From 4891120c866fcd3516b270915d0db2d31a4815e0 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 14 Jul 2006 08:58:11 +0000
Subject: [PATCH] Just fetch features for selected seqs

---
 src/jalview/io/DasSequenceFeatureFetcher.java |   28 ++++++++++++-------------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index dc51617..1295520 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -50,8 +50,8 @@ import jalview.bin.Cache;
  */
 public class DasSequenceFeatureFetcher implements Runnable
 {
-  final AlignmentI dataset;
-  final AlignFrame af;
+  SequenceI [] sequences;
+  AlignFrame af;
   StringBuffer sbuffer = new StringBuffer();
   Vector selectedSources;
 
@@ -66,12 +66,12 @@ public class DasSequenceFeatureFetcher implements Runnable
    * @param align DOCUMENT ME!
    * @param ap DOCUMENT ME!
    */
-  public DasSequenceFeatureFetcher(AlignmentI align,
+  public DasSequenceFeatureFetcher(SequenceI [] sequences,
                                    AlignFrame af,
                                    Vector selectedSources)
   {
     this.selectedSources = selectedSources;
-    this.dataset = align.getDataset();
+    this.sequences = sequences;
     this.af = af;
 
     Thread thread = new Thread(this);
@@ -145,7 +145,7 @@ public class DasSequenceFeatureFetcher implements Runnable
    * @param SourceUrl
    * @param id
    */
-  protected void createFeatureFetcher(final Sequence seq,
+  protected void createFeatureFetcher(final SequenceI seq,
                                       final String sourceUrl,
                                       String id,
                                       String nickname)  {
@@ -262,11 +262,9 @@ public class DasSequenceFeatureFetcher implements Runnable
     try
     {
       int seqIndex = 0;
-      Vector sequences = dataset.getSequences();
-      while (seqIndex < sequences.size())
+      while (seqIndex < sequences.length)
       {
-          Sequence sequence = (Sequence) sequences.get(seqIndex);
-          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),
+          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
               new String[]  {
               jalview.datamodel.DBRefSource.PDB,
               jalview.datamodel.DBRefSource.UNIPROT});
@@ -292,7 +290,7 @@ public class DasSequenceFeatureFetcher implements Runnable
                                     cs[l].getName());
 
 
-                    createFeatureFetcher(sequence,
+                    createFeatureFetcher(sequences[seqIndex],
                                          dasSource.getUrl(),
                                          ( (DBRefEntry) uprefs.get(j)).
                                          getAccessionId(),
@@ -305,19 +303,19 @@ public class DasSequenceFeatureFetcher implements Runnable
             {
               String id = null;
               // try and use the name as the sequence id
-              if (sequence.getName().indexOf("|") > -1)
+              if (sequences[seqIndex].getName().indexOf("|") > -1)
               {
-                id = sequence.getName().substring(
-                    sequence.getName().lastIndexOf("|") + 1);
+                id = sequences[seqIndex].getName().substring(
+                    sequences[seqIndex].getName().lastIndexOf("|") + 1);
               }
               else
               {
-                id = sequence.getName();
+                id = sequences[seqIndex].getName();
               }
               if (id != null)
               {
                 // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references
-                createFeatureFetcher(sequence,
+                createFeatureFetcher(sequences[seqIndex],
                                      dasSource.getUrl(),
                                      id,
                                      dasSource.getNickname());
-- 
1.7.10.2