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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;
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.Profile.StringFormat;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.AccessionID;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import java.util.Arrays;
import java.util.List;
import static org.junit.Assert.*;
public class SimpleProfileTest {
private ProteinSequence query, target;
private Profile<ProteinSequence, AminoAcidCompound> global, local, single;
@Before
public void setup() throws CompoundNotFoundException {
query = new ProteinSequence("ARND");
target = new ProteinSequence("RDG");
query.setAccession(new AccessionID("Query"));
target.setAccession(new AccessionID("Target"));
global = new SimpleProfile<ProteinSequence, AminoAcidCompound>(query, target, Arrays.asList(new Step[] {
Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP}), 0, 0, Arrays.asList(
new Step[] {Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND, Step.COMPOUND}), 0, 0);
local = new SimpleProfile<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);
single = new SimpleProfile<ProteinSequence, AminoAcidCompound>(query);
}
@Test(expected=IllegalArgumentException.class)
public void testSimpleProfile() {
new SimpleProfile<ProteinSequence, AminoAcidCompound>(query, target, Arrays.asList(new Step[] {
Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.COMPOUND, Step.GAP}), 0, 0, Arrays.asList(
new Step[] {Step.GAP, Step.COMPOUND, Step.GAP, Step.COMPOUND}), 0, 0);
}
@Test
public void testGetAlignedSequenceInt() {
assertEquals(global.getAlignedSequence(1).toString(), "ARND-");
assertEquals(global.getAlignedSequence(2).toString(), "-R-DG");
assertEquals(local.getAlignedSequence(1).toString(), "RND");
assertEquals(local.getAlignedSequence(2).toString(), "R-D");
assertEquals(single.getAlignedSequence(1).toString(), "ARND");
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetAlignedSequenceIntOutOfBounds() {
global.getAlignedSequence(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetAlignedSequenceIntOutOfBounds2() {
global.getAlignedSequence(3);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetAlignedSequenceIntOutOfBounds3() {
local.getAlignedSequence(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetAlignedSequenceIntOutOfBounds4() {
local.getAlignedSequence(3);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetAlignedSequenceIntOutOfBounds5() {
single.getAlignedSequence(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetAlignedSequenceIntOutOfBounds6() {
single.getAlignedSequence(2);
}
@Test
public void testGetAlignedSequenceS() throws CompoundNotFoundException {
assertEquals(global.getAlignedSequence(query).toString(), "ARND-");
assertEquals(global.getAlignedSequence(target).toString(), "-R-DG");
assertNull(global.getAlignedSequence(new ProteinSequence("AR")));
assertEquals(local.getAlignedSequence(query).toString(), "RND");
assertEquals(local.getAlignedSequence(target).toString(), "R-D");
assertNull(local.getAlignedSequence(new ProteinSequence("AR")));
assertEquals(single.getAlignedSequence(query).toString(), "ARND");
assertNull(single.getAlignedSequence(target));
}
@Test
public void testGetAlignedSequences() {
List<AlignedSequence<ProteinSequence, AminoAcidCompound>> list = global.getAlignedSequences();
assertEquals(list.size(), 2);
assertEquals(list.get(0).toString(), "ARND-");
assertEquals(list.get(1).toString(), "-R-DG");
list = local.getAlignedSequences();
assertEquals(list.size(), 2);
assertEquals(list.get(0).toString(), "RND");
assertEquals(list.get(1).toString(), "R-D");
list = single.getAlignedSequences();
assertEquals(list.size(), 1);
assertEquals(list.get(0).toString(), "ARND");
}
@Test
public void testGetAlignedSequencesIntArray() {
List<AlignedSequence<ProteinSequence, AminoAcidCompound>> list = global.getAlignedSequences(2, 1, 2);
