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paolopavanpaolopavan
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Added Hsp.getAlignment() test
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  • biojava-core/src/test/java/org/biojava/nbio/core/search/io

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‎biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java‎

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/*
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* To change this license header, choose License Headers in Project Properties.
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* To change this template file, choose Tools | Templates
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* and open the template in the editor.
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*/
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package org.biojava.nbio.core.search.io;
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import org.biojava.nbio.alignment.template.SequencePair;
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import org.biojava.nbio.core.search.io.blast.BlastHspBuilder;
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import org.biojava.nbio.core.sequence.DNASequence;
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import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
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import org.junit.After;
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import org.junit.AfterClass;
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import org.junit.Before;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import static org.junit.Assert.*;
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import org.junit.Ignore;
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/**
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*
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* @author pavanpa
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*/
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public class HspTest {
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Hsp hspImpl = new BlastHspBuilder()
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.setHspNum(1)
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.setHspBitScore(377.211)
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.setHspEvalue(8.04143e-093)
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.setHspQueryFrom(1)
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.setHspQueryTo(224)
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.setHspHitFrom(1035)
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.setHspHitTo(811)
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.setHspQueryFrame(-1)
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.setHspIdentity(213)
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.setHspPositive(213)
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.setHspGaps(5)
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.setHspAlignLen(227)
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.setHspQseq("CTGACGACAGCCATGCACCACCTGTCTCGACTTTCCCCCGAAGGGCACCTAATGTATCTCTACCTCGTTAGTCGGATGTCAAGACCTGGTAAGGTTTTTTCGCGTATCTTCGAATTAAACCACATACTCCACTGCTTGTGCGG-CCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGCCGTACTCCC-AGGTGGA-TACTTATTGTGTTAACTCCGGCACGGAAGG")
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.setHspHseq("CTGACGACAACCATGCACCACCTGTCTCAACTTTCCCC-GAAGGGCACCTAATGTATCTCTACTTCGTTAGTTGGATGTCAAGACCTGGTAAGGTT-CTTCGCGTTGCTTCGAATTAAACCACATACTCCACTGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGTGGATTACTTATTGTGTTAACTCCGGCACAGAAGG")
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.setHspIdentityString("||||||||| |||||||||||||||||| ||||||||| |||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||||| |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| ||||||||| ||||||| |||||||||||||||||||||||| |||||")
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.createBlastHsp();
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public HspTest() {
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}
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@BeforeClass
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public static void setUpClass() {
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}
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@AfterClass
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public static void tearDownClass() {
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}
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@Before
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public void setUp() {
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}
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@After
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public void tearDown() {
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}
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/**
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* Test of hashCode method, of class Hsp.
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*/
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@Test
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@Ignore public void testHashCode() {
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System.out.println("hashCode");
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Hsp instance = null;
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int expResult = 0;
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int result = instance.hashCode();
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assertEquals(expResult, result);
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// TODO review the generated test code and remove the default call to fail.
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fail("The test case is a prototype.");
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}
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/**
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* Test of equals method, of class Hsp.
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*/
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@Test
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@Ignore public void testEquals() {
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System.out.println("equals");
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Object o = null;
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Hsp instance = null;
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boolean expResult = false;
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boolean result = instance.equals(o);
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assertEquals(expResult, result);
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// TODO review the generated test code and remove the default call to fail.
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fail("The test case is a prototype.");
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}
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/**
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* Test of getAlignment method, of class Hsp.
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*/
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@Test
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public void testGetAlignment() {
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System.out.println("getAlignment");
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SequencePair<DNASequence, NucleotideCompound> aln = hspImpl.getAlignment();
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StringBuilder s = new StringBuilder();
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s.append(hspImpl.getHspQseq());
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s.append(String.format("%n"));
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s.append(hspImpl.getHspHseq());
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s.append(String.format("%n"));
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String expResult = s.toString();
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String result = aln.toString();
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assertEquals(expResult, result);
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}
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}

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