Skip to content

Commit ed95b34

Browse files
lafitalafita
committed
Test all String output Writer methods of MultipleAlignment
1 parent c8fb22e commit ed95b34

File tree

14 files changed

+597
-61
lines changed

14 files changed

+597
-61
lines changed

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SelectMultiplePanel.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -58,7 +58,7 @@ public SelectMultiplePanel(boolean show2boxes){
5858

5959
Box vBox = Box.createVerticalBox();
6060

61-
input = new JTextField("4hhb.A 1hlb 1thb.A 1dlw");
61+
input = new JTextField("1mbc 1hlb 1dlw 1ith.A 1thb.A 1kr7.A_0-110");
6262
Box b = getDomainPanel(input);
6363
vBox.add(b);
6464

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -261,12 +261,12 @@ else if (move < 0.85){
261261
if (debug){
262262
System.out.println("Step: "+i+": --prob: "+prob+
263263
", --score: "+AS+", --conv: "+conv);
264-
}
265-
266-
if (i%100==1){
267-
lengthHistory.add(msa.length());
268-
rmsdHistory.add(MultipleAlignmentScorer.getRMSD(msa));
269-
scoreHistory.add(mcScore);
264+
265+
if (i%100==1){
266+
lengthHistory.add(msa.length());
267+
rmsdHistory.add(MultipleAlignmentScorer.getRMSD(msa));
268+
scoreHistory.add(mcScore);
269+
}
270270
}
271271

272272
i++;

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

Lines changed: 221 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,17 @@
11
package org.biojava.nbio.structure.align.multiple;
22

3+
import java.io.BufferedReader;
4+
import java.io.FileReader;
35
import java.io.IOException;
6+
47
import org.biojava.nbio.structure.StructureException;
58
import org.junit.Test;
69

710
import static org.junit.Assert.*;
811

912
/**
10-
* Test the correctness of various Text outputs for {@link MultipleAlignment}s.
11-
* <p>
13+
* Test the correctness of various Text outputs
14+
* for {@link MultipleAlignment}s.<p>
1215
* Currently tested:
1316
* <ul><li>FASTA
1417
* <li>FatCat format
@@ -21,49 +24,236 @@
2124
*
2225
*/
2326
public class TestMultipleAlignmentWriter {
24-
27+
28+
private MultipleAlignment alignment1;
29+
private MultipleAlignment alignment2;
30+
31+
/**
32+
* Build the alignments in common for every writer output,
33+
* so that they do not have to be created each time.
34+
* @throws IOException
35+
* @throws StructureException
36+
*/
37+
public TestMultipleAlignmentWriter()
38+
throws StructureException, IOException{
39+
40+
alignment1 = TestSampleGenerator.testAlignment1();
41+
alignment2 = TestSampleGenerator.testAlignment2();
42+
}
43+
2544
@Test
26-
public void testFASTA() throws StructureException, IOException{
27-
28-
MultipleAlignment alignment = TestSampleGenerator.testAlignment1();
29-
String result = MultipleAlignmentWriter.toFASTA(alignment);
30-
System.out.println(result);
31-
32-
StringBuffer expected = new StringBuffer();
33-
expected.append(">2gox\n");
34-
expected.append("---S-tDaErLkhl--IvTpSgAgeq----NmIgMtPt-viAv---"
35-
+ "HyL-dEt-eqWe\n");
36-
expected.append(">2gox\n");
37-
expected.append("GsrS-tDAeRLkh--LiVTpSGaGEqn---MiGMtPTviA-vh--Y"
38-
+ "lDE-tEqwE-Kf\n");
39-
expected.append(">2gox\n");
40-
expected.append("GS-rsTDaERLkhl-IvTPSgAGEqnmig--MTPtVIavH-Yld-ET"
41-
+ "EqwEKf-G-LE\n");
42-
43-
assertEquals(result,expected.toString());
45+
public void testFASTA1() throws IOException{
46+
47+
String result = MultipleAlignmentWriter.toFASTA(alignment1);
48+
49+
FileReader file = new FileReader(
50+
"src/test/resources/testMSTA1.fasta");
51+
BufferedReader reader = new BufferedReader(file);
52+
String line = null;
53+
StringBuilder stringBuilder = new StringBuilder();
54+
55+
while ((line = reader.readLine()) != null) {
56+
stringBuilder.append(line);
57+
stringBuilder.append("\n");
58+
}
59+
reader.close();
60+
61+
String expected = stringBuilder.toString();
62+
assertEquals(expected,result);
63+
}
64+
65+
@Test
66+
public void testFASTA2() throws IOException {
67+
68+
String result = MultipleAlignmentWriter.toFASTA(alignment2);
69+
70+
FileReader file = new FileReader(
71+
"src/test/resources/testMSTA2.fasta");
72+
BufferedReader reader = new BufferedReader(file);
73+
String line = null;
74+
StringBuilder stringBuilder = new StringBuilder();
75+
76+
while ((line = reader.readLine()) != null) {
77+
stringBuilder.append(line);
78+
stringBuilder.append("\n");
79+
}
80+
reader.close();
81+
82+
String expected = stringBuilder.toString();
83+
assertEquals(expected,result);
84+
}
85+
86+
@Test
87+
public void testFatCat1() throws IOException{
88+
89+
String result = MultipleAlignmentWriter.toFatCat(alignment1);
90+
91+
FileReader file = new FileReader(
92+
"src/test/resources/testMSTA1.fatcat");
93+
BufferedReader reader = new BufferedReader(file);
94+
String line = null;
95+
StringBuilder stringBuilder = new StringBuilder();
96+
97+
while ((line = reader.readLine()) != null) {
98+
stringBuilder.append(line);
99+
stringBuilder.append("\n");
100+
}
101+
reader.close();
102+
103+
String expected = stringBuilder.toString();
104+
assertEquals(expected,result);
44105
}
45106

