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josemduartejosemduarte
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Less verbose test
1 parent 16d483a commit d157100

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2 files changed

+17
-15
lines changed

2 files changed

+17
-15
lines changed

‎biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java‎

Lines changed: 16 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -33,19 +33,21 @@
3333

3434
public class CookBookTest {
3535

36+
// TODO this test doesn't assert anything, i.e. it is not a test! Should fix! - JD 2016-03-07
37+
3638
private final static Logger logger = LoggerFactory.getLogger(CookBookTest.class);
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3840
@Test
3941
public void shortExample1(){
4042
String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
41-
logger.info("Molecular Weight: {}", PeptideProperties.getMolecularWeight(sequence));
43+
logger.debug("Molecular Weight: {}", PeptideProperties.getMolecularWeight(sequence));
4244
}
4345

4446
@Test
4547
public void shortExample2() throws FileNotFoundException, JAXBException{
4648
String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
4749
File aminoAcidCompositionFile = new File("./src/main/resources/AminoAcidComposition.xml");
48-
logger.info("Molecular Weight: {}", PeptideProperties.getMolecularWeight(sequence, aminoAcidCompositionFile));
50+
logger.debug("Molecular Weight: {}", PeptideProperties.getMolecularWeight(sequence, aminoAcidCompositionFile));
4951
}
5052

5153
@Test
@@ -59,7 +61,7 @@ public void shortExample3() throws Exception{
5961
AminoAcidCompositionTable table = PeptideProperties.obtainAminoAcidCompositionTable(aminoAcidCompositionFile);
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6163
for(String sequence:sequences){
62-
logger.info("Molecular Weight: {}", PeptideProperties.getMolecularWeightBasedOnXML(sequence, table));
64+
logger.debug("Molecular Weight: {}", PeptideProperties.getMolecularWeightBasedOnXML(sequence, table));
6365
}
6466
}
6567

@@ -68,12 +70,12 @@ public void shortExample4(){
6870
String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
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//Enrichment of a specific amino acid type
71-
logger.info("Composition of A: {}", PeptideProperties.getEnrichment(sequence, "A"));
73+
logger.debug("Composition of A: {}", PeptideProperties.getEnrichment(sequence, "A"));
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7375
//Enrichment of a list of amino acid types
7476
Map<String, Double> composition = PeptideProperties.getAACompositionString(sequence);
7577
for(String aa:composition.keySet()){
76-
logger.info("Composition of {}: {}", aa, composition.get(aa));
78+
logger.debug("Composition of {}: {}", aa, composition.get(aa));
7779
}
7880
}
7981

@@ -83,26 +85,26 @@ public void shortExample5(){
8385
String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTRECMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
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//Absorbance
86-
logger.info("Absorbance (Cys Reduced): {}", PeptideProperties.getAbsorbance(sequence, true));
87-
logger.info("Absorbance (Cys Not Reduced): {}", PeptideProperties.getAbsorbance(sequence, false));
88+
logger.debug("Absorbance (Cys Reduced): {}", PeptideProperties.getAbsorbance(sequence, true));
89+
logger.debug("Absorbance (Cys Not Reduced): {}", PeptideProperties.getAbsorbance(sequence, false));
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8991
//Extinction Coefficient
90-
logger.info("Extinction Coefficient (Cys Reduced): {}", PeptideProperties.getExtinctionCoefficient(sequence, true));
91-
logger.info("Extinction Coefficient (Cys Not Reduced): {}", PeptideProperties.getExtinctionCoefficient(sequence, false));
92+
logger.debug("Extinction Coefficient (Cys Reduced): {}", PeptideProperties.getExtinctionCoefficient(sequence, true));
93+
logger.debug("Extinction Coefficient (Cys Not Reduced): {}", PeptideProperties.getExtinctionCoefficient(sequence, false));
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9395
//Instability Index
94-
logger.info("Instability Index: {}", PeptideProperties.getInstabilityIndex(sequence));
96+
logger.debug("Instability Index: {}", PeptideProperties.getInstabilityIndex(sequence));
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9698
//Apliphatic Index
97-
logger.info("Apliphatic Index: {}", PeptideProperties.getApliphaticIndex(sequence));
99+
logger.debug("Apliphatic Index: {}", PeptideProperties.getApliphaticIndex(sequence));
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99101
//Average Hydropathy Value
100-
logger.info("Average Hydropathy Value: {}", PeptideProperties.getAvgHydropathy(sequence));
102+
logger.debug("Average Hydropathy Value: {}", PeptideProperties.getAvgHydropathy(sequence));
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102104
//Isoelectric Point
103-
logger.info("Isoelectric Point: {}", PeptideProperties.getIsoelectricPoint(sequence));
105+
logger.debug("Isoelectric Point: {}", PeptideProperties.getIsoelectricPoint(sequence));
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105107
//Net Charge
106-
logger.info("Net Charge at pH 7: {}", PeptideProperties.getNetCharge(sequence));
108+
logger.debug("Net Charge at pH 7: {}", PeptideProperties.getNetCharge(sequence));
107109
}
108110
}

‎biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -152,8 +152,8 @@ public void testEnrichment() {
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153153
@Test (expected = NullPointerException.class)
154154
public void testEnrichmentNull(){
155-
assertNull(PeptideProperties.getEnrichment(sequence, "1"));
156155
assertEquals(0.0, PeptideProperties.getEnrichment(sequence, ""), delta);
156+
assertNull(PeptideProperties.getEnrichment(sequence, "1"));
157157
}
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159159
@Test

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