From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 8 Dec 2005 12:04:14 +0000 (+0000)
Subject: UnknownSequences.remove moved out of loop
X-Git-Tag: Release_2_07~33
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1e99af3f3a701dd8b64d97c8811b444b0542a2ad;p=jalview.git

UnknownSequences.remove moved out of loop
---

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index d980b0a..2b6de8b 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -240,7 +240,6 @@ public class SequenceFeatureFetcher implements Runnable
         continue;
       }
 
-      unknownSequences.remove(sequence);
 
       String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence());
 
@@ -253,7 +252,6 @@ public class SequenceFeatureFetcher implements Runnable
         absStart = nonGapped.toString().indexOf(entry.getUniprotSequence().getContent());
         if(absStart == -1)
         {
-          unknownSequences.add(sequence.getName());
           sbuffer.append(sequence.getName() +
                          " SEQUENCE NOT %100 MATCH \n");
 
@@ -261,6 +259,7 @@ public class SequenceFeatureFetcher implements Runnable
         }
         else
         {
+
           if(entry.getFeature()!=null)
           {
             Enumeration e = entry.getFeature().elements();
@@ -280,6 +279,8 @@ public class SequenceFeatureFetcher implements Runnable
 
       }
 
+      unknownSequences.remove(sequence);
+
       int absEnd = absStart + nonGapped.toString().length();
       absStart += 1;