assertEquals(list.size(), 3);
assertEquals(list.get(0).toString(), "-R-DG");
assertEquals(list.get(1).toString(), "ARND-");
assertEquals(list.get(2).toString(), "-R-DG");
list = local.getAlignedSequences(2, 2, 1);
assertEquals(list.size(), 3);
assertEquals(list.get(0).toString(), "R-D");
assertEquals(list.get(1).toString(), "R-D");
assertEquals(list.get(2).toString(), "RND");
list = single.getAlignedSequences(1, 1);
assertEquals(list.size(), 2);
assertEquals(list.get(0).toString(), "ARND");
assertEquals(list.get(1).toString(), "ARND");
}
@Test
public void testGetAlignedSequencesSArray() {
List<AlignedSequence<ProteinSequence, AminoAcidCompound>> list = global.getAlignedSequences(query, query,
target);
assertEquals(list.size(), 3);
assertEquals(list.get(0).toString(), "ARND-");
assertEquals(list.get(1).toString(), "ARND-");
assertEquals(list.get(2).toString(), "-R-DG");
list = local.getAlignedSequences(target, query, target);
assertEquals(list.size(), 3);
assertEquals(list.get(0).toString(), "R-D");
assertEquals(list.get(1).toString(), "RND");
assertEquals(list.get(2).toString(), "R-D");
list = single.getAlignedSequences(query, query);
assertEquals(list.size(), 2);
assertEquals(list.get(0).toString(), "ARND");
assertEquals(list.get(1).toString(), "ARND");
}
@Test
public void testGetCompoundAtIntInt() {
assertEquals(global.getCompoundAt(1, 4).getShortName(), "D");
assertEquals(global.getCompoundAt(2, 3).getShortName(), "-");
assertEquals(local.getCompoundAt(1, 1).getShortName(), "R");
assertEquals(local.getCompoundAt(2, 2).getShortName(), "-");
assertEquals(single.getCompoundAt(1, 3).getShortName(), "N");
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtIntIntOutOfBounds() {
global.getCompoundAt(0, 4);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtIntIntOutOfBounds2() {
global.getCompoundAt(3, 4);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtIntIntOutOfBounds3() {
global.getCompoundAt(1, 0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtIntIntOutOfBounds4() {
global.getCompoundAt(2, 6);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtIntIntOutOfBounds5() {
local.getCompoundAt(0, 2);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtIntIntOutOfBounds6() {
local.getCompoundAt(3, 2);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtIntIntOutOfBounds7() {
local.getCompoundAt(1, 0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtIntIntOutOfBounds8() {
local.getCompoundAt(2, 4);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtIntIntOutOfBounds9() {
single.getCompoundAt(1, 0);
}
@Test
public void testGetCompoundAtSInt() throws CompoundNotFoundException {
assertEquals(global.getCompoundAt(query, 2).getShortName(), "R");
assertEquals(global.getCompoundAt(target, 5).getShortName(), "G");
assertNull(global.getCompoundAt(new ProteinSequence("AR"), 3));
assertEquals(local.getCompoundAt(query, 2).getShortName(), "N");
assertEquals(local.getCompoundAt(target, 3).getShortName(), "D");
assertNull(local.getCompoundAt(new ProteinSequence("AR"), 3));
assertEquals(single.getCompoundAt(query, 2).getShortName(), "R");
assertNull(single.getCompoundAt(target, 3));
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtSIntOutOfBounds() {
global.getCompoundAt(query, 0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtSIntOutOfBounds2() {
global.getCompoundAt(target, 6);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtSIntOutOfBounds3() {
local.getCompoundAt(target, 0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtSIntOutOfBounds4() {
local.getCompoundAt(query, 4);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundAtSIntOutOfBounds5() {
single.getCompoundAt(query, 0);
}
@Test
public void testGetCompoundSet() {
assertEquals(global.getCompoundSet(), AminoAcidCompoundSet.getAminoAcidCompoundSet());
