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paolopavanpaolopavan
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Further tests refinements.
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‎biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java‎

Lines changed: 125 additions & 114 deletions
Original file line numberDiff line numberDiff line change
@@ -1,114 +1,125 @@
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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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*/
6-
package org.biojava.nbio.core.search.io;
7-
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import org.biojava.nbio.alignment.template.SequencePair;
9-
import org.biojava.nbio.core.search.io.blast.BlastHspBuilder;
10-
import org.biojava.nbio.core.sequence.DNASequence;
11-
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
12-
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.*;
18-
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 {
25-
26-
Hsp hspImpl = new BlastHspBuilder()
27-
.setHspNum(1)
28-
.setHspBitScore(377.211)
29-
.setHspEvalue(8.04143e-093)
30-
.setHspQueryFrom(1)
31-
.setHspQueryTo(224)
32-
.setHspHitFrom(1035)
33-
.setHspHitTo(811)
34-
.setHspQueryFrame(-1)
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.setHspIdentity(213)
36-
.setHspPositive(213)
37-
.setHspGaps(5)
38-
.setHspAlignLen(227)
39-
.setHspQseq("CTGACGACAGCCATGCACCACCTGTCTCGACTTTCCCCCGAAGGGCACCTAATGTATCTCTACCTCGTTAGTCGGATGTCAAGACCTGGTAAGGTTTTTTCGCGTATCTTCGAATTAAACCACATACTCCACTGCTTGTGCGG-CCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGCCGTACTCCC-AGGTGGA-TACTTATTGTGTTAACTCCGGCACGGAAGG")
40-
.setHspHseq("CTGACGACAACCATGCACCACCTGTCTCAACTTTCCCC-GAAGGGCACCTAATGTATCTCTACTTCGTTAGTTGGATGTCAAGACCTGGTAAGGTT-CTTCGCGTTGCTTCGAATTAAACCACATACTCCACTGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGTGGATTACTTATTGTGTTAACTCCGGCACAGAAGG")
41-
.setHspIdentityString("||||||||| |||||||||||||||||| ||||||||| |||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||||| |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| ||||||||| ||||||| |||||||||||||||||||||||| |||||")
42-
.createBlastHsp();
43-
44-
public HspTest() {
45-
}
46-
47-
@BeforeClass
48-
public static void setUpClass() {
49-
}
50-
51-
@AfterClass
52-
public static void tearDownClass() {
53-
}
54-
55-
@Before
56-
public void setUp() {
57-
}
58-
59-
@After
60-
public void tearDown() {
61-
}
62-
63-
/**
64-
* Test of hashCode method, of class Hsp.
65-
*/
66-
@Test
67-
@Ignore public void testHashCode() {
68-
System.out.println("hashCode");
69-
Hsp instance = null;
70-
int expResult = 0;
71-
int result = instance.hashCode();
72-
assertEquals(expResult, result);
73-
// TODO review the generated test code and remove the default call to fail.
74-
fail("The test case is a prototype.");
75-
}
76-
77-
/**
78-
* Test of equals method, of class Hsp.
79-
*/
80-
@Test
81-
@Ignore public void testEquals() {
82-
System.out.println("equals");
83-
Object o = null;
84-
Hsp instance = null;
85-
boolean expResult = false;
86-
boolean result = instance.equals(o);
87-
assertEquals(expResult, result);
88-
// TODO review the generated test code and remove the default call to fail.
89-
fail("The test case is a prototype.");
90-
}
91-
92-
/**
93-
* Test of getAlignment method, of class Hsp.
94-
*/
95-
@Test
96-
public void testGetAlignment() {
97-
System.out.println("getAlignment");
98-
99-
SequencePair<DNASequence, NucleotideCompound> aln = hspImpl.getAlignment();
100-
101-
StringBuilder s = new StringBuilder();
102-
s.append(hspImpl.getHspQseq());
103-
s.append(String.format("%n"));
104-
s.append(hspImpl.getHspHseq());
105-
s.append(String.format("%n"));
106-
107-
String expResult = s.toString();
108-
109-
String result = aln.toString();
110-
111-
assertEquals(expResult, result);
112-
}
113-
114-
}
1+
/*
2+
* To change this license header, choose License Headers in Project Properties.
3+
* To change this template file, choose Tools | Templates
4+
* and open the template in the editor.
5+
*/
6+
package org.biojava.nbio.core.search.io;
