X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;fp=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=ddba94991a40f1a7927abc7131410e36cbb91e2f;hb=00c9a0c1c8c91d30d4ed03541e0135dea6e7102a;hp=2fed815eaac736fbf895a6c06dacc9cd70d8c65a;hpb=ecdbc96815298ac853543640881ef8d2384b48a1;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 2fed815..ddba949 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -1437,4 +1437,20 @@ public class AlignmentTest
     assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
     assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
   }
+
+  @Test(groups = { "Functional" })
+  public void testPadGaps()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+    a.setGapCharacter('.'); // this replaces existing gaps
+    assertEquals("ABCDEF..", seq1.getSequenceAsString());
+    a.padGaps();
+    // trailing gaps are pruned, short sequences padded with gap character
+    assertEquals("ABCDEF.", seq1.getSequenceAsString());
+    assertEquals(".JKLMNO", seq2.getSequenceAsString());
+    assertEquals(".PQR...", seq3.getSequenceAsString());
+  }
 }