+/*
+ * 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 java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
+
public class SequenceFeatureTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
- public void testCopyConstructor()
+ public void testCopyConstructors()
{
- SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
- 12.5f, "group");
+ SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+ "group");
sf1.setValue("STRAND", "+");
sf1.setValue("Note", "Testing");
- Integer count = new Integer(7);
+ Integer count = Integer.valueOf(7);
sf1.setValue("Count", count);
SequenceFeature sf2 = new SequenceFeature(sf1);
assertEquals("desc", sf2.getDescription());
assertEquals(22, sf2.getBegin());
assertEquals(33, sf2.getEnd());
+ assertEquals(12.5f, sf2.getScore());
assertEquals("+", sf2.getValue("STRAND"));
assertEquals("Testing", sf2.getValue("Note"));
// shallow clone of otherDetails map - contains the same object values!
assertSame(count, sf2.getValue("Count"));
+
+ /*
+ * copy constructor modifying begin/end/group/score
+ */
+ SequenceFeature sf3 = new SequenceFeature(sf1, 11, 14, "group2", 17.4f);
+ assertEquals("type", sf3.getType());
+ assertEquals("desc", sf3.getDescription());
+ assertEquals(11, sf3.getBegin());
+ assertEquals(14, sf3.getEnd());
+ assertEquals(17.4f, sf3.getScore());
+ assertEquals("+", sf3.getValue("STRAND"));
+ assertEquals("Testing", sf3.getValue("Note"));
+ // shallow clone of otherDetails map - contains the same object values!
+ assertSame(count, sf3.getValue("Count"));
+
+ /*
+ * copy constructor modifying type/begin/end/group/score
+ */
+ SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12, 15,
+ "group3", -9.1f);
+ assertEquals("Disulfide bond", sf4.getType());
+ assertTrue(sf4.isContactFeature());
+ assertEquals("desc", sf4.getDescription());
+ assertEquals(12, sf4.getBegin());
+ assertEquals(15, sf4.getEnd());
+ assertEquals(-9.1f, sf4.getScore());
+ assertEquals("+", sf4.getValue("STRAND"));
+ assertEquals("Testing", sf4.getValue("Note"));
+ // shallow clone of otherDetails map - contains the same object values!
+ assertSame(count, sf4.getValue("Count"));
}
/**
@Test(groups = { "Functional" })
public void testGetValue()
{
- SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33,
- 12.5f, "group");
+ SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+ "group");
sf1.setValue("STRAND", "+");
assertEquals("+", sf1.getValue("STRAND"));
assertNull(sf1.getValue("strand")); // case-sensitive
assertEquals(".", sf1.getValue("unknown", "."));
- Integer i = new Integer(27);
+ Integer i = Integer.valueOf(27);
assertSame(i, sf1.getValue("Unknown", i));
}
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());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetDetailsReport()
+ {
+ SequenceI seq = new Sequence("TestSeq", "PLRFQMD");
+ String seqName = seq.getName();
+
+ // single locus, no group, no score
+ SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22,
+ null);
+ String expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22</td></tr>"
+ + "<tr><td>Type</td><td>variant</td><td></td></tr>"
+ + "<tr><td>Description</td><td>G,C</td><td></td></tr></table>";
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+
+ // contact feature
+ sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
+ null);
+ expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>28:31</td></tr>"
+ + "<tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>"
+ + "<tr><td>Description</td><td>a description</td><td></td></tr></table>";
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+
+ sf = new SequenceFeature("variant", "G,C", 22, 33, 12.5f, "group");
+ sf.setValue("Parent", "ENSG001");
+ sf.setValue("Child", "ENSP002");
+ expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22-33</td></tr>"
+ + "<tr><td>Type</td><td>variant</td><td></td></tr>"
+ + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
+ + "<tr><td>Score</td><td>12.5</td><td></td></tr>"
+ + "<tr><td>Group</td><td>group</td><td></td></tr>"
+ + "<tr><td>Child</td><td></td><td>ENSP002</td></tr>"
+ + "<tr><td>Parent</td><td></td><td>ENSG001</td></tr></table>";
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+
+ /*
+ * feature with embedded html link in description
+ */
+ String desc = "<html>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></html>";
+ sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot");
+ expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>8-83</td></tr>"
+ + "<tr><td>Type</td><td>Pfam</td><td></td></tr>"
+ + "<tr><td>Description</td><td>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></td><td></td></tr>"
+ + "<tr><td>Group</td><td>Uniprot</td><td></td></tr></table>";
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+ }
+
+ /**
+ * Feature details report for a virtual feature should include original and
+ * mapped locations, and also derived peptide consequence if it can be
+ * determined
+ */
+ @Test(groups = { "Functional" })
+ public void testGetDetailsReport_virtualFeature()
+ {
+ SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
+ SequenceI seq = new Sequence("TestSeq/8-14", "PLRFQMD");
+ MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
+ 3, 1);
+ Mapping mapping = new Mapping(seq, map);
+ List<SequenceFeature> features = new ArrayList<>();
+ // vary ttg (Leu) to ttc (Phe)
+ SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
+ null);
+ sf.setValue("alleles", "G,C"); // needed to compute peptide consequence!
+ features.add(sf);
+
+ MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
+
+ String expected = "<br><table><tr><td>Location</td><td>Cds</td><td>106</td></tr>"
+ + "<tr><td>Peptide Location</td><td>TestSeq</td><td>9</td></tr>"
+ + "<tr><td>Type</td><td>variant</td><td></td></tr>"
+ + "<tr><td>Description</td><td>G,C</td><td></td></tr>"
+ + "<tr><td>Consequence</td><td><i>Translated by Jalview</i></td><td>p.Leu9Phe</td></tr>"
+ + "<tr><td>alleles</td><td></td><td>G,C</td></tr>"
+ + "</table>";
+
+ assertEquals(expected, sf.getDetailsReport(seq.getName(), mf));
+
+
+ /*
+ * exon feature extending beyond mapped range; mapped location should be
+ * restricted to peptide mapped range limit i.e. 10-13
+ */
+ SequenceFeature sf2 = new SequenceFeature("exon", "exon 1", 109, 230, null);
+ features.add(sf2);
+ expected = "<br><table><tr><td>Location</td><td>Cds</td><td>109-230</td></tr>"
+ + "<tr><td>Peptide Location</td><td>TestSeq</td><td>10-13</td></tr>"
+ + "<tr><td>Type</td><td>exon</td><td></td></tr>"
+ + "<tr><td>Description</td><td>exon 1</td><td></td></tr>"
+ + "</table>";
+ assertEquals(expected, sf2.getDetailsReport(seq.getName(), mf));
+ }
}
git://source.jalview.org / jalview.git / blobdiff