X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FCigarArrayTest.java;h=7bee4234505156a85e0700995cdbc5a9d7753880;hb=3bc97fb559bcd28299532021c5b62b0ca62d4d3b;hp=12f31fc40431cbc327b1a3c5446cce7f515b2baa;hpb=3adf08ae85605e3896ecedfc770bed9f47f13416;p=jalview.git

diff --git a/test/jalview/datamodel/CigarArrayTest.java b/test/jalview/datamodel/CigarArrayTest.java
index 12f31fc..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
@@ -75,11 +90,11 @@ public class CigarArrayTest
     assertEquals(result, "2D9M5D3M");
 
     // group starts at last hidden col
-    /*    sg1.setStartRes(6);
+    sg1.setStartRes(6);
     cig = new CigarArray(al, hc, sg1);
     result = cig.getCigarstring();
     assertEquals(result, "1D9M5D3M");
-    */
+
     // group starts just after hidden region
     sg1.setStartRes(7);
     cig = new CigarArray(al, hc, sg1);