X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FDBRefFetcher.java;h=d57f3be2e97716dcd1208f0e59bdc85c098a5189;hb=fbb18baad3919cbf94fcb5159bbd5269d6af18b4;hp=4488d02c96127b147a9de0e97f677caa7ea344df;hpb=3bff9f93376444b36ca6b69d30193e10ea3c07ab;p=jalview.git

diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index 4488d02..d57f3be 100644
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -135,13 +135,13 @@ public class DBRefFetcher implements Runnable
              seqIndex++, i++)
         {
           Sequence sequence = (Sequence) sequences.get(seqIndex);
-          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {
+          DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {
               jalview.datamodel.DBRefSource.UNIPROT});
           if (uprefs!=null)
           {
             // we know the id for this entry, so don't note its ID in the unknownSequences list
-            for (int j=0,k=uprefs.size(); j<k; j++)
-              ids.add(((DBRefEntry) uprefs.get(j)).getAccessionId());
+            for (int j=0,k=uprefs.length; j<k; j++)
+              ids.add(uprefs[j].getAccessionId());
             unknownSequences.add(sequence);
           } else {
             if (!ids.contains(sequence.getName()))
@@ -244,7 +244,7 @@ public class DBRefFetcher implements Runnable
     if(!file.exists())
       return;
 
-    SequenceI sequence = null;
+    SequenceI [] sequence = null;
 
     Vector entries = getUniprotEntries(file);
 
@@ -254,43 +254,45 @@ public class DBRefFetcher implements Runnable
     {
       entry = (UniprotEntry) entries.elementAt(i);
       String idmatch = entry.getAccession().elementAt(0).toString();
-      sequence = dataset.findName(idmatch);
+      sequence = dataset.findSequenceMatch(idmatch);
 
-      if (sequence == null)
+      if (sequence.length==0)
       {
         //Sequence maybe Name, not Accession
         idmatch = entry.getName().elementAt(0).toString();
-        sequence = dataset.findName(idmatch);
+        sequence = dataset.findSequenceMatch(idmatch);
       }
 
-      if(sequence!=null)
-        ids.remove(sequence.getName());
+      if(sequence.length>0)
+        ids.remove(sequence[0].getName());
 
-      else  if (sequence == null && uniprotFlag)
+      else  if (sequence.length==0 && uniprotFlag)
       {
           StringBuffer upid = new StringBuffer("UniProt/Swiss-Prot|");
           for(int u=0; u<entry.getAccession().size(); u++)
             upid.append(entry.getAccession().elementAt(u)+"|");
 
-          sequence = dataset.findName(upid+idmatch);
+          sequence = dataset.findSequenceMatch(upid+idmatch);
           ids.remove(idmatch);
       }
 
-      if(sequence ==null)
+      if(sequence.length==0)
       {
         System.out.println(idmatch+" not found");
         continue;
       }
 
+      for(int m=0; m<sequence.length; m++)
+      {
 
-      sequence.addDBRef(new DBRefEntry(DBRefSource.UNIPROT,
-                                       "1.0",
+      sequence[m].addDBRef(new DBRefEntry(DBRefSource.UNIPROT,
+                                       "0",
                                        entry.getAccession().elementAt(0).toString()));
 
-      System.out.println("Adding dbref to "+sequence.getName()+" : "+
+      System.out.println("Adding dbref to "+sequence[m].getName()+" : "+
                          entry.getAccession().elementAt(0).toString());
 