46107
@Test
47-
public void testFatCat(){
48-
49-
108+
public void testFatCat2() throws IOException{
109+
110+
String result = MultipleAlignmentWriter.toFatCat(alignment2);
111+
112+
FileReader file = new FileReader(
113+
"src/test/resources/testMSTA2.fatcat");
114+
BufferedReader reader = new BufferedReader(file);
115+
String line = null;
116+
StringBuilder stringBuilder = new StringBuilder();
117+
118+
while ((line = reader.readLine()) != null) {
119+
stringBuilder.append(line);
120+
stringBuilder.append("\n");
121+
}
122+
reader.close();
123+
124+
String expected = stringBuilder.toString();
125+
assertEquals(expected,result);
126+
}
127+
128+
@Test
129+
public void testAlignedResidues1() throws IOException{
130+
131+
String result = MultipleAlignmentWriter.toAlignedResidues(alignment1);
132+
133+
FileReader file = new FileReader(
134+
"src/test/resources/testMSTA1_alnres.tsv");
135+
BufferedReader reader = new BufferedReader(file);
136+
String line = null;
137+
StringBuilder stringBuilder = new StringBuilder();
138+
139+
while ((line = reader.readLine()) != null) {
140+
stringBuilder.append(line);
141+
stringBuilder.append("\n");
142+
}
143+
reader.close();
144+
145+
String expected = stringBuilder.toString();
146+
assertEquals(expected,result);
50147
}
51148

52149
@Test
53-
public void testAlignedResidues(){
54-
150+
public void testAlignedResidues2() throws IOException{
151+
152+
String result = MultipleAlignmentWriter.toAlignedResidues(alignment2);
153+
154+
FileReader file = new FileReader(
155+
"src/test/resources/testMSTA2_alnres.tsv");
156+
BufferedReader reader = new BufferedReader(file);
157+
String line = null;
158+
StringBuilder stringBuilder = new StringBuilder();
159+
160+
while ((line = reader.readLine()) != null) {
161+
stringBuilder.append(line);
162+
stringBuilder.append("\n");
163+
}
164+
reader.close();
165+
166+
String expected = stringBuilder.toString();
167+
assertEquals(expected,result);
168+
}
169+
170+
@Test
171+
public void testTransformMatrices1() throws IOException{
55172

173+
String result = MultipleAlignmentWriter.
174+
toTransformMatrices(alignment1);
175+
176+
FileReader file = new FileReader(
177+
"src/test/resources/testMSTA1.transforms");
178+
BufferedReader reader = new BufferedReader(file);
179+
String line = null;
180+
StringBuilder stringBuilder = new StringBuilder();
181+
182+
while ((line = reader.readLine()) != null) {
183+
stringBuilder.append(line);
184+
stringBuilder.append("\n");
185+
}
186+
reader.close();
187+
188+
String expected = stringBuilder.toString();
189+
assertEquals(expected,result);
56190
}
57191

58192
@Test
59-
public void testTransformMatrices(){
60-
193+
public void testTransformMatrices2() throws IOException{
61194

195+
String result = MultipleAlignmentWriter.
196+
toTransformMatrices(alignment2);
197+
System.out.println(result);
198+
199+
FileReader file = new FileReader(
200+
"src/test/resources/testMSTA2.transforms");
201+
BufferedReader reader = new BufferedReader(file);
202+
String line = null;
203+
StringBuilder stringBuilder = new StringBuilder();
204+
205+
while ((line = reader.readLine()) != null) {
206+
stringBuilder.append(line);
207+
stringBuilder.append("\n");
208+
}
209+
reader.close();
210+
211+
String expected = stringBuilder.toString();
212+
assertEquals(expected,result);
213+
214+
}
215+
216+
@Test
217+
public void testXMLformat1() throws IOException{
218+
219+
MultipleAlignmentEnsemble ensemble = alignment1.getEnsemble();
220+
String result = MultipleAlignmentWriter.toXML(ensemble);
221+
222+
FileReader file = new FileReader(
223+
"src/test/resources/testMSTA1.xml");
224+
BufferedReader reader = new BufferedReader(file);
225+
String line = null;
226+
StringBuilder stringBuilder = new StringBuilder();
227+
228+
while ((line = reader.readLine()) != null) {
229+
stringBuilder.append(line);
230+
stringBuilder.append("\n");
231+
}
232+
reader.close();
233+
234+
String expected = stringBuilder.toString();
235+
assertEquals(expected,result);
62236
}
63237

64238
@Test
65-
public void testXMLformat(){
66-
67-
239+
public void testXMLformat2() throws IOException{
240+
241+
MultipleAlignmentEnsemble ensemble = alignment2.getEnsemble();
242+
String result = MultipleAlignmentWriter.toXML(ensemble);
243+
244+
FileReader file = new FileReader(
245+
"src/test/resources/testMSTA2.xml");
246+
BufferedReader reader = new BufferedReader(file);
247+
String line = null;
248+
StringBuilder stringBuilder = new StringBuilder();
249+
250+
while ((line = reader.readLine()) != null) {
251+
stringBuilder.append(line);
252+
stringBuilder.append("\n");
253+
}
254+
reader.close();
255+
256+
String expected = stringBuilder.toString();
257+
assertEquals(expected,result);
68258
}
69259
}

0 commit comments

Comments
 (0)