From 142aafdd26883e2c97a880eb40c8005748b15a3e Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 4 Dec 2012 10:17:11 +0000
Subject: [PATCH] JAL-1028 tidy and refactor external processing and mapping
 to separate functions

---
 src/MCview/PDBfile.java |  120 ++++++++++++++++++++++++-----------------------
 1 file changed, 62 insertions(+), 58 deletions(-)

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 9c30e67..1b3aa8b 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -33,9 +33,7 @@ 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
@@ -204,62 +202,7 @@ 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");
@@ -280,6 +223,67 @@ public class PDBfile extends jalview.io.AlignFile
     }
   }
 
+  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.
    * 
-- 
1.7.10.2