-      String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence());
+      String nonGapped = AlignSeq.extractGaps("-. ", sequence[m].getSequence()).toUpperCase();
 
       int absStart = entry.getUniprotSequence().getContent().indexOf(
           nonGapped.toString());
@@ -301,28 +303,26 @@ public class DBRefFetcher implements Runnable
         absStart = nonGapped.toString().indexOf(entry.getUniprotSequence().getContent());
         if(absStart == -1)
         {
-          sbuffer.append(sequence.getName() +
+          sbuffer.append(sequence[m].getName() +
                          " SEQUENCE NOT %100 MATCH \n");
 
           continue;
         }
-        else
-        {
 
-          if(entry.getFeature()!=null)
+        if (entry.getFeature() != null)
+        {
+          Enumeration e = entry.getFeature().elements();
+          while (e.hasMoreElements())
           {
-            Enumeration e = entry.getFeature().elements();
-            while (e.hasMoreElements())
-            {
-              SequenceFeature sf = (SequenceFeature) e.nextElement();
-              sf.setBegin(sf.getBegin() + absStart + 1);
-              sf.setEnd(sf.getEnd() + absStart + 1);
-            }
+            SequenceFeature sf = (SequenceFeature) e.nextElement();
+            sf.setBegin(sf.getBegin() + absStart + 1);
+            sf.setEnd(sf.getEnd() + absStart + 1);
           }
 
-          sbuffer.append(sequence.getName() +
-                         " HAS "+absStart+" PREFIXED RESIDUES COMPARED TO UNIPROT - ANY SEQUENCE FEATURES"
-                        +" HAVE BEEN ADJUSTED ACCORDINGLY \n");
+          sbuffer.append(sequence[m].getName() +
+                         " HAS " + absStart +
+              " PREFIXED RESIDUES COMPARED TO UNIPROT - ANY SEQUENCE FEATURES"
+                         + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
           absStart = 0;
         }
 
@@ -338,57 +338,22 @@ public class DBRefFetcher implements Runnable
       while(e.hasMoreElements())
       {
         PDBEntry pdb = (PDBEntry)e.nextElement();
-        if(!pdb.getType().equals("PDB"))
+        if(!pdb.getType().equals(DBRefSource.PDB))
           continue;
 
-        onlyPdbEntries.addElement(pdb);
-      }
+        sequence[m].addDBRef(new DBRefEntry(DBRefSource.PDB,
+                                       "0",
+                                       pdb.getId()));
 
-      sequence.setPDBId(onlyPdbEntries);
-
-      if (entry.getFeature()!=null) {
-        //e = entry.getFeature().elements();
-      //  while (e.hasMoreElements())
-        {
-        //  SequenceFeature sf = (SequenceFeature) e.nextElement();
-         // sf.setFeatureGroup("Uniprot");
-        //  sequence.addSequenceFeature( sf );
-        }
+        onlyPdbEntries.addElement(pdb);
       }
-      sequence.setStart(absStart);
-      sequence.setEnd(absEnd);
-
 
-      int n = 0;
-      SequenceI seq2;
-      while (n < align.getHeight())
-      {
-        //This loop enables multiple sequences with the same
-        //id to have features added and seq limits updated
-        seq2 = align.getSequenceAt(n);
-        if (seq2.getName().equals(idmatch))
-        {
-          nonGapped = AlignSeq.extractGaps("-. ", seq2.getSequence());
+      sequence[m].setPDBId(onlyPdbEntries);
 
-          absStart = sequence.getSequence().indexOf(nonGapped);
-          absEnd = absStart + nonGapped.toString().length() - 1;
+      sequence[m].setStart(absStart);
+      sequence[m].setEnd(absEnd);
 
-          // This is the Viewd alignment sequences
-          // No need to tell the user of the dataset updates
-          if ( (seq2.getStart() != absStart+sequence.getStart())
-             || (seq2.getEnd() != absEnd+sequence.getStart()))
-          {
-            sbuffer.append("Updated: " + seq2.getName() + " " +
-                           seq2.getStart() + "/" + seq2.getEnd() +
-                           "  to  " + (absStart + sequence.getStart()) + "/" +
-                           (absEnd + sequence.getStart()) + "\n");
-
-            seq2.setStart(absStart + sequence.getStart());
-            seq2.setEnd(absEnd + sequence.getStart());
-          }
-        }
 
-        n++;
       }
     }
   }