From c9c74c082bdd9323850a864144dc8a9b36399157 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 14 Aug 2006 15:09:43 +0000
Subject: [PATCH] Do a loop for multiple seq matches

---
 src/jalview/io/DBRefFetcher.java |   77 ++++++++++----------------------------
 1 file changed, 20 insertions(+), 57 deletions(-)

diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index 17526ac..23e5bf6 100644
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -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,
+      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());
 
       int absStart = entry.getUniprotSequence().getContent().indexOf(
           nonGapped.toString());
@@ -301,7 +303,7 @@ 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;
@@ -317,7 +319,7 @@ public class DBRefFetcher implements Runnable
             sf.setEnd(sf.getEnd() + absStart + 1);
           }
 
-          sbuffer.append(sequence.getName() +
+          sbuffer.append(sequence[m].getName() +
                          " HAS " + absStart +
               " PREFIXED RESIDUES COMPARED TO UNIPROT - ANY SEQUENCE FEATURES"
                          + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
@@ -339,58 +341,19 @@ public class DBRefFetcher implements Runnable
         if(!pdb.getType().equals(DBRefSource.PDB))
           continue;
 
-        sequence.addDBRef(new DBRefEntry(DBRefSource.PDB,
+        sequence[m].addDBRef(new DBRefEntry(DBRefSource.PDB,
                                        "0",
                                        pdb.getId()));
 
         onlyPdbEntries.addElement(pdb);
       }
 
-      sequence.setPDBId(onlyPdbEntries);
+      sequence[m].setPDBId(onlyPdbEntries);
 
-      if (entry.getFeature()!=null) {
-        //e = entry.getFeature().elements();
-      //  while (e.hasMoreElements())
-        {
-        //  SequenceFeature sf = (SequenceFeature) e.nextElement();
-         // sf.setFeatureGroup("Uniprot");
-        //  sequence.addSequenceFeature( sf );
-        }
-      }
-      sequence.setStart(absStart);
-      sequence.setEnd(absEnd);
+      sequence[m].setStart(absStart);
+      sequence[m].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());
-
-          absStart = sequence.getSequence().indexOf(nonGapped);
-          absEnd = absStart + nonGapped.toString().length() - 1;
-
-          // 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++;
       }
     }
   }
-- 
1.7.10.2