From 3adf08ae85605e3896ecedfc770bed9f47f13416 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 26 Sep 2017 16:35:23 +0100
Subject: [PATCH] JAL-2742 CigarArray constructor unit test

---
 test/jalview/datamodel/CigarArrayTest.java |  126 ++++++++++++++++++++++++++++
 1 file changed, 126 insertions(+)
 create mode 100644 test/jalview/datamodel/CigarArrayTest.java

diff --git a/test/jalview/datamodel/CigarArrayTest.java b/test/jalview/datamodel/CigarArrayTest.java
new file mode 100644
index 0000000..12f31fc
--- /dev/null
+++ b/test/jalview/datamodel/CigarArrayTest.java
@@ -0,0 +1,126 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class CigarArrayTest
+{
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = "Functional")
+  public void TestConstructor()
+  {
+    SequenceI seq1 = new Sequence("sq1",
+            "ASFDDABACBACBACBACBACBACBABCABCBACBABCAB");
+    Sequence seq2 = new Sequence("sq2",
+            "TTTTTTACBCBABCABCABCABCBACBACBABCABCABCBA");
+
+    // construct alignment
+    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+
+    // hide columns
+    HiddenColumns hc = new HiddenColumns();
+    hc.hideColumns(3, 6);
+    hc.hideColumns(16, 20);
+
+    // select group
+    SequenceGroup sg1 = new SequenceGroup();
+    sg1.addSequence(seq1, false);
+    sg1.setStartRes(2);
+    sg1.setEndRes(23);
+
+    CigarArray cig = new CigarArray(al, hc, sg1);
+    String result = cig.getCigarstring();
+    assertEquals(result, "1M4D9M5D3M");
+
+    // group starts at hidden cols
+    sg1.setStartRes(3);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "4D9M5D3M");
+
+    // group starts at last but 1 hidden col
+    sg1.setStartRes(5);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M5D3M");
+
+    // group starts at last hidden col
+    /*    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);
+    result = cig.getCigarstring();
+    assertEquals(result, "9M5D3M");
+
+    // group ends just before start of hidden region
+    sg1.setStartRes(5);
+    sg1.setEndRes(15);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M");
+
+    // group ends at start of hidden region
+    sg1.setEndRes(16);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M1D");
+
+    // group ends 1 after start of hidden region
+    sg1.setEndRes(17);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M2D");
+
+    // group ends at end of hidden region
+    sg1.setEndRes(20);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M5D");
+
+    // group ends just after end of hidden region
+    sg1.setEndRes(21);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M5D1M");
+
+    // group ends 2 after end of hidden region
+    sg1.setEndRes(22);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M5D2M");
+  }
+}
-- 
1.7.10.2