7+
8+
import org.biojava.nbio.alignment.template.SequencePair;
9+
import org.biojava.nbio.core.search.io.blast.BlastHspBuilder;
10+
import org.biojava.nbio.core.sequence.DNASequence;
11+
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
12+
import org.junit.After;
13+
import org.junit.AfterClass;
14+
import org.junit.Before;
15+
import org.junit.BeforeClass;
16+
import org.junit.Test;
17+
import static org.junit.Assert.*;
18+
import org.junit.Ignore;
19+
20+
/**
21+
*
22+
* @author pavanpa
23+
*/
24+
public class HspTest {
25+
26+
Hsp hspImpl = new BlastHspBuilder()
27+
.setHspNum(1)
28+
.setHspBitScore(377.211)
29+
.setHspEvalue(8.04143e-093)
30+
.setHspQueryFrom(1)
31+
.setHspQueryTo(224)
32+
.setHspHitFrom(1035)
33+
.setHspHitTo(811)
34+
.setHspQueryFrame(-1)
35+
.setHspIdentity(213)
36+
.setHspPositive(213)
37+
.setHspGaps(5)
38+
.setHspAlignLen(227)
39+
.setHspQseq("CTGACGACAGCCATGCACCACCTGTCTCGACTTTCCCCCGAAGGGCACCTAATGTATCTCTACCTCGTTAGTCGGATGTCAAGACCTGGTAAGGTTTTTTCGCGTATCTTCGAATTAAACCACATACTCCACTGCTTGTGCGG-CCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGCCGTACTCCC-AGGTGGA-TACTTATTGTGTTAACTCCGGCACGGAAGG")
40+
.setHspHseq("CTGACGACAACCATGCACCACCTGTCTCAACTTTCCCC-GAAGGGCACCTAATGTATCTCTACTTCGTTAGTTGGATGTCAAGACCTGGTAAGGTT-CTTCGCGTTGCTTCGAATTAAACCACATACTCCACTGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGTGGATTACTTATTGTGTTAACTCCGGCACAGAAGG")
41+
.setHspIdentityString("||||||||| |||||||||||||||||| ||||||||| |||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||||| |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| ||||||||| ||||||| |||||||||||||||||||||||| |||||")
42+
.createBlastHsp();
43+
44+
public HspTest() {
45+
}
46+
47+
@BeforeClass
48+
public static void setUpClass() {
49+
}
50+
51+
@AfterClass
52+
public static void tearDownClass() {
53+
}
54+
55+
@Before
56+
public void setUp() {
57+
}
58+
59+
@After
60+
public void tearDown() {
61+
}
62+
63+
/**
64+
* Test of hashCode method, of class Hsp.
65+
*/
66+
@Test
67+
public void testHashCode() {
68+
System.out.println("hashCode");
69+
Hsp instance = hspImpl;
70+
int expResult = 879126434;
71+
int result = instance.hashCode();
72+
assertEquals(expResult, result);
73+
}
74+
75+
/**
76+
* Test of equals method, of class Hsp.
77+
*/
78+
@Test
79+
public void testEquals() {
80+
System.out.println("equals");
81+
Object o = new BlastHspBuilder()
82+
.setHspNum(1)
83+
.setHspBitScore(377.211)
84+
.setHspEvalue(8.04143e-093)
85+
.setHspQueryFrom(1)
86+
.setHspQueryTo(224)
87+
.setHspHitFrom(1035)
88+
.setHspHitTo(811)
89+
.setHspQueryFrame(-1)
90+
.setHspIdentity(213)
91+
.setHspPositive(213)
92+
.setHspGaps(5)
93+
.setHspAlignLen(227)
94+
.setHspQseq("CTGACGACAGCCATGCACCACCTGTCTCGACTTTCCCCCGAAGGGCACCTAATGTATCTCTACCTCGTTAGTCGGATGTCAAGACCTGGTAAGGTTTTTTCGCGTATCTTCGAATTAAACCACATACTCCACTGCTTGTGCGG-CCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGCCGTACTCCC-AGGTGGA-TACTTATTGTGTTAACTCCGGCACGGAAGG")
95+
.setHspHseq("CTGACGACAACCATGCACCACCTGTCTCAACTTTCCCC-GAAGGGCACCTAATGTATCTCTACTTCGTTAGTTGGATGTCAAGACCTGGTAAGGTT-CTTCGCGTTGCTTCGAATTAAACCACATACTCCACTGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGTGGATTACTTATTGTGTTAACTCCGGCACAGAAGG")
96+
.setHspIdentityString("||||||||| |||||||||||||||||| ||||||||| |||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||||| |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| ||||||||| ||||||| |||||||||||||||||||||||| |||||")
97+
.createBlastHsp();
98+
Hsp instance = hspImpl;
99+
100+
assertEquals(o, instance);
101+
}
102+
103+
/**
104+
* Test of getAlignment method, of class Hsp.
105+
*/
106+
@Test
107+
public void testGetAlignment() {
108+
System.out.println("getAlignment");
109+
110+
SequencePair<DNASequence, NucleotideCompound> aln = hspImpl.getAlignment();
111+
112+
StringBuilder s = new StringBuilder();
113+
s.append(hspImpl.getHspQseq());
114+
s.append(String.format("%n"));
115+
s.append(hspImpl.getHspHseq());
116+
s.append(String.format("%n"));
117+
118+
String expResult = s.toString();
119+
120+
String result = aln.toString();
121+
122+
assertEquals(expResult, result);
123+
}
124+
125+
}

