@Test
public void testSmallFasta() {
try {
InputStream inStream = this.getClass().getResourceAsStream("/test.fasta");
FastaReader<ProteinSequence, AminoAcidCompound> fastaReader =
new FastaReader<ProteinSequence, AminoAcidCompound>(
inStream,
new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
LinkedHashMap<String, ProteinSequence> b;
int nrSeq = 0;
while ((b = fastaReader.process(10)) != null) {
for (String key : b.keySet()) {
nrSeq++;
// #282 would result in an endless loop
// this makes sure it has been fixed.
assertTrue(
"Looks like there is a problem with termination of processing of the FASTA file!",
nrSeq < 15);
}
}
} catch (Exception ex) {
ex.printStackTrace();
java.util.logging.Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, null, ex);
fail(ex.getMessage());
}
}
@Test
public void testSmallFasta2() {
try {
InputStream inStream = this.getClass().getResourceAsStream("/test.fasta");
FastaReader<ProteinSequence, AminoAcidCompound> fastaReader =
new FastaReader<ProteinSequence, AminoAcidCompound>(
inStream,
new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
int nrSeq = 0;
LinkedHashMap<String, ProteinSequence> b = fastaReader.process();
assertNotNull(b);
// #282 make sure that process() still works
assertTrue(b.keySet().size() == 10);
} catch (Exception ex) {
ex.printStackTrace();
java.util.logging.Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, null, ex);
fail(ex.getMessage());
}
}
@Before
public void setUp() {
if (!Boolean.parseBoolean(System.getProperty("test.solr.verbose"))) {
java.util.logging.Logger.getLogger("org.apache.solr")
.setLevel(java.util.logging.Level.SEVERE);
Utils.setLog4jLogLevel(org.apache.log4j.Level.WARN);
}
testDataParentPath = System.getProperty("test.data.path");
testConfigFname = System.getProperty("test.config.file");
// System.out.println("-----testDataParentPath = "+testDataParentPath);
}