Merge branch 'develop' into bug/JAL-4421_customise_volume_name_of_DMG_installers

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

diff --git a/test/jalview/analysis/AlignSeqTest.java b/test/jalview/analysis/AlignSeqTest.java
index a9a9730..03bdd0b 100644 (file)
--- a/test/jalview/analysis/AlignSeqTest.java
+++ b/test/jalview/analysis/AlignSeqTest.java
@@ -76,4 +76,16 @@ public class AlignSeqTest
     String s = "aArRnNzZxX *.-?";
     assertArrayEquals(expected, as.indexEncode(s));
   }
+  @Test(groups= {"Functional"})
+  public void testGlobalAlignment()
+  {
+    String seq1="CAGCTAGCG",seq2="CCATACGA";
+    Sequence sq1=new Sequence("s1",seq1),sq2=new Sequence("s2",seq2);
+    // AlignSeq doesn't report the unaligned regions at either end of sequences
+    //String alseq1="-CAGCTAGCG-",alseq2="CCA--TA-CGA";
+    // so we check we have the aligned segment correct only
+    String alseq1="CAGCTAGCG",alseq2="CA--TA-CG";
+    AlignSeq as = AlignSeq.doGlobalNWAlignment(sq1,sq2,AlignSeq.DNA);
+    assertEquals(as.getAStr1()+"\n"+as.getAStr2(),alseq1+"\n"+alseq2);
+  }
 }