X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fanalysis%2FAlignSeqTest.java;h=a9a9730c3bfcc52b95c52b9ee67b192970e84f37;hb=037c9d3e4d7f914cedecb5dc82b5f85d605ab018;hp=b9e866d191a6647e397b97d0ec196d9c832d172c;hpb=e0f478e7dd73384609bd596f7edf6106dc7d9330;p=jalview.git

diff --git a/test/jalview/analysis/AlignSeqTest.java b/test/jalview/analysis/AlignSeqTest.java
index b9e866d..a9a9730 100644
--- a/test/jalview/analysis/AlignSeqTest.java
+++ b/test/jalview/analysis/AlignSeqTest.java
@@ -52,13 +52,14 @@ 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" })
   public void testIndexEncode_nucleotide()
   {
-    AlignSeq as = new AlignSeq(new Sequence("s1", "TTAG"), new Sequence(
-            "s2", "ACGT"), AlignSeq.DNA);
+    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, -1, -1, 10, -1 };
     String s = "aAcCgGtTuUiIxXrRyYnN .-?";
@@ -68,10 +69,10 @@ public class AlignSeqTest
   @Test(groups = { "Functional" })
   public void testIndexEncode_peptide()
   {
-    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, -1, -1,
-        -1, 23, -1 };
+    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, -1, 23,
+        -1, -1, -1 };
     String s = "aArRnNzZxX *.-?";
     assertArrayEquals(expected, as.indexEncode(s));
   }