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

[jalview.git] / test / jalview / ext / so / SequenceOntologyTest.java

diff --git a/test/jalview/ext/so/SequenceOntologyTest.java b/test/jalview/ext/so/SequenceOntologyTest.java
deleted file mode 100644 (file)
index 31e1887..0000000
--- a/test/jalview/ext/so/SequenceOntologyTest.java
+++ /dev/null
@@ -1,135 +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.ext.so;
-
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.gui.JvOptionPane;
-import jalview.io.gff.SequenceOntologyI;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class SequenceOntologyTest
-{
-
-  @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
-  {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-  }
-
-  private SequenceOntologyI so;
-
-  @BeforeClass(alwaysRun = true)
-  public void setUp()
-  {
-    long now = System.currentTimeMillis();
-    try
-    {
-      so = new SequenceOntology();
-    } catch (Throwable t)
-    {
-      System.out.println("SOTest error ");
-      t.printStackTrace(System.err);
-    }
-    long elapsed = System.currentTimeMillis() - now;
-    System.out.println("Load and cache of Sequence Ontology took "
-            + elapsed + "ms");
-  }
-
-  @Test(groups = "Functional")
-  public void testIsA()
-  {
-    assertFalse(so.isA(null, null));
-    assertFalse(so.isA(null, "SO:0000087"));
-    assertFalse(so.isA("SO:0000087", null));
-    assertFalse(so.isA("complete", "garbage"));
-
-    assertTrue(so.isA("SO:0000087", "SO:0000704"));
-    assertFalse(so.isA("SO:0000704", "SO:0000087"));
-    assertTrue(so.isA("SO:0000736", "SO:0000735"));
-
-    // same thing:
-    assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
-    // direct parent:
-    assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
-    // grandparent:
-    assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
-    // great-grandparent:
-    assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
-
-    // same thing by name / description:
-    assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
-    assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
-    assertTrue(so.isA("SO:0000084", "SO:0000084"));
-
-    // SO name to description:
-    assertTrue(so.isA("SO:0000084", "organelle_sequence"));
-    assertTrue(so.isA("SO:0000084", "sequence_location"));
-    assertTrue(so.isA("SO:0000084", "sequence_attribute"));
-
-    // description to SO name:
-    assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
-    assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
-    assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
-  }
-
-  @Test(groups = "Functional")
-  public void testIsCDS()
-  {
-    assertTrue(so.isA("CDS", "CDS"));
-    assertTrue(so.isA("CDS_predicted", "CDS"));
-    assertTrue(so.isA("transposable_element_CDS", "CDS"));
-    assertTrue(so.isA("edited_CDS", "CDS"));
-    assertTrue(so.isA("CDS_independently_known", "CDS"));
-    assertTrue(so.isA("CDS_fragment", "CDS"));
-    assertFalse(so.isA("CDS_region", "CDS"));// part_of
-    assertFalse(so.isA("polypeptide", "CDS")); // derives_from
-  }
-
-  @Test(groups = "Functional")
-  public void testIsSequenceVariant()
-  {
-    assertFalse(so.isA("CDS", "sequence_variant"));
-    assertTrue(so.isA("sequence_variant", "sequence_variant"));
-
-    /*
-     * these should all be sub-types of sequence_variant
-     */
-    assertTrue(so.isA("structural_variant", "sequence_variant"));
-    assertTrue(so.isA("feature_variant", "sequence_variant"));
-    assertTrue(so.isA("gene_variant", "sequence_variant"));
-    assertTrue(so.isA("transcript_variant", "sequence_variant"));
-    assertTrue(so.isA("NMD_transcript_variant", "sequence_variant"));
-    assertTrue(so.isA("missense_variant", "sequence_variant"));
-    assertTrue(so.isA("synonymous_variant", "sequence_variant"));
-    assertTrue(so.isA("frameshift_variant", "sequence_variant"));
-    assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant"));
-    assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant"));
-    assertTrue(so.isA("stop_gained", "sequence_variant"));
-    assertTrue(so.isA("stop_lost", "sequence_variant"));
-    assertTrue(so.isA("inframe_deletion", "sequence_variant"));
-    assertTrue(so.isA("inframe_insertion", "sequence_variant"));
-  }
-}