From e7a099f0fa94511b2bfe092533a0b75e99fc3d29 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 23 Apr 2007 11:44:46 +0000
Subject: [PATCH] Only fetch refs for seelcted sequences

---
 src/jalview/io/DBRefFetcher.java              |   21 ++++++++++++++-------
 src/jalview/io/DasSequenceFeatureFetcher.java |    3 +--
 2 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index 437fee7..6d589f9 100644
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -36,7 +36,7 @@ import jalview.gui.*;
 public class DBRefFetcher
     implements Runnable
 {
-  AlignmentI dataset;
+  SequenceI [] dataset;
   AlignFrame af;
   CutAndPasteTransfer output = new CutAndPasteTransfer();
   StringBuffer sbuffer = new StringBuffer();
@@ -80,10 +80,18 @@ public class DBRefFetcher
    * @param align DOCUMENT ME!
    * @param ap DOCUMENT ME!
    */
-  public DBRefFetcher(AlignmentI align, AlignFrame af)
+  public DBRefFetcher(SequenceI [] seqs, AlignFrame af)
   {
     this.af = af;
-    this.dataset = align.getDataset();
+    SequenceI [] ds = new SequenceI[seqs.length];
+    for (int i = 0; i < seqs.length; i++)
+    {
+      if(seqs[i].getDatasetSequence()!=null)
+        ds[i] = seqs[i].getDatasetSequence();
+      else
+        ds[i] = seqs[i];
+    }
+    this.dataset = ds;
   }
 
   public boolean fetchDBRefs(boolean waitTillFinished)
@@ -157,16 +165,15 @@ public class DBRefFetcher
     try
     {
       int seqIndex = 0;
-      Vector sequences = dataset.getSequences();
 
-      while (seqIndex < sequences.size())
+      while (seqIndex < dataset.length)
       {
         StringBuffer queryString = new StringBuffer("uniprot:");
 
-        for (int i = 0; (seqIndex < sequences.size()) && (i < 50);
+        for (int i = 0; (seqIndex < dataset.length) && (i < 50);
              seqIndex++, i++)
         {
-          Sequence sequence = (Sequence) sequences.get(seqIndex);
+          SequenceI sequence = dataset[seqIndex];
           DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.
               getDBRef(), new String[]
               {
diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 33791ad..c8b5d3e 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -130,8 +130,7 @@ public class DasSequenceFeatureFetcher
   {
     public void run()
     {
-      new DBRefFetcher(
-          af.getViewport().getAlignment(), af).fetchDBRefs(true);
+      new DBRefFetcher(sequences, af).fetchDBRefs(true);
       startFetching();
     }
   }
-- 
1.7.10.2