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275 lines (232 loc) · 8.97 KB
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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on June 15, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.core.alignment;
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.junit.Before;
import org.junit.Test;
import java.util.Arrays;
import static org.junit.Assert.assertEquals;
public class SimpleSequencePairTest {
private ProteinSequence query, target;
private SequencePair<ProteinSequence, AminoAcidCompound> global, local;
@Before
public void setup() throws CompoundNotFoundException {
query = new ProteinSequence("ARND");
target = new ProteinSequence("RDG");
global = new SimpleSequencePair<ProteinSequence, AminoAcidCompound>(query, target, Arrays.asList(new Step[] {
Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP}), Arrays.asList(new Step[] {
Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND}));
local = new SimpleSequencePair<ProteinSequence, AminoAcidCompound>(query, target, Arrays.asList(new Step[] {
Step.COMPOUND, Step.COMPOUND, Step.COMPOUND}), 1, 0, Arrays.asList(new Step[] { Step.COMPOUND,
Step.GAP, Step.COMPOUND}), 0, 1);
}
@Test
public void testGetCompoundInQueryAt() {
assertEquals(global.getCompoundInQueryAt(1).getShortName(), "A");
assertEquals(global.getCompoundInQueryAt(2).getShortName(), "R");
assertEquals(global.getCompoundInQueryAt(3).getShortName(), "N");
assertEquals(global.getCompoundInQueryAt(4).getShortName(), "D");
assertEquals(global.getCompoundInQueryAt(5).getShortName(), "-");
assertEquals(local.getCompoundInQueryAt(1).getShortName(), "R");
assertEquals(local.getCompoundInQueryAt(2).getShortName(), "N");
assertEquals(local.getCompoundInQueryAt(3).getShortName(), "D");
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundInQueryAtOutOfBounds() {
global.getCompoundInQueryAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundInQueryAtOutOfBounds2() {
global.getCompoundInQueryAt(6);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundInQueryAtOutOfBounds3() {
local.getCompoundInQueryAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundInQueryAtOutOfBounds4() {
local.getCompoundInQueryAt(4);
}
@Test
public void testGetCompoundInTargetAt() {
assertEquals(global.getCompoundInTargetAt(1).getShortName(), "-");
assertEquals(global.getCompoundInTargetAt(2).getShortName(), "R");
assertEquals(global.getCompoundInTargetAt(3).getShortName(), "-");
assertEquals(global.getCompoundInTargetAt(4).getShortName(), "D");
assertEquals(global.getCompoundInTargetAt(5).getShortName(), "G");
assertEquals(local.getCompoundInTargetAt(1).getShortName(), "R");
assertEquals(local.getCompoundInTargetAt(2).getShortName(), "-");
assertEquals(local.getCompoundInTargetAt(3).getShortName(), "D");
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundInTargetAtOutOfBounds() {
global.getCompoundInTargetAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundInTargetAtOutOfBounds2() {
global.getCompoundInTargetAt(6);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundInTargetAtOutOfBounds3() {
local.getCompoundInTargetAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundInTargetAtOutOfBounds4() {
local.getCompoundInTargetAt(4);
}
@Test
public void testGetIndexInQueryAt() {
assertEquals(global.getIndexInQueryAt(1), 1);
assertEquals(global.getIndexInQueryAt(2), 2);
assertEquals(global.getIndexInQueryAt(3), 3);
assertEquals(global.getIndexInQueryAt(4), 4);
assertEquals(global.getIndexInQueryAt(5), 4);
assertEquals(local.getIndexInQueryAt(1), 2);
assertEquals(local.getIndexInQueryAt(2), 3);
assertEquals(local.getIndexInQueryAt(3), 4);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInQueryAtOutOfBounds() {
global.getIndexInQueryAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInQueryAtOutOfBounds2() {
global.getIndexInQueryAt(6);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInQueryAtOutOfBounds3() {
local.getIndexInQueryAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInQueryAtOutOfBounds4() {
local.getIndexInQueryAt(4);
}
@Test
public void testGetIndexInQueryForTargetAt() {
assertEquals(global.getIndexInQueryForTargetAt(1), 2);
assertEquals(global.getIndexInQueryForTargetAt(2), 4);
assertEquals(global.getIndexInQueryForTargetAt(3), 4);
assertEquals(local.getIndexInQueryForTargetAt(1), 2);
assertEquals(local.getIndexInQueryForTargetAt(2), 4);
assertEquals(local.getIndexInQueryForTargetAt(3), 4);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInQueryForTargetAtOutOfBounds() {
global.getIndexInQueryForTargetAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInQueryForTargetAtOutOfBounds2() {
global.getIndexInQueryForTargetAt(4);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInQueryForTargetAtOutOfBounds3() {
local.getIndexInQueryForTargetAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInQueryForTargetAtOutOfBounds4() {
local.getIndexInQueryForTargetAt(4);
}
@Test
public void testGetIndexInTargetAt() {
assertEquals(global.getIndexInTargetAt(1), 1);
assertEquals(global.getIndexInTargetAt(2), 1);
assertEquals(global.getIndexInTargetAt(3), 1);
assertEquals(global.getIndexInTargetAt(4), 2);
assertEquals(global.getIndexInTargetAt(5), 3);
assertEquals(local.getIndexInTargetAt(1), 1);
assertEquals(local.getIndexInTargetAt(2), 1);
assertEquals(local.getIndexInTargetAt(3), 2);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInTargetAtOutOfBounds() {
global.getIndexInTargetAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInTargetAtOutOfBounds2() {
global.getIndexInTargetAt(6);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInTargetAtOutOfBounds3() {
local.getIndexInTargetAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInTargetAtOutOfBounds4() {
local.getIndexInTargetAt(4);
}
@Test
public void testGetIndexInTargetForQueryAt() {
assertEquals(global.getIndexInTargetForQueryAt(1), 1);
assertEquals(global.getIndexInTargetForQueryAt(2), 1);
assertEquals(global.getIndexInTargetForQueryAt(3), 1);
assertEquals(global.getIndexInTargetForQueryAt(4), 2);
assertEquals(local.getIndexInTargetForQueryAt(1), 1);
assertEquals(local.getIndexInTargetForQueryAt(2), 1);
assertEquals(local.getIndexInTargetForQueryAt(3), 1);
assertEquals(local.getIndexInTargetForQueryAt(4), 2);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInTargetForQueryAtOutOfBounds() {
global.getIndexInTargetForQueryAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInTargetForQueryAtOutOfBounds2() {
global.getIndexInTargetForQueryAt(5);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInTargetForQueryAtOutOfBounds3() {
local.getIndexInTargetForQueryAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndexInTargetForQueryAtOutOfBounds4() {
local.getIndexInTargetForQueryAt(5);
}
@Test
public void testGetNumIdenticals() {
assertEquals(global.getNumIdenticals(), 2);
assertEquals(local.getNumIdenticals(), 2);
}
@Test
public void testGetPercentageOfIdentity() {
assertEquals(global.getPercentageOfIdentity(false), 1.0, 0.01);
assertEquals(local.getPercentageOfIdentity(false), 1.0, 0.01);
}
@Test
public void testGetNumSimilars() {
assertEquals(global.getNumSimilars(), 2);
assertEquals(local.getNumSimilars(), 2);
}
@Test
public void testGetQuery() {
assertEquals(global.getQuery().getOriginalSequence(), query);
assertEquals(local.getQuery().getOriginalSequence(), query);
}
@Test
public void testGetTarget() {
assertEquals(global.getTarget().getOriginalSequence(), target);
assertEquals(local.getTarget().getOriginalSequence(), target);
}
}