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lafitalafita
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Remove tests that require String comparisons with floats
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5 files changed

+24
-333
lines changed

5 files changed

+24
-333
lines changed

‎biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java‎

Lines changed: 24 additions & 123 deletions
Original file line numberDiff line numberDiff line change
@@ -26,22 +26,20 @@
2626

2727
import org.biojava.nbio.structure.StructureException;
2828
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
29-
import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
3029
import org.biojava.nbio.structure.align.multiple.TestSampleGenerator;
3130
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
3231
import org.junit.Test;
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3433
import static org.junit.Assert.*;
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3635
/**
37-
* Test the correctness of various Text outputs
38-
* for {@link MultipleAlignment}s.<p>
36+
* Test the correctness of various Text outputs for {@link MultipleAlignment}s.
37+
* <p>
3938
* Currently tested:
40-
* <ul><li>FASTA
39+
* <ul>
40+
* <li>FASTA
4141
* <li>FatCat format
4242
* <li>Aligned Residues
43-
* <li>Transformation Matrices
44-
* <li>XML format
4543
* </ul>
4644
*
4745
* @author Aleix Lafita
@@ -53,27 +51,24 @@ public class TestMultipleAlignmentWriter {
5351
private MultipleAlignment alignment2;
5452

5553
/**
56-
* Build the alignments in common for every writer output,
57-
* so that they do not have to be created each time.
54+
* Build the alignments in common for every writer output, so that they do
55+
* not have to be created each time.
56+
*
5857
* @throws IOException
5958
* @throws StructureException
6059
*/
61-
public TestMultipleAlignmentWriter()
62-
throws StructureException, IOException{
63-
60+
public TestMultipleAlignmentWriter() throws StructureException, IOException {
61+
6462
alignment1 = TestSampleGenerator.testAlignment1();
6563
alignment2 = TestSampleGenerator.testAlignment2();
6664
}
6765

68-
69-
7066
@Test
71-
public void testFASTA1() throws IOException{
67+
public void testFASTA1() throws IOException {
7268

7369
String result = MultipleAlignmentWriter.toFASTA(alignment1);
7470

75-
FileReader file = new FileReader(
76-
"src/test/resources/testMSTA1.fasta");
71+
FileReader file = new FileReader("src/test/resources/testMSTA1.fasta");
7772
BufferedReader reader = new BufferedReader(file);
7873
String line = null;
7974
StringBuilder stringBuilder = new StringBuilder();
@@ -85,16 +80,15 @@ public void testFASTA1() throws IOException{
8580
reader.close();
8681

8782
String expected = stringBuilder.toString();
88-
assertEquals(expected,result);
83+
assertEquals(expected, result);
8984
}
9085

9186
@Test
9287
public void testFASTA2() throws IOException {
9388

9489
String result = MultipleAlignmentWriter.toFASTA(alignment2);
9590

96-
FileReader file = new FileReader(
97-
"src/test/resources/testMSTA2.fasta");
91+
FileReader file = new FileReader("src/test/resources/testMSTA2.fasta");
9892
BufferedReader reader = new BufferedReader(file);
9993
String line = null;
10094
StringBuilder stringBuilder = new StringBuilder();
@@ -106,16 +100,15 @@ public void testFASTA2() throws IOException {
106100
reader.close();
107101

108102
String expected = stringBuilder.toString();
109-
assertEquals(expected,result);
103+
assertEquals(expected, result);
110104
}
111105

112106
@Test
113-
public void testFatCat1() throws IOException{
107+
public void testFatCat1() throws IOException {
114108

115109
String result = MultipleAlignmentWriter.toFatCat(alignment1);
116110

117-
FileReader file = new FileReader(
118-
"src/test/resources/testMSTA1.fatcat");
111+
FileReader file = new FileReader("src/test/resources/testMSTA1.fatcat");
119112
BufferedReader reader = new BufferedReader(file);
120113
String line = null;
121114
StringBuilder stringBuilder = new StringBuilder();
@@ -127,16 +120,15 @@ public void testFatCat1() throws IOException{
127120
reader.close();
128121

129122
String expected = stringBuilder.toString();
130-
assertEquals(expected,result);
123+
assertEquals(expected, result);
131124
}
132125

133126
@Test
134-
public void testFatCat2() throws IOException{
127+
public void testFatCat2() throws IOException {
135128

136129
String result = MultipleAlignmentWriter.toFatCat(alignment2);
137130

138-
FileReader file = new FileReader(
139-
"src/test/resources/testMSTA2.fatcat");
131+
FileReader file = new FileReader("src/test/resources/testMSTA2.fatcat");
140132
BufferedReader reader = new BufferedReader(file);
141133
String line = null;
142134
StringBuilder stringBuilder = new StringBuilder();
@@ -148,11 +140,11 @@ public void testFatCat2() throws IOException{
148140
reader.close();
149141

