return annotated rna sequences from rnaml returned from annotate3d

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index e3df0db..0ab28f6 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -31,7 +31,9 @@ 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;
@@ -68,7 +70,7 @@ public class PDBfile extends jalview.io.AlignFile
     id = safeName(getDataName());
 
     chains = new Vector();
-
+    ArrayList<SequenceI> rna=new ArrayList<SequenceI>();
     PDBChain tmpchain;
     String line = null;
     boolean modelFlag = false;
@@ -185,28 +187,9 @@ public class PDBfile extends jalview.io.AlignFile
         seqs.addElement(chainseq);
        if(isRNA(chainseq)==true)
        {
-          String path =inFile.getPath();
-          System.out.println("this is a PDB format and RNA sequence");
-          Annotate3D an3d = new Annotate3D(path);
-          System.out.println(id);
-          //BufferedWriter r = an3d.getReader();
-          
-         // BufferedReader in = new BufferedReader(new FileReader("temp.rnaml"));
-          
-          //String str;
-         // while ((str = in.readLine()) != null) {
-                   // System.out.println(str);
-                   // System.out.println("toto");
-
-                   // }
-          //String type = "File";
-          //RnamlFile rnaml =new RnamlFile("temp.rnaml",type);
-          System.out.println("Create rnamfile object");
-          //rnaml.parse("temp");
-          //this.annotations =rnaml.getAnnot();
-          
+         rna.add(chainseq);
        }
-        
+         
         AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
         
         if (chainannot != null)
@@ -219,6 +202,70 @@ 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;p<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");