/*
* 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 .
* 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 testCopyConstructors()
{
SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, 12.5f,
"group");
sf1.setValue("STRAND", "+");
sf1.setValue("Note", "Testing");
Integer count = Integer.valueOf(7);
sf1.setValue("Count", count);
SequenceFeature sf2 = new SequenceFeature(sf1);
assertEquals("type", sf2.getType());
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"));
}
/**
* Tests for retrieving a 'miscellaneous details' property value, with or
* without a supplied default
*/
@Test(groups = { "Functional" })
public void testGetValue()
{
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 = Integer.valueOf(27);
assertSame(i, sf1.getValue("Unknown", i));
}
/**
* Tests the method that returns 1 / -1 / 0 for strand "+" / "-" / other
*/
@Test(groups = { "Functional" })
public void testGetStrand()
{
SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
"group");
assertEquals(0, sf.getStrand());
sf.setValue("STRAND", "+");
assertEquals(1, sf.getStrand());
sf.setValue("STRAND", "-");
assertEquals(-1, sf.getStrand());
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 = "
Location | TestSeq | 22 |
"
+ "Type | variant | |
"
+ "Description | G,C | |
";
assertEquals(expected, sf.getDetailsReport(seqName, null));
// contact feature
sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
null);
expected = "
Location | TestSeq | 28:31 |
"
+ "Type | Disulphide Bond | |
"
+ "Description | a description | |
";
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 = "
Location | TestSeq | 22-33 |
"
+ "Type | variant | |
"
+ "Description | G,C | |
"
+ "Score | 12.5 | |
"
+ "Group | group | |
"
+ "Child | | ENSP002 |
"
+ "Parent | | ENSG001 |
";
assertEquals(expected, sf.getDetailsReport(seqName, null));
/*
* feature with embedded html link in description
*/
String desc = "Fer2 Status: True Positive Pfam 8_8";
sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot");
expected = "
Location | TestSeq | 8-83 |
"
+ "Type | Pfam | |
"
+ "Description | Fer2 Status: True Positive Pfam 8_8 | |
"
+ "Group | Uniprot | |
";
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 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 = "
Location | Cds | 106 |
"
+ "Peptide Location | TestSeq | 9 |
"
+ "Type | variant | |
"
+ "Description | G,C | |
"
+ "Consequence | Translated by Jalview | p.Leu9Phe |
"
+ "alleles | | G,C |
" + "
";
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 = "
Location | Cds | 109-230 |
"
+ "Peptide Location | TestSeq | 10-13 |
"
+ "Type | exon | |
"
+ "Description | exon 1 | |
"
+ "
";
assertEquals(expected, sf2.getDetailsReport(seq.getName(), mf));
}
}