDB format and RNA sequence");
+    Annotate3D an3d = new Annotate3D();
+    AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
+    replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+  }
   private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
 //    System.out.println("this is a PDB format and RNA sequence");
     Annotate3D an3d = new Annotate3D();