X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignSeqTest.java;h=bd827f96d7b5d70dd314b2d0f656c4740a790451;hb=b2a2c2070f14d18d67b07b030d70073a21b7a4e3;hp=c12f544073460703bb258d51510c0dc2080c28ea;hpb=69b6e688c0a87bffc1fc7ae970fa0f8cd2976007;p=jalview.git

diff --git a/test/jalview/analysis/AlignSeqTest.java b/test/jalview/analysis/AlignSeqTest.java
index c12f544..bd827f9 100644
--- a/test/jalview/analysis/AlignSeqTest.java
+++ b/test/jalview/analysis/AlignSeqTest.java
@@ -52,6 +52,7 @@ public class AlignSeqTest
     assertEquals(AlignSeq.extractGaps(" -", " AC-G.T"), "ACG.T");
     assertEquals(AlignSeq.extractGaps(" -.", " AC-G.T ."), "ACGT");
     assertEquals(AlignSeq.extractGaps("-", " AC-G.T"), " ACG.T");
+    assertEquals(AlignSeq.extractGaps("-. ", " -. .-"), "");
   }
 
   @Test(groups = { "Functional" })
@@ -60,7 +61,7 @@ public class AlignSeqTest
     AlignSeq as = new AlignSeq(new Sequence("s1", "TTAG"), new Sequence(
             "s2", "ACGT"), AlignSeq.DNA);
     int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6,
-        7, 7, 8, 8, 9, 9, 10, -1, 11, -1 };
+        7, 7, 8, 8, 9, 9, -1, -1, 10, -1 };
     String s = "aAcCgGtTuUiIxXrRyYnN .-?";
     assertArrayEquals(expected, as.indexEncode(s));
   }
@@ -70,7 +71,7 @@ public class AlignSeqTest
   {
     AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"), new Sequence(
             "s2", "RQW"), AlignSeq.PEP);
-    int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, 23, 24,
+    int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, -1, 23,
         -1, -1, -1 };
     String s = "aArRnNzZxX *.-?";
     assertArrayEquals(expected, as.indexEncode(s));