X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;fp=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=2104d4a404d8fa6af7c2be4a194edbc9ee278846;hb=efde43fab576590026bbe0ced39e13426aa6532f;hp=5039deb58517843c09ebfefc7bb249ef5510ca0c;hpb=135d3c8e51d19e221e68134a3cd7290fa9c783a8;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 5039deb..2104d4a 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -1,5 +1,7 @@
 package jalview.analysis;
 
+import static org.junit.Assert.assertTrue;
+
 import org.junit.Test;
 
 import jalview.datamodel.Alignment;
@@ -23,8 +25,16 @@ public class AlignmentUtilsTests
     System.out.println(new AppletFormatAdapter().formatSequences("Clustal", al, true));
     for (int flnk=-1;flnk<25; flnk++)
     {
+      AlignmentI exp;
       System.out.println("\nFlank size: "+flnk);
-      System.out.println(new AppletFormatAdapter().formatSequences("Clustal", AlignmentUtils.expandContext(al, flnk), true));
+      System.out.println(new AppletFormatAdapter().formatSequences("Clustal", exp=AlignmentUtils.expandContext(al, flnk), true));
+      if (flnk==-1) {
+        for (SequenceI sq:exp.getSequences())
+      {
+          String ung = sq.getSequenceAsString().replaceAll("-+", "");
+          assertTrue("Flanking sequence not the same as original dataset sequence.\n"+ung+"\n"+sq.getDatasetSequence().getSequenceAsString(),ung.equalsIgnoreCase(sq.getDatasetSequence().getSequenceAsString()));
+      }
+      }
     }    
   }
 }