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test MSA
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Lines changed: 60 additions & 11 deletions

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‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -180,7 +180,7 @@ public String toString() {
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// helper methods
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/**
183-
* Helper method that does all the formating work
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* Helper method that does all the formatting work
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* @param width
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* @param header
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* @param idFormat

‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignmentTest.java‎

Lines changed: 58 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -28,24 +28,34 @@
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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.compound.NucleotideCompound;
31-
import org.junit.Before;
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import org.junit.Test;
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import org.biojava.nbio.core.sequence.template.LightweightProfile;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.params.ParameterizedTest;
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import org.junit.jupiter.params.provider.EnumSource;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Set;
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import java.util.stream.Collectors;
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37-
import static org.junit.Assert.assertEquals;
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import static org.junit.jupiter.api.Assertions.*;
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public class MultipleSequenceAlignmentTest {
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class MultipleSequenceAlignmentTest {
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private MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msaProteins;
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private MultipleSequenceAlignment<DNASequence,NucleotideCompound> msaDNA;
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44-
@Before
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public void setup() throws CompoundNotFoundException {
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private static final String aaSeq = "ARNDCEQGHILKMFPSTWYVBZJX";
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@BeforeEach
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void setup() throws CompoundNotFoundException {
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msaProteins = new MultipleSequenceAlignment<>();
4755
for (int i = 0; i < 8; i++) {
48-
msaProteins.addAlignedSequence(new ProteinSequence("ARNDCEQGHILKMFPSTWYVBZJX"));
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ProteinSequence ps = new ProteinSequence(aaSeq);
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ps.setAccession(new AccessionID(i+""));
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msaProteins.addAlignedSequence(ps);
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}
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msaDNA = new MultipleSequenceAlignment<>();
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for (int i = 0; i < 7; i++) {
@@ -54,7 +64,46 @@ public void setup() throws CompoundNotFoundException {
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}
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@Test
57-
public void testGetCompoundsAt() {
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void allSequencesMustBeSameLength() throws CompoundNotFoundException {
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ProteinSequence differentLength = new ProteinSequence("ARNDC");
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assertThrows(IllegalArgumentException.class, ()->msaProteins.addAlignedSequence(differentLength));
70+
}
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72+
@Test
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void addRemoveAlignments() throws CompoundNotFoundException {
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assertEquals(8, msaProteins.getSize());
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assertEquals(8, msaProteins.getAlignedSequences().size());
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assertEquals(aaSeq.length(), msaProteins.getLength());
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msaProteins.removeAlignedSequence(new ProteinSequence(aaSeq));
78+
assertEquals(7, msaProteins.getSize());
79+
assertEquals(7, msaProteins.getAlignedSequences().size());
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}
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82+
@ParameterizedTest
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@EnumSource(LightweightProfile.StringFormat.class)
84+
void formattedAlignmentToString(LightweightProfile.StringFormat format){
85+
String formatted = msaProteins.toString(format);
86+
assertTrue(formatted.length() > 0);
87+
}
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@Test
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void alignmentToBasicString(){
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String alnStr = msaProteins.toString();
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String [] lines = alnStr.split(System.lineSeparator());
93+
assertEquals(8, lines.length);
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95+
//lines all same length
96+
Set<Integer> collect = Arrays.stream(lines).map(String::length).collect(Collectors.toSet());
97+
assertEquals(1, collect.size());
98+
}
99+
@Test
100+
void alignmentToWidth() {
101+
String alnStr = msaProteins.toString(10);
102+
assertEquals(29, alnStr.split(System.lineSeparator()).length);
103+
}
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@Test
106+
void testGetCompoundsAt() {
58107
AminoAcidCompound aminoAcid = AminoAcidCompoundSet.getAminoAcidCompoundSet().getCompoundForString("N");
59108
List<AminoAcidCompound> colProteins = new ArrayList<>();
60109
for (int i = 0; i < 8; i++) {
@@ -69,4 +118,5 @@ public void testGetCompoundsAt() {
69118
assertEquals(msaDNA.getCompoundsAt(3), colDNA);
70119
}
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121+
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}

‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/SequenceTestUtils.java‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -15,8 +15,7 @@ public class SequenceTestUtils {
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*/
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static GeneSequence anyGeneSequence() throws CompoundNotFoundException {
1717
ChromosomeSequence chr = new ChromosomeSequence(ChromosomeSequenceTest.CHROMOSOME_SEQ);
18-
GeneSequence gene = new GeneSequence(chr, new AccessionID("someGeneId"), 10, 200, Strand.POSITIVE);
19-
return gene;
18+
return new GeneSequence(chr, new AccessionID("someGeneId"), 10, 200, Strand.POSITIVE);
2019
}
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/**

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