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remove GenericFastaHeaderParser main- duplicate of unit test
1 parent b83e1b8 commit c640463

2 files changed

Lines changed: 2 additions & 112 deletions

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‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java‎

Lines changed: 1 addition & 88 deletions
Original file line numberDiff line numberDiff line change
@@ -171,92 +171,5 @@ public void parseHeader(String header, S sequence) {
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}
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/**
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*
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* @param args
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*/
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public static void main(String[] args) {
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logger.info("parseHeader");
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String header = "";
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ProteinSequence sequence = null;
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try {
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sequence = new ProteinSequence("");
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} catch (CompoundNotFoundException e) {
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// this should not happen, in case it does we log error
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logger.error("Could not create empty protein sequence. Error: {}. This is most likely a bug.",e.getMessage());
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}
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GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound> instance =
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new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>();
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header = "gi|gi-number|gb|accession|locus";
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instance.parseHeader(header, sequence);
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logger.info("accession = {}", sequence.getAccession());
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logger.info("Data source: {} = {}", sequence.getAccession().getDataSource(), DataSource.GENBANK);
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header = "gi|gi-number|emb|accession|locus";
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instance.parseHeader(header, sequence);
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logger.info("accession = {}", sequence.getAccession());
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logger.info("Data source: {} = {}", sequence.getAccession().getDataSource(), DataSource.ENA);
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header = "gi|gi-number|dbj|accession|locus";
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instance.parseHeader(header, sequence);
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logger.info("accession = {}", sequence.getAccession());
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logger.info("Data source: {} = {}", sequence.getAccession().getDataSource(), DataSource.DDBJ);
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header = "pir||entry";
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instance.parseHeader(header, sequence);
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logger.info("entry = {}", sequence.getAccession());
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logger.info("Data source: {} = {}", sequence.getAccession().getDataSource(), DataSource.NBRF);
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header = "prf||name";
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instance.parseHeader(header, sequence);
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logger.info("name = {}", sequence.getAccession());
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logger.info("Data source: {}", sequence.getAccession().getDataSource(), DataSource.PRF);
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header = "sp|accession|name";
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instance.parseHeader(header, sequence);
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logger.info("accession = ", sequence.getAccession());
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logger.info("Data source: {} = {}", sequence.getAccession().getDataSource(), DataSource.UNIPROT);
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header = "pdb|entry|chain";
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instance.parseHeader(header, sequence);
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logger.info("entry:chain = ", sequence.getAccession());
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logger.info("Data source: {} = {}", sequence.getAccession().getDataSource(), DataSource.PDB1);
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header = "entry:chain|PDBID|CHAIN|SEQUENCE";
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instance.parseHeader(header, sequence);
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logger.info("entry:chain = {}", sequence.getAccession());
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logger.info("Data source: {} = {}", sequence.getAccession().getDataSource(), DataSource.PDB2);
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header = "PDB:1ECY_A mol:protein length:142 ECOTIN";
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instance.parseHeader(header, sequence);
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logger.info("1ECY_A = {}", sequence.getAccession());
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logger.info("Data source: {} = {}", sequence.getAccession().getDataSource(), DataSource.PDBe);
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header = "pat|country|number";
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instance.parseHeader(header, sequence);
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logger.info("number = {}", sequence.getAccession());
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logger.info("Data source: {}", sequence.getAccession().getDataSource(), DataSource.PATENTS);
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header = "bbs|number";
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instance.parseHeader(header, sequence);
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logger.info("number = {}", sequence.getAccession());
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logger.info("Data source: {} = {}", sequence.getAccession().getDataSource(), DataSource.GENINFO);
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header = "gnl|database|identifier";
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instance.parseHeader(header, sequence);
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logger.info("identifier = {}", sequence.getAccession());
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logger.info("Data source: {} = {}", sequence.getAccession().getDataSource(), DataSource.GENERAL);
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header = "ref|accession|locus";
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instance.parseHeader(header, sequence);
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logger.info("accession = {}", sequence.getAccession());
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logger.info("Data source: {} = {}", sequence.getAccession().getDataSource(), DataSource.NCBI);
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header = "lcl|identifier";
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instance.parseHeader(header, sequence);
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logger.info("identifier = {}", sequence.getAccession());
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logger.info("Data source: {} = {}", sequence.getAccession().getDataSource(), DataSource.LOCAL);
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}
174+
262175
}

‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java‎

Lines changed: 1 addition & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -36,27 +36,6 @@
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*/
3737
public class GenericFastaHeaderParserTest {
3838

39-
private final static Logger logger = LoggerFactory.getLogger(GenericFastaHeaderParserTest.class);
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public GenericFastaHeaderParserTest() {
42-
}
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@BeforeClass
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public static void setUpClass() throws Exception {
46-
}
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@AfterClass
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public static void tearDownClass() throws Exception {
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}
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@Before
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public void setUp() {
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}
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@After
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public void tearDown() {
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}
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6039
/**
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* GenBank gi|gi-number|gb|accession|locus
6241
* ENA Data Library gi|gi-number|emb|accession|locus
@@ -77,7 +56,6 @@ public void tearDown() {
7756
*/
7857
@Test
7958
public void testParseHeader() throws CompoundNotFoundException {
80-
logger.info("parseHeader");
8159
String header = "";
8260
ProteinSequence sequence = new ProteinSequence("");
8361
GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound> instance = new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>();
@@ -151,7 +129,6 @@ public void testParseHeader() throws CompoundNotFoundException {
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instance.parseHeader(header, sequence);
152130
assertEquals("identifier", sequence.getAccession().getID());
153131
assertEquals(sequence.getAccession().getDataSource(), DataSource.LOCAL);
154-
// TODO review the generated test code and remove the default call to fail.
155-
//fail("The test case is a prototype.");
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156133
}
157134
}

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