X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=4fc88141cff64812809c1c38911fb422a269d79a;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=9c30e675d018a571585bf7fdfad2f50cbbb1edce;hpb=90c1537ec500264f2ac89d64bb75a7ce14fa0181;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 9c30e67..4fc8814 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,19 +1,22 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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.
+ * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package MCview;
 
@@ -22,21 +25,9 @@ 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.AppletFormatAdapter;
 import jalview.io.FileParse;
-import jalview.io.RnamlFile;
-import jalview.ws.jws1.Annotate3D;
 
 public class PDBfile extends jalview.io.AlignFile
 {
@@ -49,12 +40,12 @@ 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 IOException
   {
     super(inFile, inType);
   }
 
-  public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PDBfile(FileParse source) throws IOException
   {
     super(source);
   }
@@ -64,13 +55,13 @@ public class PDBfile extends jalview.io.AlignFile
     return null;
   }
 
-  public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  public void parse() throws IOException
   {
     // 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;
@@ -170,7 +161,9 @@ public class PDBfile extends jalview.io.AlignFile
         PDBEntry entry = new PDBEntry();
         entry.setId(id);
         entry.setProperty(new Hashtable());
-        entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+        if (((PDBChain)chains.elementAt(i)).id!=null) {
+          entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+        }
         if (inFile != null)
         {
           entry.setFile(inFile.getAbsolutePath());
@@ -188,6 +181,8 @@ public class PDBfile extends jalview.io.AlignFile
        if(isRNA(chainseq)==true)
        {
          rna.add(chainseq);
+       } else {
+         prot.add(chainseq);
        }
          
         AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
@@ -204,62 +199,25 @@ 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()));
-            }
-          }
-        }
+        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();
+        
+      };
+      if (prot.size()>0)
+      try {
+        processPdbFileWithJmol(prot);
       } catch (Exception x)
       {
         System.err.println("Exceptions when dealing with RNA in pdb file");
@@ -279,7 +237,94 @@ public class PDBfile extends jalview.io.AlignFile
       }
     }
   }
-
+  private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
+  {
+    try {
+      Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+      if (cl!=null)
+      {
+        Object jmf = cl.getConstructor(new Class[] {FileParse.class}).newInstance(new Object[] {new FileParse(getDataName(),type)});
+        Alignment al = new Alignment((SequenceI[]) cl.getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));
+        cl.getMethod("addAnnotations",new Class[] {Alignment.class}).invoke(jmf, al);
+        replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+      }
+    } catch (ClassNotFoundException q)
+    {}
+  }
+  private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
+//    System.out.println("this is a PDB format and RNA sequence");
+    // note: we use reflection here so that the applet can compile and run without the HTTPClient bits and pieces needed for accessing Annotate3D web service
+    try {
+    Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+    if (cl!=null)
+    {
+      // TODO: use the PDB ID of the structure if one is available, to save bandwidth and avoid uploading the whole structure to the service
+      Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(new Object[] {});
+      AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor", new Class[] { FileParse.class}).invoke(annotate3d, new Object[] { new FileParse(getDataName(),type)}));
+      replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+    }
+    } catch (ClassNotFoundException x)
+    {
+      //ignore classnotfounds - occurs in applet
+    };
+  }
+  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++;
+            }
+          }
+          if (sq.getAnnotation()!=null) {
+            annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+          }
+        }
+      }
+    }
+  }
   /**
    * make a friendly ID string.
    *