X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=302f3b22e9bafc1fa3b9958c237dc4b757d64088;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=4fc88141cff64812809c1c38911fb422a269d79a;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 4fc8814..302f3b2 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -61,7 +61,7 @@ public class PDBfile extends jalview.io.AlignFile
     id = safeName(getDataName());
 
     chains = new Vector();
-    ArrayList<SequenceI> rna=new ArrayList<SequenceI>(), prot=new ArrayList<SequenceI>();
+    ArrayList<SequenceI> rna = new ArrayList<SequenceI>(), prot = new ArrayList<SequenceI>();
     PDBChain tmpchain;
     String line = null;
     boolean modelFlag = false;
@@ -161,8 +161,10 @@ public class PDBfile extends jalview.io.AlignFile
         PDBEntry entry = new PDBEntry();
         entry.setId(id);
         entry.setProperty(new Hashtable());
-        if (((PDBChain)chains.elementAt(i)).id!=null) {
-          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)
         {
@@ -178,52 +180,63 @@ 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);
-       }
-         
+        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();
-        
-      };
-      if (prot.size()>0)
-      try {
-        processPdbFileWithJmol(prot);
-      } catch (Exception x)
-      {
-        System.err.println("Exceptions when dealing with RNA in pdb file");
-        x.printStackTrace();
-        
-      };
+      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();
+
+        }
+      ;
+      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");
@@ -237,94 +250,125 @@ public class PDBfile extends jalview.io.AlignFile
       }
     }
   }
-  private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
+
+  private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
+          throws Exception
   {
-    try {
+    try
+    {
       Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
-      if (cl!=null)
+      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);
+        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);
     }
+  }
+
+  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
-    };
+      // ignore classnotfounds - occurs in applet
+    }
+    ;
   }
-  private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
+
+  private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains,
+          AlignmentI al, String dnaOrProtein)
   {
-    if (al!=null && al.getHeight()>0)
+    if (al != null && al.getHeight() > 0)
     {
-      ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
-      ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
-      
-      for (SequenceI sq:ochains)
+      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())
+        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)
+          AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq,
+                  dnaOrProtein);
+          if (bestm == null || aseq.getMaxScore() > bestscore)
           {
-            bestscore=aseq.getMaxScore();
-            bestaseq= aseq;
-            bestm=msq;
+            bestscore = aseq.getMaxScore();
+            bestaseq = aseq;
+            bestm = msq;
           }
         }
-        System.out.println("Best Score for "+(matches.size()+1)+" :"+bestscore);
+        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++)
+      for (int p = 0, pSize = seqs.size(); p < pSize; p++)
       {
-        SequenceI sq,sp=seqs.get(p);
+        SequenceI sq, sp = seqs.get(p);
         int q;
-        if ((q=ochains.indexOf(sp))>-1)
+        if ((q = ochains.indexOf(sp)) > -1)
         {
-          seqs.set(p, sq=matches.get(q));
+          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();)
+          int inspos = -1;
+          for (int ap = 0; ap < annotations.size();)
           {
-            if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
-              if (inspos==-1)
+            if (((AlignmentAnnotation) annotations.get(ap)).sequenceRef == sp)
+            {
+              if (inspos == -1)
               {
-                inspos=ap;
+                inspos = ap;
               }
               annotations.remove(ap);
-            } else {
+            }
+            else
+            {
               ap++;
             }
           }
-          if (sq.getAnnotation()!=null) {
+          if (sq.getAnnotation() != null)
+          {
             annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
           }
         }
       }
     }
   }
+
   /**
    * make a friendly ID string.
    * 
@@ -394,17 +438,19 @@ 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;
-	  
-	  
+    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;
+
   }
 }