+/*
+ * 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.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class SequenceFeatureTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testCopyConstructor()
{
sf.setValue("STRAND", ".");
assertEquals(0, sf.getStrand());
}
+
+ /**
+ * Tests for equality, and that equal objects have the same hashCode
+ */
+ @Test(groups = { "Functional" })
+ public void testEqualsAndHashCode()
+ {
+ SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
+ 12.5f, "group");
+ sf1.setValue("ID", "id");
+ sf1.setValue("Name", "name");
+ sf1.setValue("Parent", "parent");
+ sf1.setStrand("+");
+ sf1.setPhase("1");
+ SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33,
+ 12.5f, "group");
+ sf2.setValue("ID", "id");
+ sf2.setValue("Name", "name");
+ sf2.setValue("Parent", "parent");
+ sf2.setStrand("+");
+ sf2.setPhase("1");
+
+ assertFalse(sf1.equals(null));
+ assertTrue(sf1.equals(sf2));
+ assertTrue(sf2.equals(sf1));
+ assertEquals(sf1.hashCode(), sf2.hashCode());
+
+ // changing type breaks equals:
+ SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33,
+ 12.5f, "group");
+ SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33,
+ 12.5f, "group");
+ assertFalse(sf3.equals(sf4));
+
+ // changing description breaks equals:
+ String restores = sf2.getDescription();
+ sf2.setDescription("Desc");
+ assertFalse(sf1.equals(sf2));
+ sf2.setDescription(restores);
+
+ // changing score breaks equals:
+ float restoref = sf2.getScore();
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
+ sf2.getFeatureGroup(), 10f);
+ assertFalse(sf1.equals(sf2));
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
+ sf2.getFeatureGroup(), restoref);
+
+ // NaN doesn't match a number
+ restoref = sf2.getScore();
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
+ sf2.getFeatureGroup(), Float.NaN);
+ assertFalse(sf1.equals(sf2));
+
+ // NaN matches NaN
+ sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
+ sf1.getFeatureGroup(), Float.NaN);
+ assertTrue(sf1.equals(sf2));
+ sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(),
+ sf1.getFeatureGroup(), restoref);
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(),
+ sf2.getFeatureGroup(), restoref);
+
+ // changing start position breaks equals:
+ int restorei = sf2.getBegin();
+ sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(), sf2.getScore());
+ assertFalse(sf1.equals(sf2));
+ sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(),
+ sf2.getFeatureGroup(), sf2.getScore());
+
+ // changing end position breaks equals:
+ restorei = sf2.getEnd();
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), 32,
+ sf2.getFeatureGroup(), sf2.getScore());
+ assertFalse(sf1.equals(sf2));
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), restorei,
+ sf2.getFeatureGroup(), sf2.getScore());
+
+ // changing feature group breaks equals:
+ restores = sf2.getFeatureGroup();
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group", sf2.getScore());
+ assertFalse(sf1.equals(sf2));
+ sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores, sf2.getScore());
+
+ // changing ID breaks equals:
+ restores = (String) sf2.getValue("ID");
+ sf2.setValue("ID", "id2");
+ assertFalse(sf1.equals(sf2));
+ sf2.setValue("ID", restores);
+
+ // changing Name breaks equals:
+ restores = (String) sf2.getValue("Name");
+ sf2.setValue("Name", "Name");
+ assertFalse(sf1.equals(sf2));
+ sf2.setValue("Name", restores);
+
+ // changing Parent breaks equals:
+ restores = (String) sf1.getValue("Parent");
+ sf1.setValue("Parent", "Parent");
+ assertFalse(sf1.equals(sf2));
+ sf1.setValue("Parent", restores);
+
+ // changing strand breaks equals:
+ restorei = sf2.getStrand();
+ sf2.setStrand("-");
+ assertFalse(sf1.equals(sf2));
+ sf2.setStrand(restorei == 1 ? "+" : "-");
+
+ // changing phase breaks equals:
+ restores = sf1.getPhase();
+ sf1.setPhase("2");
+ assertFalse(sf1.equals(sf2));
+ sf1.setPhase(restores);
+
+ // restore equality as sanity check:
+ assertTrue(sf1.equals(sf2));
+ assertTrue(sf2.equals(sf1));
+ assertEquals(sf1.hashCode(), sf2.hashCode());
+
+ // changing status doesn't change equals:
+ sf1.setStatus("new");
+ assertTrue(sf1.equals(sf2));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsContactFeature()
+ {
+ SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+ "group");
+ assertFalse(sf.isContactFeature());
+ sf = new SequenceFeature("", "desc", 22, 33, 12.5f, "group");
+ assertFalse(sf.isContactFeature());
+ sf = new SequenceFeature(null, "desc", 22, 33, 12.5f, "group");
+ assertFalse(sf.isContactFeature());
+ sf = new SequenceFeature("Disulfide Bond", "desc", 22, 33, 12.5f,
+ "group");
+ assertTrue(sf.isContactFeature());
+ sf = new SequenceFeature("disulfide bond", "desc", 22, 33, 12.5f,
+ "group");
+ assertTrue(sf.isContactFeature());
+ sf = new SequenceFeature("Disulphide Bond", "desc", 22, 33, 12.5f,
+ "group");
+ assertTrue(sf.isContactFeature());
+ sf = new SequenceFeature("disulphide bond", "desc", 22, 33, 12.5f,
+ "group");
+ assertTrue(sf.isContactFeature());
+ }
}
git://source.jalview.org / jalview.git / blobdiff