From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 11 Oct 2017 11:08:25 +0000 (+0100)
Subject: JAL-2742 minor test updates following review
X-Git-Tag: Release_2_10_3b1~111^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=19a6c92c82afe36f99e485a88237681861045430;p=jalview.git

JAL-2742 minor test updates following review
---

diff --git a/test/jalview/datamodel/CigarArrayTest.java b/test/jalview/datamodel/CigarArrayTest.java
index 7b5c090..20dcc96 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");
@@ -58,6 +58,16 @@ public class CigarArrayTest
     sg1.setStartRes(2);
     sg1.setEndRes(23);
 
+    // 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.
+
     CigarArray cig = new CigarArray(al, hc, sg1);
     String result = cig.getCigarstring();
     assertEquals(result, "1M4D9M5D3M");