JAL-1466 improved test and patched off by one that deleted one dataset residue from...

[jalview.git] / test / jalview / analysis / AlignmentUtilsTests.java

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 5039deb..2104d4a 100644 (file)
--- 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()));
+      }
+      }
     }    
   }
 }