X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=581901a5450a2f9655ea2bf278ab694c988f27db;hb=f5a2fd32ad34d909ba7326ab40c1709cf00bdf32;hp=1fd9f1c1078b210f835dab27133f9745e558d8c6;hpb=cb37b13542829ad0406c5f0ff8349334f83c31ae;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 1fd9f1c..581901a 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -74,6 +74,8 @@ public class DBRefFetcher implements Runnable
 
   SequenceFetcher sfetcher;
 
+  private SequenceI[] alseqs;
+
   public DBRefFetcher()
   {
   }
@@ -106,9 +108,11 @@ public class DBRefFetcher implements Runnable
   public DBRefFetcher(SequenceI[] seqs, AlignFrame af, String[] sources)
   {
     this.af = af;
+    alseqs = new SequenceI[seqs.length];
     SequenceI[] ds = new SequenceI[seqs.length];
     for (int i = 0; i < seqs.length; i++)
     {
+      alseqs[i] = seqs[i];
       if (seqs[i].getDatasetSequence() != null)
         ds[i] = seqs[i].getDatasetSequence();
       else
@@ -496,27 +500,31 @@ public class DBRefFetcher implements Runnable
       DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry
               .getDBRef(), new String[]
       { dbSource });
+      if (entryRefs==null) {
+        System.err.println("Dud dbSource string ? no entryrefs selected for "+dbSource+ " on "+entry.getName());
+        continue;
+      }
       for (int j = 0; j < entryRefs.length; j++)
-      {
-        String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString();
-        // match up on accessionId
-        if (seqRefs.containsKey(accessionId.toUpperCase()))
         {
-          Vector seqs = (Vector) seqRefs.get(accessionId);
-          for (int jj = 0; jj < seqs.size(); jj++)
+          String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString();
+          // match up on accessionId
+          if (seqRefs.containsKey(accessionId.toUpperCase()))
           {
-            sequence = (SequenceI) seqs.elementAt(jj);
-            if (!sequenceMatches.contains(sequence))
+            Vector seqs = (Vector) seqRefs.get(accessionId);
+            for (int jj = 0; jj < seqs.size(); jj++)
             {
-              sequenceMatches.addElement(sequence);
+              sequence = (SequenceI) seqs.elementAt(jj);
+              if (!sequenceMatches.contains(sequence))
+              {
+                sequenceMatches.addElement(sequence);
+              }
             }
           }
         }
-      }
-      if (sequenceMatches.size() == 0)
-      {
-        // failed to match directly on accessionId==query so just compare all
-        // sequences to entry
+        if (sequenceMatches.size() == 0)
+        {
+          // failed to match directly on accessionId==query so just compare all
+          // sequences to entry
         Enumeration e = seqRefs.keys();
         while (e.hasMoreElements())
         {
@@ -608,8 +616,9 @@ public class DBRefFetcher implements Runnable
           // absStart+sequence.getStart()+entrySeq.length()-1},
           // new int[] { entry.getStart(), entry.getEnd() }, 1, 1);
           // relocate local features for updated start
-          if (updateRefFrame && sequence.getSequenceFeatures() != null)
-          {
+          if (updateRefFrame) {
+            if (sequence.getSequenceFeatures() != null)
+            {
             SequenceFeature[] sf = sequence.getSequenceFeatures();
             int start = sequence.getStart();
             int end = sequence.getEnd();
@@ -624,6 +633,7 @@ public class DBRefFetcher implements Runnable
                 sf[sfi].setEnd(sf[sfi].getEnd() + startShift);
               }
             }
+            }
           }
         }
 
@@ -638,6 +648,22 @@ public class DBRefFetcher implements Runnable
           // finally, update local sequence reference frame if we're allowed
           sequence.setStart(absStart);
           sequence.setEnd(absEnd);
+          // search for alignment sequences to update coordinate frame for
+          for (int alsq = 0; alsq<alseqs.length; alsq++)
+          {
+            if (alseqs[alsq].getDatasetSequence()==sequence)
+            {
+              String ngAlsq = AlignSeq.extractGaps("-. ",
+                      alseqs[alsq].getSequenceAsString()).toUpperCase();
+              int oldstrt = alseqs[alsq].getStart();
+              alseqs[alsq].setStart(sequence.getSequenceAsString().toUpperCase().indexOf(ngAlsq)+sequence.getStart());
+              if (oldstrt != alseqs[alsq].getStart()) {
+                alseqs[alsq].setEnd(ngAlsq.length()+alseqs[alsq].getStart()-1);
+              }
+            }
+          }
+          // TODO:  search for all other references to this dataset sequence, and update start/end
+          // TODO: update all AlCodonMappings which involve this alignment sequence (e.g. Q30167 cdna translation from exon2 product (vamsas demo)
         }
         // and remove it from the rest
         // TODO: decide if we should remove annotated sequence from set