X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=99d55b02b7e7db63d499ad2fff1c6dd065aa4c6c;hb=7d00e99455868f5895682506e495d4e12e8c2fc2;hp=30f7e425ec55fee0b28e03675699ba12439be1ca;hpb=9bfd2651e3fd3dbadf67f5831f56fb86b4626a46;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 30f7e42..99d55b0 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 
@@ -22,8 +22,11 @@ import java.util.*;
 
 import java.awt.*;
 
+
+import jalview.analysis.AlignSeq;
 import jalview.datamodel.*;
 import jalview.io.FileParse;
+import jalview.ws.jws1.Annotate3D;
 
 public class PDBfile extends jalview.io.AlignFile
 {
@@ -36,12 +39,12 @@ 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 Exception
   {
     super(inFile, inType);
   }
 
-  public PDBfile(FileParse source) throws IOException
+  public PDBfile(FileParse source) throws Exception
   {
     super(source);
   }
@@ -51,23 +54,23 @@ public class PDBfile extends jalview.io.AlignFile
     return null;
   }
 
-  public void parse() throws IOException
+  public void parse() throws Exception
   {
     // TODO set the filename sensibly - try using data source name.
     id = safeName(getDataName());
 
-      chains = new Vector();
+    chains = new Vector();
+    ArrayList<SequenceI> rna=new ArrayList<SequenceI>(), prot=new ArrayList<SequenceI>();
+    PDBChain tmpchain;
+    String line = null;
+    boolean modelFlag = false;
+    boolean terFlag = false;
+    String lastID = "";
 
-      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)
@@ -156,6 +159,8 @@ 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());
@@ -170,30 +175,124 @@ public class PDBfile extends jalview.io.AlignFile
         // maintain reference to
         // dataset
         seqs.addElement(chainseq);
+       if(isRNA(chainseq)==true)
+       {
+         rna.add(chainseq);
+       } else {
+         prot.add(chainseq);
+       }
+         
         AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+        
         if (chainannot != null)
         {
           for (int ai = 0; ai < chainannot.length; ai++)
           {
+        
             chainannot[ai].visible = VisibleChainAnnotation;
             annotations.addElement(chainannot[ai]);
           }
         }
       }
+      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");
       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);
       }
     }
   }
-
+  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.
    * 
@@ -263,4 +362,17 @@ 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;
+	  
+	  
+  }
 }