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 e3df0db..99d55b0 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -22,18 +22,10 @@ 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.*;
 import jalview.io.FileParse;
-import jalview.io.RnamlFile;
 import jalview.ws.jws1.Annotate3D;
 
 public class PDBfile extends jalview.io.AlignFile
@@ -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>(), prot=new ArrayList<SequenceI>();
     PDBChain tmpchain;
     String line = null;
     boolean modelFlag = false;
@@ -185,28 +177,11 @@ 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(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();
-          
+         rna.add(chainseq);
+       } else {
+         prot.add(chainseq);
        }
-        
+         
         AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
         
         if (chainannot != null)
@@ -219,6 +194,24 @@ public class PDBfile extends jalview.io.AlignFile
           }
         }
       }
+      if (rna.size()>0)
+      try {
+        processPdbFileWithAnnotate3d(rna);
+      } catch (Exception x)
+      {
+        System.err.println("Exceptions when dealing with RNA in pdb file");
+        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");
@@ -232,7 +225,74 @@ 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();
+    AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
+    replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+  }
+  private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
+  {
+    if (al!=null && al.getHeight()>0)
+    {
+      ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
+      ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
+      
+      for (SequenceI sq:ochains)
+      {
+        SequenceI bestm=null;
+        AlignSeq bestaseq=null;
+        int bestscore=0;
+        for (SequenceI msq:al.getSequences())
+        {
+          AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, dnaOrProtein);
+          if (bestm==null || aseq.getMaxScore()>bestscore)
+          {
+            bestscore=aseq.getMaxScore();
+            bestaseq= aseq;
+            bestm=msq;
+          }
+        }
+        System.out.println("Best Score for "+(matches.size()+1)+" :"+bestscore);
+        matches.add(bestm);
+        aligns.add(bestaseq);
+        al.deleteSequence(bestm);
+      }
+      for (int p=0,pSize=seqs.size();p<pSize;p++)
+      {
+        SequenceI sq,sp=seqs.get(p);
+        int q;
+        if ((q=ochains.indexOf(sp))>-1)
+        {
+          seqs.set(p, sq=matches.get(q));
+          sq.setName(sp.getName());
+          sq.setDescription(sp.getDescription());
+          sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
+          int inspos=-1;
+          for (int ap=0;ap<annotations.size();)
+          {
+            if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
+              if (inspos==-1)
+              {
+                inspos=ap;
+              }
+              annotations.remove(ap);
+            } else {
+              ap++;
+            }
+          }
+          annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+        }
+      }
+    }
+  }
   /**
    * make a friendly ID string.
    *