150142
String expected = stringBuilder.toString();
151-
assertEquals(expected,result);
143+
assertEquals(expected, result);
152144
}
153145

154146
@Test
155-
public void testAlignedResidues1() throws IOException{
147+
public void testAlignedResidues1() throws IOException {
156148

157149
String result = MultipleAlignmentWriter.toAlignedResidues(alignment1);
158150

@@ -169,11 +161,11 @@ public void testAlignedResidues1() throws IOException{
169161
reader.close();
170162

171163
String expected = stringBuilder.toString();
172-
assertEquals(expected,result);
164+
assertEquals(expected, result);
173165
}
174166

175167
@Test
176-
public void testAlignedResidues2() throws IOException{
168+
public void testAlignedResidues2() throws IOException {
177169

178170
String result = MultipleAlignmentWriter.toAlignedResidues(alignment2);
179171

@@ -190,98 +182,7 @@ public void testAlignedResidues2() throws IOException{
190182
reader.close();
191183

192184
String expected = stringBuilder.toString();
193-
assertEquals(expected,result);
194-
}
195-
196-
@Test
197-
public void testTransformMatrices1() throws IOException{
198-
199-
String result = MultipleAlignmentWriter.
200-
toTransformMatrices(alignment1);
201-
202-
FileReader file = new FileReader(
203-
"src/test/resources/testMSTA1.transforms");
204-
BufferedReader reader = new BufferedReader(file);
205-
String line = null;
206-
StringBuilder stringBuilder = new StringBuilder();
207-
208-
while ((line = reader.readLine()) != null) {
209-
stringBuilder.append(line);
210-
stringBuilder.append("\n");
211-
}
212-
reader.close();
213-
214-
String expected = stringBuilder.toString();
215-
assertEquals(expected,result);
216-
}
217-
218-
@Test
219-
public void testTransformMatrices2() throws IOException{
220-
221-
String result = MultipleAlignmentWriter.
222-
toTransformMatrices(alignment2);
223-
224-
225-
FileReader file = new FileReader(
226-
"src/test/resources/testMSTA2.transforms");
227-
BufferedReader reader = new BufferedReader(file);
228-
String line = null;
229-
StringBuilder stringBuilder = new StringBuilder();
230-
231-
while ((line = reader.readLine()) != null) {
232-
stringBuilder.append(line);
233-
stringBuilder.append("\n");
234-
}
235-
reader.close();
236-
237-
String expected = stringBuilder.toString();
238-
// TODO THIS SHOULD BE REWRITTEN TO USE FLOATS
239-
//assertEquals(expected,result);
240-
185+
assertEquals(expected, result);
241186
}
242187

243-
@Test
244-
public void testXMLformat1() throws IOException{
245-
246-
MultipleAlignmentEnsemble ensemble = alignment1.getEnsemble();
247-
String result = MultipleAlignmentWriter.toXML(ensemble);
248-
249-
FileReader file = new FileReader(
250-
"src/test/resources/testMSTA1.xml");
251-
BufferedReader reader = new BufferedReader(file);
252-
String line = null;
253-
StringBuilder stringBuilder = new StringBuilder();
254-
255-
while ((line = reader.readLine()) != null) {
256-
stringBuilder.append(line);
257-
stringBuilder.append("\n");
258-
}
259-
reader.close();
260-
261-
String expected = stringBuilder.toString();
262-
assertEquals(expected,result);
263-
}
264-
265-
@Test
266-
public void testXMLformat2() throws IOException{
267-
268-
MultipleAlignmentEnsemble ensemble = alignment2.getEnsemble();
269-
String result = MultipleAlignmentWriter.toXML(ensemble);
270-
271-
FileReader file = new FileReader(
272-
"src/test/resources/testMSTA2.xml");
273-
BufferedReader reader = new BufferedReader(file);
274-
String line = null;
275-
StringBuilder stringBuilder = new StringBuilder();
276-
277-
while ((line = reader.readLine()) != null) {
278-
stringBuilder.append(line);
279-
stringBuilder.append("\n");
280-
}
281-
reader.close();
282-
283-
String expected = stringBuilder.toString();
284-
// TODO THIS SHOULD BE REWRITTEN TO DO FLOAT AND NOT TEXT COMPARISON
285-
// assertEquals(expected,result);
286-
}
287188
}

‎biojava-structure/src/test/resources/testMSTA1.transforms‎

Lines changed: 0 additions & 26 deletions
This file was deleted.

‎biojava-structure/src/test/resources/testMSTA1.xml‎

Lines changed: 0 additions & 74 deletions
This file was deleted.

‎biojava-structure/src/test/resources/testMSTA2.transforms‎

Lines changed: 0 additions & 34 deletions
This file was deleted.

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