UnknownSequences.remove moved out of loop

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