Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

[jalview.git] / test / jalview / datamodel / CigarArrayTest.java

diff --git a/test/jalview/datamodel/CigarArrayTest.java b/test/jalview/datamodel/CigarArrayTest.java
index 7b5c090..7bee423 100644 (file)
--- 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