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revoke deleted tests
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‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/LocationParserTest.java‎

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/*
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* BioJava development code
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*
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* This code may be freely distributed and modified under the
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* terms of the GNU Lesser General Public Licence. This should
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* be distributed with the code. If you do not have a copy,
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* see:
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*
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* http://www.gnu.org/copyleft/lesser.html
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*
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* Copyright for this code is held jointly by the individual
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* authors. These should be listed in @author doc comments.
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*
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* For more information on the BioJava project and its aims,
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* or to join the biojava-l mailing list, visit the home page
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* at:
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*
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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.core.sequence.location;
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import org.biojava.nbio.core.sequence.AccessionID;
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import org.biojava.nbio.core.sequence.Strand;
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import org.biojava.nbio.core.sequence.location.template.Location;
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import org.junit.Assert;
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import org.junit.Ignore;
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import org.junit.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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/**
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* TODO: Temporary test is switched off. Currently results are messy:
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*
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* <code>
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* to test: complement(order(1,2..34,complement(34..45),A00001.5:34..45)) expected: 1..45(.) received: 1..45(.)
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* to test: 1 expected: 1..1(+) received: 1..1(+)
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* to test: 1..10 expected: 1..10(+) received: 1..10(+)
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* to test: 1^2 expected: 1^2(+) received: 1^2(+)
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* to test: complement(1..10) expected: 1..10(-) received: 1..10(-)
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* to test: join(1..2,7..8) expected: 1..8(+) received: 1..8(+)
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* to test: complement(join(1..2,7..8)) expected: 1..8(-) received: 1..8(-)
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* to test: join(complement(1..2),complement(7..8)) expected: 1..8(-) received: 1..8(-)
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* to test: join(1..2,join(4..5,complement(6..8)) expected: 1..8(.) received: 1..8(.)
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* to test: join(5..10,1..3) expected: 5..13(+ - circular) received: 1..10(+)
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* </code>
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*
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* Serialisation to string should be fixed as well.
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*
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*
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* @author Jacek Grzebyta
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*/
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public class LocationParserTest {
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public static final InsdcParser PARSER = new InsdcParser();
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private Logger log = LoggerFactory.getLogger(getClass());
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@Test
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@Ignore
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public void basicLocationTests() {
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assertInsdcLoc("1", new SimpleLocation(1, 1, Strand.POSITIVE));
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assertInsdcLoc("1..10", new SimpleLocation(1, 10, Strand.POSITIVE));
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assertInsdcLoc("1^2", new SimpleLocation(
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new SimplePoint(1),
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new SimplePoint(2),
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Strand.POSITIVE, false, true));
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assertInsdcLoc("complement(1..10)", new SimpleLocation(1, 10, Strand.NEGATIVE));
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assertInsdcLoc("join(1..2,7..8)", new InsdcLocations.GroupLocation(
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new SimplePoint(1), new SimplePoint(8), Strand.POSITIVE,
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new SimpleLocation(1, 2, Strand.POSITIVE),
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new SimpleLocation(7, 8, Strand.POSITIVE)));
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assertInsdcLoc("complement(join(1..2,7..8))", new InsdcLocations.GroupLocation(
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new SimplePoint(1), new SimplePoint(8), Strand.NEGATIVE,
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new SimpleLocation(1, 2, Strand.NEGATIVE),
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new SimpleLocation(7, 8, Strand.NEGATIVE)));
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//Reverse relationship
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assertInsdcLoc("join(complement(1..2),complement(7..8))", new InsdcLocations.GroupLocation(
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new SimplePoint(1), new SimplePoint(8), Strand.NEGATIVE,
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new SimpleLocation(1, 2, Strand.NEGATIVE),
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new SimpleLocation(7, 8, Strand.NEGATIVE)));
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//Complex sub relations
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//should tests be designed for both modes?
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//PARSER.setComplexFeaturesAppendMode(InsdcParser.complexFeaturesAppendEnum.HIERARCHICAL);
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assertInsdcLoc("join(1..2,join(4..5,complement(6..8))", new InsdcLocations.GroupLocation(
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new SimplePoint(1), new SimplePoint(8), Strand.UNDEFINED,
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new SimpleLocation(1, 2, Strand.POSITIVE),
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new SimpleLocation(4, 8, Strand.UNDEFINED,
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new SimpleLocation(4, 5, Strand.POSITIVE),
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new SimpleLocation(6, 8, Strand.NEGATIVE))));
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assertInsdcLoc("join(5..10,1..3)", new InsdcLocations.GroupLocation(
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new SimplePoint(5), new SimplePoint(13), Strand.POSITIVE,
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true, //Circular genome
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new SimpleLocation(5, 10, Strand.POSITIVE),
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new SimpleLocation(1, 3, Strand.POSITIVE)));
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assertInsdcLoc("order(1..2,7..8)", new InsdcLocations.OrderLocation(
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new SimplePoint(1), new SimplePoint(8), Strand.POSITIVE,
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new SimpleLocation(1, 2, Strand.POSITIVE),
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new SimpleLocation(7, 8, Strand.POSITIVE)));
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}
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@Test
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@Ignore
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public void moreComplex() {
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assertInsdcLoc("complement(order(1,2..34,complement(34..45),A00001.5:34..45))",
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new InsdcLocations.OrderLocation(
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new SimplePoint(1), new SimplePoint(45), Strand.UNDEFINED,
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new SimpleLocation(1, 1, Strand.NEGATIVE),
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new SimpleLocation(2, 34, Strand.NEGATIVE),
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new SimpleLocation(34, 45, Strand.POSITIVE),
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new SimpleLocation(
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new SimplePoint(34), new SimplePoint(45),
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Strand.NEGATIVE,
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new AccessionID("A00001.5", PARSER.getDataSource()))));
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}
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public void assertInsdcLoc(String stringLoc, Location expected) {
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Location actual = PARSER.parse(stringLoc);
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log.info("to test: {}\texpected: {}\treceived: {}", stringLoc, expected.toString(), actual.toString());
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Assert.assertEquals("Asserting locations are the same", expected.toString(), actual.toString());
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}
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}

‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/LocationTest.java‎

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/*
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* BioJava development code
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*
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* This code may be freely distributed and modified under the
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* terms of the GNU Lesser General Public Licence. This should
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* be distributed with the code. If you do not have a copy,
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* see:
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*
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* http://www.gnu.org/copyleft/lesser.html
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*
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* Copyright for this code is held jointly by the individual
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* authors. These should be listed in @author doc comments.
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*
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* For more information on the BioJava project and its aims,
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* or to join the biojava-l mailing list, visit the home page
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* at:
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*
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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.core.sequence.location;
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import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
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import org.biojava.nbio.core.sequence.DNASequence;
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import org.biojava.nbio.core.sequence.Strand;
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import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
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import org.biojava.nbio.core.sequence.location.template.Location;
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import org.biojava.nbio.core.sequence.template.Sequence;
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import org.junit.Test;
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import java.util.Arrays;
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import java.util.List;
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import static org.biojava.nbio.core.sequence.Strand.UNDEFINED;
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import static org.junit.Assert.assertEquals;
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public class LocationTest {
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@Test
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public void testSubLocations() throws CompoundNotFoundException {
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List<SimpleLocation> expected = Arrays.asList(
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new SimpleLocation(1, 2, Strand.UNDEFINED),
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new SimpleLocation(3, 6, Strand.UNDEFINED),
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new SimpleLocation(7, 10, Strand.UNDEFINED),
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new SimpleLocation(11, 20, UNDEFINED));
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Location location = new SimpleLocation(1, 20, UNDEFINED,
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new SimpleLocation(1, 10, UNDEFINED,
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new SimpleLocation(1, 6, UNDEFINED,
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new SimpleLocation(1, 2, UNDEFINED), new SimpleLocation(3, 6, UNDEFINED)),
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new SimpleLocation(7, 10, UNDEFINED)),
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new SimpleLocation(11, 20, UNDEFINED));
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List<Location> actual = location.getRelevantSubLocations();
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assertEquals("Checking sublocations iterate as expected", toStr(expected), toStr(actual));
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String expectedDna = "AACCCCTTTTGGGGGGGGGG";
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Sequence<NucleotideCompound> s = new DNASequence(expectedDna + "CC");
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Sequence<NucleotideCompound> subSeq = location.getSubSequence(s);
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assertEquals("Checking subseq as expected", expectedDna, subSeq.getSequenceAsString());
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}
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@Test
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public void testBasicCircularLocation() throws CompoundNotFoundException {
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Location circularLocation = new SimpleLocation(
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new SimplePoint(3), new SimplePoint(52), Strand.POSITIVE, true,
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new SimpleLocation(3, 20, Strand.POSITIVE),
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new SimpleLocation(1, 20, Strand.POSITIVE),
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new SimpleLocation(1, 12, Strand.POSITIVE));
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assertEquals("Checking length as expected", circularLocation.getLength(), 50);
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String expectedDna = "CCCCTTTTGGGGGGGGGGAACCCCTTTTGGGGGGGGGGAACCCCTTTTGG";
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DNASequence s = new DNASequence("AACCCCTTTTGGGGGGGGGG");
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Sequence<NucleotideCompound> subSeq = circularLocation.getSubSequence(s);
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assertEquals("Checking subseq as expected", expectedDna, subSeq.getSequenceAsString());
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Location newCircularLocation = Location.Tools.circularLocation(
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3, 52, Strand.POSITIVE, 20);
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//Check this is the right set of coords even to use!
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Location negativeCoordsCircularLocation = Location.Tools.circularLocation(
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58,9, Strand.POSITIVE, 20);
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assertEquals("location objects should be equivalent", circularLocation, newCircularLocation);
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assertEquals("location objects should be equivalent even if they are on the wrong coord system", circularLocation.getSubLocations(), negativeCoordsCircularLocation.getSubLocations());
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assertEquals("Checking subseq as expected", expectedDna,
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newCircularLocation.getSubSequence(s).getSequenceAsString());
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}
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@Test
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public void testWithStrandSwitch() throws CompoundNotFoundException {
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DNASequence s = new DNASequence("AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAATTTCCCG");
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Location location = new SimpleLocation(1, 50, Strand.UNDEFINED,
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new SimpleLocation(1, 10, Strand.POSITIVE), //AAAAAAAAAA
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new SimpleLocation(19, 23, Strand.NEGATIVE), //GGGAA
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new SimpleLocation(45, 50, Strand.POSITIVE)); //TTCCCG
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String expectedDna = "AAAAAAAAAAGGGAATTCCCG";
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Sequence<NucleotideCompound> subSeq = location.getRelevantSubSequence(s);
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assertEquals("Checking subseq as expected", expectedDna, subSeq.getSequenceAsString());
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}
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@Test
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public void testStrandFlip() {
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Location l = new SimpleLocation(3,17,Strand.POSITIVE);
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Location r = Location.Tools.location(18, 4, Strand.POSITIVE, 20);
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assertEquals("Locations should be the same even though they were expressed differently", l, r);
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}
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@Test(expected = IllegalStateException.class)
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public void badLocations() {
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new SimpleLocation(10, 1, Strand.UNDEFINED);
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}
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@Test
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public void modulateCircular() {
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int length = 20;
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assertEquals("Checking modulation", 12, Location.Tools.modulateCircularIndex(52, length));
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assertEquals("Checking modulation", 1, Location.Tools.modulateCircularIndex(21, length));
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assertEquals("Checking modulation", 3, Location.Tools.modulateCircularIndex(3, length));
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}
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@Test
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public void completePasses() {
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assertEquals("Checking passes", 4, Location.Tools.completeCircularPasses(52, 10));
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assertEquals("Checking passes", 2, Location.Tools.completeCircularPasses(36, 10));
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}
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private <L extends Location> String toStr(List<L> locations) {
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StringBuilder sb = new StringBuilder();
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for (L l : locations) {
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sb.append(l).append("|");
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}
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return sb.toString();
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}
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}

‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/location/TargetedLocationParserTest.java‎

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/*
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* BioJava development code
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*
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* This code may be freely distributed and modified under the
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* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
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*
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* http://www.gnu.org/copyleft/lesser.html
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*
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* Copyright for this code is held jointly by the individual
12+
* authors. These should be listed in @author doc comments.
13+
*
14+
* For more information on the BioJava project and its aims,
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* or to join the biojava-l mailing list, visit the home page
16+
* at:
17+
*
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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.core.sequence.location;
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import org.biojava.nbio.core.sequence.DataSource;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
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import org.biojava.nbio.core.sequence.location.template.Location;
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import org.biojava.nbio.core.sequence.template.CompoundSet;
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import org.junit.Assert;
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import org.junit.Test;
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import org.junit.runner.RunWith;
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import org.junit.runners.Parameterized;
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import java.util.Arrays;
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import java.util.Collection;
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/**
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*
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* @author Jacek Grzebyta
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*/
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@RunWith(Parameterized.class)
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public class TargetedLocationParserTest {
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private Data request;
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public static class Data {
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private String Insdc;
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/**
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* Parser data input. Based on that input it should be able to identity the origin and wanted target
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* @param gi origin GI number
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* @param originType origin compound set type
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* @param Insdc string with INSDC notation
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* @param compound wanted compound type {@see CompoundSet}
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*/
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public Data(String gi, CompoundSet<?> originType, String Insdc, CompoundSet<?> compound) {
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this.Insdc = Insdc;
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}
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};
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@Parameterized.Parameters
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public static Collection<Data[]> getLocations() throws Exception {
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Data[][] out = new Data[][]{
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{new Data("7525057", AminoAcidCompoundSet.getAminoAcidCompoundSet(),
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"join(complement(NC_000932.1:69611..69724),NC_000932.1:139856..140087,NC_000932.1:140625..140650)", DNACompoundSet.getDNACompoundSet())},
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{new Data("7525059", AminoAcidCompoundSet.getAminoAcidCompoundSet(),
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"NC_000932.1:72371..73897", DNACompoundSet.getDNACompoundSet())},
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{new Data("7525073", DNACompoundSet.getDNACompoundSet() ,
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"complement(NC_000932.1:84005..84283)", DNACompoundSet.getDNACompoundSet())},
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{new Data("7525012", DNACompoundSet.getDNACompoundSet(),
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"complement(9938..11461)", DNACompoundSet.getDNACompoundSet())}
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};
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return Arrays.asList(out);
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}
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public TargetedLocationParserTest(Data request) {
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this.request = request;
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}
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@Test
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public void locationTest() throws Exception {
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InsdcParser parser = new InsdcParser(DataSource.GENBANK);
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Location loc = parser.parse(request.Insdc);
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Assert.assertNotNull(loc);
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if (loc.isComplex()) {
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Assert.assertFalse(loc.getSubLocations().isEmpty());
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} else {
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}
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}
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}

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