assertEquals(local.getCompoundSet(), AminoAcidCompoundSet.getAminoAcidCompoundSet());
assertEquals(single.getCompoundSet(), AminoAcidCompoundSet.getAminoAcidCompoundSet());
}
@Test
public void testGetCompoundsAt() {
List<AminoAcidCompound> column = global.getCompoundsAt(5);
assertEquals(column.size(), 2);
assertEquals(column.get(0).getShortName(), "-");
assertEquals(column.get(1).getShortName(), "G");
column = local.getCompoundsAt(2);
assertEquals(column.size(), 2);
assertEquals(column.get(0).getShortName(), "N");
assertEquals(column.get(1).getShortName(), "-");
column = single.getCompoundsAt(2);
assertEquals(column.size(), 1);
assertEquals(column.get(0).getShortName(), "R");
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundsAtOutOfBounds() {
global.getCompoundsAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundsAtOutOfBounds2() {
global.getCompoundsAt(6);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundsAtOutOfBounds3() {
local.getCompoundsAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundsAtOutOfBounds4() {
local.getCompoundsAt(4);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundsAtOutOfBounds5() {
single.getCompoundsAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetCompoundsAtOutOfBounds6() {
single.getCompoundsAt(5);
}
@Test
public void testGetIndexOf() {
AminoAcidCompoundSet cs = AminoAcidCompoundSet.getAminoAcidCompoundSet();
assertEquals(global.getIndexOf(cs.getCompoundForString("A")), 1);
assertEquals(global.getIndexOf(cs.getCompoundForString("R")), 2);
assertEquals(global.getIndexOf(cs.getCompoundForString("N")), 3);
assertEquals(global.getIndexOf(cs.getCompoundForString("D")), 4);
assertEquals(global.getIndexOf(cs.getCompoundForString("G")), 5);
assertEquals(global.getIndexOf(cs.getCompoundForString("-")), 1);
assertEquals(global.getIndexOf(cs.getCompoundForString("E")), -1);
assertEquals(local.getIndexOf(cs.getCompoundForString("R")), 1);
assertEquals(local.getIndexOf(cs.getCompoundForString("N")), 2);
assertEquals(local.getIndexOf(cs.getCompoundForString("D")), 3);
assertEquals(local.getIndexOf(cs.getCompoundForString("-")), 2);
assertEquals(local.getIndexOf(cs.getCompoundForString("K")), -1);
assertEquals(single.getIndexOf(cs.getCompoundForString("A")), 1);
assertEquals(single.getIndexOf(cs.getCompoundForString("R")), 2);
assertEquals(single.getIndexOf(cs.getCompoundForString("N")), 3);
assertEquals(single.getIndexOf(cs.getCompoundForString("D")), 4);
assertEquals(single.getIndexOf(cs.getCompoundForString("G")), -1);
}
@Test
public void testGetIndicesAt() {
assertArrayEquals(global.getIndicesAt(1), new int[] {1, 1});
assertArrayEquals(global.getIndicesAt(2), new int[] {2, 1});
assertArrayEquals(global.getIndicesAt(3), new int[] {3, 1});
assertArrayEquals(global.getIndicesAt(4), new int[] {4, 2});
assertArrayEquals(global.getIndicesAt(5), new int[] {4, 3});
assertArrayEquals(local.getIndicesAt(1), new int[] {2, 1});
assertArrayEquals(local.getIndicesAt(2), new int[] {3, 1});
assertArrayEquals(local.getIndicesAt(3), new int[] {4, 2});
assertArrayEquals(single.getIndicesAt(1), new int[] {1});
assertArrayEquals(single.getIndicesAt(2), new int[] {2});
assertArrayEquals(single.getIndicesAt(3), new int[] {3});
assertArrayEquals(single.getIndicesAt(4), new int[] {4});
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndicesAtOutOfBounds() {
global.getIndicesAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndicesAtOutOfBounds2() {
global.getIndicesAt(6);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndicesAtOutOfBounds3() {
local.getIndicesAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndicesAtOutOfBounds4() {
local.getIndicesAt(4);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndicesAtOutOfBounds5() {
single.getIndicesAt(0);
}
@Test(expected=IndexOutOfBoundsException.class)
public void testGetIndicesAtOutOfBounds6() {