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

Lines changed: 6 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -51,11 +51,13 @@ public void tearDown() {
5151
public void testGetFileExtensions() {
5252
System.out.println("getFileExtensions");
5353
BlastTabularParser instance = new BlastTabularParser();
54-
List<String> expResult = null;
54+
55+
List<String> expResult = new ArrayList();
56+
expResult.add("blasttabular");
57+
expResult.add("blasttxt");
58+
5559
List<String> result = instance.getFileExtensions();
5660
assertEquals(expResult, result);
57-
// TODO review the generated test code and remove the default call to fail.
58-
fail("The test case is a prototype.");
5961
}
6062

6163
/**
@@ -67,8 +69,6 @@ public void testSetFile() {
6769
File f = null;
6870
BlastTabularParser instance = new BlastTabularParser();
6971
instance.setFile(f);
70-
// TODO review the generated test code and remove the default call to fail.
71-
fail("The test case is a prototype.");
7272
}
7373

7474
/**
@@ -167,17 +167,6 @@ public void testCreateObjects() throws Exception {
167167
assertEquals(expHsp1hit1res1, hsp1Hit1Res1);
168168
}
169169

170-
/**
171-
* Test of storeObjects method, of class BlastTabularParser.
172-
*/
173-
@Test
174-
public void testStoreObjects() throws Exception {
175-
System.out.println("storeObjects");
176-
List<Result> results = null;
177-
BlastTabularParser instance = new BlastTabularParser();
178-
instance.storeObjects(results);
179-
// TODO review the generated test code and remove the default call to fail.
180-
fail("The test case is a prototype.");
181-
}
170+
182171

183172
}

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

Lines changed: 2 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -131,14 +131,11 @@ public void testCreateObjects() throws Exception {
131131
* Test of getFileExtensions method, of class BlastXMLQuery.
132132
*/
133133
@Test
134-
@Ignore public void testGetFileExtensions() {
134+
public void testGetFileExtensions() {
135135
System.out.println("getFileExtensions");
136136
BlastXMLQuery instance = new BlastXMLQuery();
137-
List<String> expResult = null;
138137
List<String> result = instance.getFileExtensions();
139-
assertEquals(expResult, result);
140-
// TODO review the generated test code and remove the default call to fail.
141-
fail("The test case is a prototype.");
138+
assertTrue(result.contains("blastxml"));
142139
}
143140

144141
/**

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