X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FCodingUtilsTest.java;fp=test%2Fjalview%2Fanalysis%2FCodingUtilsTest.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=b66c499f9a0556608b4706a66b8bc82236a83315;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/test/jalview/analysis/CodingUtilsTest.java b/test/jalview/analysis/CodingUtilsTest.java
deleted file mode 100644
index b66c499..0000000
--- a/test/jalview/analysis/CodingUtilsTest.java
+++ /dev/null
@@ -1,100 +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.analysis;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.gui.JvOptionPane;
-
-import java.util.Arrays;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class CodingUtilsTest
-{
-
-  @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
-  {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-  }
-
-  @Test(groups = { "Functional" })
-  public void testDecodeCodon()
-  {
-    assertTrue(Arrays.equals(new char[] { 'A', 'A', 'A' },
-            CodingUtils.decodeCodon(0)));
-    assertTrue(Arrays.equals(new char[] { 'A', 'A', 'C' },
-            CodingUtils.decodeCodon(1)));
-    assertTrue(Arrays.equals(new char[] { 'A', 'A', 'G' },
-            CodingUtils.decodeCodon(2)));
-    assertTrue(Arrays.equals(new char[] { 'A', 'A', 'T' },
-            CodingUtils.decodeCodon(3)));
-    assertTrue(Arrays.equals(new char[] { 'A', 'C', 'A' },
-            CodingUtils.decodeCodon(4)));
-    assertTrue(Arrays.equals(new char[] { 'C', 'A', 'A' },
-            CodingUtils.decodeCodon(16)));
-    assertTrue(Arrays.equals(new char[] { 'G', 'G', 'G' },
-            CodingUtils.decodeCodon(42)));
-    assertTrue(Arrays.equals(new char[] { 'T', 'T', 'T' },
-            CodingUtils.decodeCodon(63)));
-  }
-
-  @Test(groups = { "Functional" })
-  public void testDecodeNucleotide()
-  {
-    assertEquals('A', CodingUtils.decodeNucleotide(0));
-    assertEquals('C', CodingUtils.decodeNucleotide(1));
-    assertEquals('G', CodingUtils.decodeNucleotide(2));
-    assertEquals('T', CodingUtils.decodeNucleotide(3));
-    assertEquals('0', CodingUtils.decodeNucleotide(4));
-  }
-
-  @Test(groups = { "Functional" })
-  public void testEncodeCodon()
-  {
-    assertTrue(CodingUtils.encodeCodon('Z') < 0);
-    assertEquals(0, CodingUtils.encodeCodon('a'));
-    assertEquals(0, CodingUtils.encodeCodon('A'));
-    assertEquals(1, CodingUtils.encodeCodon('c'));
-    assertEquals(1, CodingUtils.encodeCodon('C'));
-    assertEquals(2, CodingUtils.encodeCodon('g'));
-    assertEquals(2, CodingUtils.encodeCodon('G'));
-    assertEquals(3, CodingUtils.encodeCodon('t'));
-    assertEquals(3, CodingUtils.encodeCodon('T'));
-    assertEquals(3, CodingUtils.encodeCodon('u'));
-    assertEquals(3, CodingUtils.encodeCodon('U'));
-
-    assertEquals(-1, CodingUtils.encodeCodon(null));
-    assertEquals(0, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'A' }));
-    assertEquals(1, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'C' }));
-    assertEquals(2, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'G' }));
-    assertEquals(3, CodingUtils.encodeCodon(new char[] { 'A', 'A', 'T' }));
-    assertEquals(4, CodingUtils.encodeCodon(new char[] { 'A', 'C', 'A' }));
-    assertEquals(16, CodingUtils.encodeCodon(new char[] { 'C', 'A', 'A' }));
-    assertEquals(42, CodingUtils.encodeCodon(new char[] { 'G', 'G', 'G' }));
-    assertEquals(63, CodingUtils.encodeCodon(new char[] { 'T', 'T', 'T' }));
-  }
-
-}