single.getIndicesAt(5);
}
@Test
public void testGetLastIndexOf() {
AminoAcidCompoundSet cs = AminoAcidCompoundSet.getAminoAcidCompoundSet();
assertEquals(global.getLastIndexOf(cs.getCompoundForString("A")), 1);
assertEquals(global.getLastIndexOf(cs.getCompoundForString("R")), 2);
assertEquals(global.getLastIndexOf(cs.getCompoundForString("N")), 3);
assertEquals(global.getLastIndexOf(cs.getCompoundForString("D")), 4);
assertEquals(global.getLastIndexOf(cs.getCompoundForString("G")), 5);
assertEquals(global.getLastIndexOf(cs.getCompoundForString("-")), 5);
assertEquals(global.getLastIndexOf(cs.getCompoundForString("E")), -1);
assertEquals(local.getLastIndexOf(cs.getCompoundForString("R")), 1);
assertEquals(local.getLastIndexOf(cs.getCompoundForString("N")), 2);
assertEquals(local.getLastIndexOf(cs.getCompoundForString("D")), 3);
assertEquals(local.getLastIndexOf(cs.getCompoundForString("-")), 2);
assertEquals(local.getLastIndexOf(cs.getCompoundForString("K")), -1);
assertEquals(single.getLastIndexOf(cs.getCompoundForString("A")), 1);
assertEquals(single.getLastIndexOf(cs.getCompoundForString("R")), 2);
assertEquals(single.getLastIndexOf(cs.getCompoundForString("N")), 3);
assertEquals(single.getLastIndexOf(cs.getCompoundForString("D")), 4);
assertEquals(single.getLastIndexOf(cs.getCompoundForString("G")), -1);
}
@Test
public void testGetLength() {
assertEquals(global.getLength(), 5);
assertEquals(local.getLength(), 3);
assertEquals(single.getLength(), 4);
}
@Test
public void testGetOriginalSequences() {
List<ProteinSequence> list = global.getOriginalSequences();
assertEquals(list.size(), 2);
assertEquals(list.get(0), query);
assertEquals(list.get(1), target);
list = local.getOriginalSequences();
assertEquals(list.size(), 2);
assertEquals(list.get(0), query);
assertEquals(list.get(1), target);
list = single.getOriginalSequences();
assertEquals(list.size(), 1);
assertEquals(list.get(0), query);
}
@Test
public void testGetSize() {
assertEquals(global.getSize(), 2);
assertEquals(local.getSize(), 2);
assertEquals(single.getSize(), 1);
}
@Ignore // TODO SimpleProfile.getSubProfile(Location)
@Test
public void testGetSubProfile() {
fail("Not yet implemented");
}
@Test
public void testIsCircular() {
assertFalse(global.isCircular());
assertFalse(local.isCircular());
assertFalse(single.isCircular());
}
@Test
public void testToStringInt() {
assertEquals(global.toString(3), String.format(
" 1 3%n" +
"Query 1 ARN 3%n" +
" | %n"+
"Target 1 -R- 1%n" +
"%n" +
" 4 5%n" +
"Query 4 D- 4%n" +
" | %n"+
"Target 2 DG 3%n"));
assertEquals(local.toString(4), String.format(
" 1 3%n" +
"Query 2 RND 4%n" +
" | |%n"+
"Target 1 R-D 2%n"));
assertEquals(single.toString(4), String.format(
" 1 4%n" +
"Query 1 ARND 4%n" ));
}
@Test
public void testToStringFormatted() {
assertEquals(global.toString(StringFormat.ALN), String.format(
"CLUSTAL W MSA from BioJava%n%n" +
"Query ARND- 4%n" +
" | | %n"+
"Target -R-DG 3%n"));
assertEquals(local.toString(StringFormat.FASTA), String.format(
">Query%n" +
"RND%n" +
">Target%n" +
"R-D%n"));
assertEquals(single.toString(StringFormat.MSF), String.format(
"MSA from BioJava%n%n" +
" MSF: 4 Type: P Check: 735 ..%n%n" +
" Name: Query Len: 4 Check: 735 Weight: 1.0%n" +
"%n//%n%n" +
"Query ARND%n"));
}
@Test
public void testToString() {
assertEquals(global.toString(), String.format("ARND-%n-R-DG%n"));
assertEquals(local.toString(), String.format("RND%nR-D%n"));
assertEquals(single.toString(), String.format("ARND%n"));
}
@Test
public void testIterator() {
for (AlignedSequence<ProteinSequence, AminoAcidCompound> s : global) {
assertEquals(s.toString().length(), 5);
}
for (AlignedSequence<ProteinSequence, AminoAcidCompound> s : local) {
assertEquals(s.toString().length(), 3);
}
for (AlignedSequence<ProteinSequence, AminoAcidCompound> s : single) {
assertEquals(s.toString().length(), 4);
}
}
}