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Added first prototype of tests
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‎biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastHitTest.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.blast;
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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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/**
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*
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* @author pavanpa
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*/
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public class BlastHitTest {
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public BlastHitTest() {
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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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@Test
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public void testSomeMethod() {
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// TODO review the generated test code and remove the default call to fail.
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}
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}

‎biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastHspTest.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.blast;
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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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/**
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*
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* @author pavanpa
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*/
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public class BlastHspTest {
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public BlastHspTest() {
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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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@Test
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public void testSomeMethod() {
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// TODO review the generated test code and remove the default call to fail.
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}
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}

‎biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLQueryTest.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.blast;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.OutputStream;
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import java.net.URL;
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import java.util.ArrayList;
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import java.util.List;
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import org.biojava.nbio.core.search.io.Hit;
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import org.biojava.nbio.core.search.io.Hsp;
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import org.biojava.nbio.core.search.io.Result;
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import org.biojava.nbio.core.sequence.io.util.ClasspathResource;
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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 BlastXMLQueryTest {
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public BlastXMLQueryTest() {
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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 setFile method, of class BlastXMLQuery.
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*/
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@Test
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public void testSetFile() {
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System.out.println("setFile");
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File f = null;
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BlastXMLQuery instance = new BlastXMLQuery();
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instance.setFile(f);
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}
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/**
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* Test of createObjects method, of class BlastXMLQuery.
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*/
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@Test
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public void testCreateObjects() throws Exception {
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System.out.println("createObjects");
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String resource = "/org/biojava/nbio/core/search/io/blast/testBlastReport.xml";
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URL resourceURL = getClass().getResource(resource);
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File file = new File(resourceURL.getFile());
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BlastXMLQuery instance = new BlastXMLQuery();
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instance.setFile(file);
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//instance.setQueryReferences(null);
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//instance.setDatabaseReferences(null);
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ArrayList<Result> result = instance.createObjects(Double.MAX_VALUE);
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// test with random manual selected results
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BlastHsp hsp1hit1res1 = 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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BlastHit hit1res1 = new BlastHitBuilder()
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.setHitNum(1)
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.setHitId("gnl|BL_ORD_ID|2006")
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.setHitDef("gi|265679047|ref|NR_029355.1| Clostridium methylpentosum DSM 5476 strain R2 16S ribosomal RNA, partial sequence")
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.setHitAccession("2006")
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.setHitLen(1435)
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.createBlastHit();
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BlastResult res1 = new BlastResultBuilder()
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.setProgram("blastn")
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.setVersion("BLASTN 2.2.29+")
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.setReference("Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), &quot;A greedy algorithm for aligning DNA sequences&quot;, J Comput Biol 2000; 7(1-2):203-14.")
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.setQueryID("Query_1")
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.setQueryDef("42DKN:00022:00047")
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.setQueryLength(226)
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.createBlastResult();
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Result expRes1 = result.get(0);
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Hit expHit1res1 = expRes1.iterator().next();
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Hsp expHsp1hit1res1 = expHit1res1.iterator().next();
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// result test
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assertEquals(expRes1, res1);
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// hit test
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assertEquals(expHit1res1, hit1res1);
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// hsp test
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assertEquals(expHsp1hit1res1, hsp1hit1res1);
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}
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/**
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* Test of getFileExtensions method, of class BlastXMLQuery.
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*/
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@Test
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@Ignore public void testGetFileExtensions() {
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System.out.println("getFileExtensions");
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BlastXMLQuery instance = new BlastXMLQuery();
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List<String> expResult = null;
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List<String> result = instance.getFileExtensions();
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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 setQueryReferences method, of class BlastXMLQuery.
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*/
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@Test
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@Ignore public void testSetQueryReferences() {
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System.out.println("setQueryReferences");
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List sequences = null;
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BlastXMLQuery instance = new BlastXMLQuery();
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instance.setQueryReferences(sequences);
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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 setDatabaseReferences method, of class BlastXMLQuery.
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*/
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@Test
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@Ignore public void testSetDatabaseReferences() {
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System.out.println("setDatabaseReferences");
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List sequences = null;
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BlastXMLQuery instance = new BlastXMLQuery();
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instance.setDatabaseReferences(sequences);
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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 storeObjects method, of class BlastXMLQuery.
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*/
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@Test
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public void testStoreObjects() throws Exception {
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// not implemented yet
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}
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private File unpackResourceFile(String resource) {
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File file = null;
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URL res = getClass().getResource(resource);
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if (res == null) {
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throw new RuntimeException(" not supported");
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}
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if (res.toString().startsWith("jar:")) {
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try {
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InputStream input = getClass().getResourceAsStream(resource);
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file = File.createTempFile("javawrapped", ".exe");
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//if (!DEBUG) file.deleteOnExit();
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file.setExecutable(true, true);
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OutputStream out = new FileOutputStream(file);
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int read;
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byte[] bytes = new byte[1024];
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while ((read = input.read(bytes)) != -1) {
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out.write(bytes, 0, read);
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}
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out.close();
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out.flush();
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} catch (IOException ex) {
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throw new RuntimeException("Resource not available for this OS!");
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}
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} else {
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//this will probably work in your IDE, but not from a JAR
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file = new File(res.getFile());
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}
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if (file == null) {
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throw new RuntimeException("Error: File " + file + " not found!");
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}
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return file;
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}
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}

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