From 976c518ffa15791c680156dd357d33f5a06c3a54 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 5 Jan 2017 16:31:55 +0000
Subject: [PATCH] JAL-2374 unit test for (modified) Alignment.findGroup()

---
 test/jalview/datamodel/AlignmentTest.java |   59 +++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index d2f4b4d..618bac5 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -1131,4 +1131,63 @@ public class AlignmentTest
     assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to);
   }
 
+  @Test(groups = { "Functional" })
+  public void testFindGroup()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI");
+    SequenceI seq2 = new Sequence("seq2", "---JKLMNO---");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 });
+
+    assertNull(a.findGroup(null, 0));
+    assertNull(a.findGroup(seq1, 1));
+    assertNull(a.findGroup(seq1, -1));
+
+    /*
+     * add a group consisting of just "DEF"
+     */
+    SequenceGroup sg1 = new SequenceGroup();
+    sg1.addSequence(seq1, false);
+    sg1.setStartRes(3);
+    sg1.setEndRes(5);
+    a.addGroup(sg1);
+
+    assertNull(a.findGroup(seq1, 2)); // position not in group
+    assertNull(a.findGroup(seq1, 6)); // position not in group
+    assertNull(a.findGroup(seq2, 5)); // sequence not in group
+    assertSame(a.findGroup(seq1, 3), sg1); // yes
+    assertSame(a.findGroup(seq1, 4), sg1);
+    assertSame(a.findGroup(seq1, 5), sg1);
+
+    /*
+     * add a group consisting of 
+     * EF--
+     * KLMN
+     */
+    SequenceGroup sg2 = new SequenceGroup();
+    sg2.addSequence(seq1, false);
+    sg2.addSequence(seq2, false);
+    sg2.setStartRes(4);
+    sg2.setEndRes(7);
+    a.addGroup(sg2);
+
+    assertNull(a.findGroup(seq1, 2)); // unchanged
+    assertSame(a.findGroup(seq1, 3), sg1); // unchanged
+    /*
+     * if a residue is in more than one group, method returns
+     * the first found (in order groups were added)
+     */
+    assertSame(a.findGroup(seq1, 4), sg1);
+    assertSame(a.findGroup(seq1, 5), sg1);
+
+    /*
+     * seq2 only belongs to the second group
+     */
+    assertSame(a.findGroup(seq2, 4), sg2);
+    assertSame(a.findGroup(seq2, 5), sg2);
+    assertSame(a.findGroup(seq2, 6), sg2);
+    assertSame(a.findGroup(seq2, 7), sg2);
+    assertNull(a.findGroup(seq2, 3));
+    assertNull(a.findGroup(seq2, 8));
+  }
+
 }
-- 
1.7.10.2