X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=9c30e675d018a571585bf7fdfad2f50cbbb1edce;hb=90c1537ec500264f2ac89d64bb75a7ce14fa0181;hp=bb4817420c4f2d01905aa423c4d40d5193c2ff05;hpb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index bb48174..9c30e67 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,13 +1,13 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -29,9 +29,14 @@ 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.AppletFormatAdapter;
 import jalview.io.FileParse;
+import jalview.io.RnamlFile;
+import jalview.ws.jws1.Annotate3D;
 
 public class PDBfile extends jalview.io.AlignFile
 {
@@ -44,12 +49,12 @@ public class PDBfile extends jalview.io.AlignFile
    */
   boolean VisibleChainAnnotation = false;
 
-  public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+  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
+  public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
   {
     super(source);
   }
@@ -59,23 +64,23 @@ 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());
-  
-      chains = new Vector();
 
-      PDBChain tmpchain;
-      String line=null;
-      boolean modelFlag = false;
-      boolean terFlag = false;
-      String lastID = "";
+    chains = new Vector();
+    ArrayList<SequenceI> rna=new ArrayList<SequenceI>();
+    PDBChain tmpchain;
+    String line = null;
+    boolean modelFlag = false;
+    boolean terFlag = false;
+    String lastID = "";
 
-      int index = 0;
-      String atomnam = null;
-      try
-      {
+    int index = 0;
+    String atomnam = null;
+    try
+    {
       while ((line = nextLine()) != null)
       {
         if (line.indexOf("HEADER") == 0)
@@ -164,6 +169,8 @@ public class PDBfile extends jalview.io.AlignFile
         dataset.setName(id + "|" + dataset.getName());
         PDBEntry entry = new PDBEntry();
         entry.setId(id);
+        entry.setProperty(new Hashtable());
+        entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
         if (inFile != null)
         {
           entry.setFile(inFile.getAbsolutePath());
@@ -180,9 +187,9 @@ public class PDBfile extends jalview.io.AlignFile
         seqs.addElement(chainseq);
        if(isRNA(chainseq)==true)
        {
-    	   System.out.println("this is a PDB format and RNA sequence");
+         rna.add(chainseq);
        }
-        
+         
         AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
         
         if (chainannot != null)
@@ -195,14 +202,78 @@ public class PDBfile extends jalview.io.AlignFile
           }
         }
       }
+      if (rna.size()>0)
+      try {
+        String path =inFile.getPath();
+        System.out.println("this is a PDB format and RNA sequence");
+        Annotate3D an3d = new Annotate3D();
+        AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
+        if (al!=null && al.getHeight()>0)
+        {
+          ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
+          ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
+          for (SequenceI sq:rna)
+          {
+            SequenceI bestm=null;
+            AlignSeq bestaseq=null;
+            int bestscore=0;
+            for (SequenceI msq:al.getSequences())
+            {
+              AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, AlignSeq.DNA);
+              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=rna.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));
+              //sq.setSequenceFeatures(sp.getSequenceFeatures());
+              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()));
+            }
+          }
+        }
+      } 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");
       throw new IOException("Out of memory loading PDB File");
-    }
-    catch (NumberFormatException ex)
+    } catch (NumberFormatException ex)
     {
-      if (line!=null) {
+      if (line != null)
+      {
         System.err.println("Couldn't read number from line:");
         System.err.println(line);
       }