JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/test/jalview/datamodel/CigarArrayTest.java b/test/jalview/datamodel/CigarArrayTest.java
deleted file mode 100644 (file)
index 7bee423..0000000
--- a/test/jalview/datamodel/CigarArrayTest.java
+++ /dev/null
@@ -1,141 +0,0 @@
-/*
- * 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);
-
-    // 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
-    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");
-  }
-}