/**
* @param header
* @param fastaEntry
* @return
* @throws Exception
*/
@Override
public DetermineTaxonomyIdResult getTaxonomyId(
DetermineTaxonomyIdParams determineTaxonomyIdParams) throws Exception {
DetermineTaxonomyIdResult determineTaxonomyIdResult = new DetermineTaxonomyIdResult();
Integer taxonomyId = null;
// String headerName = header.getName();
// String headerDescription = header.getDescription();
String fullHeaderString = determineTaxonomyIdParams.getHeaderFullString();
if (fullHeaderString == null) {
} else {
Matcher gm = null;
// Check to see if they have header ending with "[species name]" (bracket species pattern).
// If so, use that name
gm = this.uniprotPattern3.matcher(fullHeaderString);
if (gm.matches()) {
String speciesName = gm.group(1);
// try the common names first
if (speciesName.equals("Escherichia coli K12")) taxonomyId = 83333;
else if (speciesName.equals("Escherichia coli")) taxonomyId = 562;
else if (speciesName.equals("Arabidopsis thaliana")) taxonomyId = 3702;
else if (speciesName.equals("Bos taurus")) taxonomyId = 9913;
else if (speciesName.equals("Caenorhabditis elegans")) taxonomyId = 6239;
else if (speciesName.equals("Chlamydomonas reinhardtii")) taxonomyId = 3055;
else if (speciesName.equals("Danio rerio")) taxonomyId = 7955;
else if (speciesName.equals("Dictyostelium discoideum")) taxonomyId = 44689;
else if (speciesName.equals("Drosophila melanogaster")) taxonomyId = 7227;
else if (speciesName.equals("Hepatitis C virus")) taxonomyId = 11103;
else if (speciesName.equals("H**o sapiens")) taxonomyId = 9606;
else if (speciesName.equals("Mus musculus")) taxonomyId = 10090;
else if (speciesName.equals("Mycoplasma pneumoniae")) taxonomyId = 2104;
else if (speciesName.equals("Oryza sativa")) taxonomyId = 4530;
else if (speciesName.equals("Plasmodium falciparum")) taxonomyId = 5833;
else if (speciesName.equals("Pneumocystis carinii")) taxonomyId = 4754;
else if (speciesName.equals("Rattus norvegicus")) taxonomyId = 10116;
else if (speciesName.equals("Saccharomyces cerevisiae")) taxonomyId = 4932;
else if (speciesName.equals("Schizosaccharomyces pombe")) taxonomyId = 4896;
else if (speciesName.equals("Takifugu rubripes")) taxonomyId = 31033;
else if (speciesName.equals("Xenopus laevis")) taxonomyId = 8355;
else if (speciesName.equals("Zea mays")) taxonomyId = 4577;
}
}
determineTaxonomyIdResult.setTaxonomyId(taxonomyId);
return determineTaxonomyIdResult;
}
/**
* @param header
* @param fastaEntry
* @return
* @throws Exception
*/
@Override
public DetermineTaxonomyIdResult getTaxonomyId(
DetermineTaxonomyIdParams determineTaxonomyIdParams) throws Exception {
DetermineTaxonomyIdResult determineTaxonomyIdResult = new DetermineTaxonomyIdResult();
Integer taxonomyId = null;
String fullHeaderString = determineTaxonomyIdParams.getHeaderFullString();
if (fullHeaderString == null) {
} else {
Matcher gm = null;
// Check to see if they have header ending with "[species name]" (bracket species pattern).
// If so, use that name
gm = this.bracketSpeciesPattern.matcher(fullHeaderString);
if (gm.matches()) {
String speciesName = gm.group(1);
try {
// try the common names first
if (speciesName.equals("Escherichia coli K12")) taxonomyId = 83333;
else if (speciesName.equals("Escherichia coli")) taxonomyId = 562;
else if (speciesName.equals("Arabidopsis thaliana")) taxonomyId = 3702;
else if (speciesName.equals("Bos taurus")) taxonomyId = 9913;
else if (speciesName.equals("Caenorhabditis elegans")) taxonomyId = 6239;
else if (speciesName.equals("Chlamydomonas reinhardtii")) taxonomyId = 3055;
else if (speciesName.equals("Danio rerio")) taxonomyId = 7955;
else if (speciesName.equals("Dictyostelium discoideum")) taxonomyId = 44689;
else if (speciesName.equals("Drosophila melanogaster")) taxonomyId = 7227;
else if (speciesName.equals("Hepatitis C virus")) taxonomyId = 11103;
else if (speciesName.equals("H**o sapiens")) taxonomyId = 9606;
else if (speciesName.equals("Mus musculus")) taxonomyId = 10090;
else if (speciesName.equals("Mycoplasma pneumoniae")) taxonomyId = 2104;
else if (speciesName.equals("Oryza sativa")) taxonomyId = 4530;
else if (speciesName.equals("Plasmodium falciparum")) taxonomyId = 5833;
else if (speciesName.equals("Pneumocystis carinii")) taxonomyId = 4754;
else if (speciesName.equals("Rattus norvegicus")) taxonomyId = 10116;
else if (speciesName.equals("Saccharomyces cerevisiae")) taxonomyId = 4932;
else if (speciesName.equals("Schizosaccharomyces pombe")) taxonomyId = 4896;
else if (speciesName.equals("Takifugu rubripes")) taxonomyId = 31033;
else if (speciesName.equals("Xenopus laevis")) taxonomyId = 8355;
else if (speciesName.equals("Zea mays")) taxonomyId = 4577;
else {
// having failed the common names, look it up in the database
int id = NCBITaxonomySearcher.getInstance().getSpeciesByName(speciesName);
if (id != 0) {
taxonomyId = id;
}
}
} catch (Exception e) {
// Never get this exception since the regex pattern only applies to digits after the "="
String msg =
"Error processing FASTA header that contains species name surrounded by '[]'."
+ " species name value (delim '|'): |"
+ speciesName
+ "|.";
// log.error( msg );
log.error(msg, e);
throw e;
}
}
}
determineTaxonomyIdResult.setTaxonomyId(taxonomyId);
return determineTaxonomyIdResult;
}
