X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FCigarArrayTest.java;h=7bee4234505156a85e0700995cdbc5a9d7753880;hb=4d2867aa88b5ae02ef34a505794c650038fd3591;hp=7b5c090f7f24a81ea4b1d07a322b3b671f1c2ee2;hpb=f63a01dac2f6e2ee30929c56da582c9621ef8d1b;p=jalview.git

diff --git a/test/jalview/datamodel/CigarArrayTest.java b/test/jalview/datamodel/CigarArrayTest.java
index 7b5c090..7bee423 100644
--- a/test/jalview/datamodel/CigarArrayTest.java
+++ b/test/jalview/datamodel/CigarArrayTest.java
@@ -37,7 +37,7 @@ public class CigarArrayTest
   }
 
   @Test(groups = "Functional")
-  public void TestConstructor()
+  public void testConstructor()
   {
     SequenceI seq1 = new Sequence("sq1",
             "ASFDDABACBACBACBACBACBACBABCABCBACBABCAB");
@@ -58,8 +58,23 @@ public class CigarArrayTest
     sg1.setStartRes(2);
     sg1.setEndRes(23);
 
-    CigarArray cig = new CigarArray(al, hc, sg1);
+    // Cigar array meanings:
+    // M = match
+    // D = deletion
+    // I = insertion
+    // number preceding M/D/I is the number of residues which
+    // match/are deleted/are inserted
+    // In the CigarArray constructor only matches or deletions are created, as
+    // we are comparing a sequence to its own subsequence (the group) + hidden
+    // columns.
+
+    // no hidden columns case
+    CigarArray cig = new CigarArray(al, null, sg1);
     String result = cig.getCigarstring();
+    assertEquals(result, "22M");
+
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
     assertEquals(result, "1M4D9M5D3M");
 
     // group starts at hidden cols