From 19a6c92c82afe36f99e485a88237681861045430 Mon Sep 17 00:00:00 2001 From: kiramt Date: Wed, 11 Oct 2017 12:08:25 +0100 Subject: [PATCH 1/1] JAL-2742 minor test updates following review --- test/jalview/datamodel/CigarArrayTest.java | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) 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"); -- 1.7.10.2