use of org.nextprot.api.commons.constants.AnnotationCategory in project nextprot-api by calipho-sib.
the class RawStatementDaoTest method findModificationEffectCategory.
@Test
public void findModificationEffectCategory() {
AnnotationCategory category = AnnotationCategory.PHENOTYPIC_VARIATION;
Annotation isoAnnotation = new Annotation();
isoAnnotation.setAnnotationCategory(category);
assertEquals(isoAnnotation.getCategory(), "phenotypic-variation");
}
use of org.nextprot.api.commons.constants.AnnotationCategory in project nextprot-api by calipho-sib.
the class AnnotationServiceImpl method bioPhyChemPropsToAnnotationList.
private List<Annotation> bioPhyChemPropsToAnnotationList(String entryName, List<AnnotationProperty> props) {
List<Annotation> annotations = new ArrayList<>(props.size());
List<Isoform> isoforms = isoformService.findIsoformsByEntryName(entryName);
for (AnnotationProperty property : props) {
Annotation annotation = new Annotation();
AnnotationCategory model = AnnotationCategory.getByDbAnnotationTypeName(property.getName());
String description = property.getValue();
annotation.setAnnotationId(property.getAnnotationId() + IdentifierOffset.BIOPHYSICOCHEMICAL_ANNOTATION_OFFSET);
annotation.setCategory(model.getDbAnnotationTypeName());
annotation.setDescription(description);
annotation.setEvidences(new ArrayList<>());
annotation.setQualityQualifier("GOLD");
annotation.setUniqueName(entryName + "_" + model.getApiTypeName());
annotation.addTargetingIsoforms(newAnnotationIsoformSpecificityList(annotation.getAnnotationId(), isoforms));
annotations.add(annotation);
}
return annotations;
}
use of org.nextprot.api.commons.constants.AnnotationCategory in project nextprot-api by calipho-sib.
the class AnnotationFieldBuilder method init.
@Override
protected void init(Entry entry) {
// Function with canonical first
List<String> function_canonical = EntryUtils.getFunctionInfoWithCanonicalFirst(entry);
for (String finfo : function_canonical) {
addField(Fields.FUNCTION_DESC, finfo);
addField(Fields.ANNOTATIONS, finfo);
}
List<Annotation> annots = entry.getAnnotations();
for (Annotation currannot : annots) {
String category = currannot.getCategory();
AnnotationCategory apiCategory = currannot.getAPICategory();
String quality = currannot.getQualityQualifier();
if (apiCategory.equals(AnnotationCategory.FUNCTION_INFO) || apiCategory.equals(AnnotationCategory.EXPRESSION_PROFILE))
// and tissue specificity values are indexed under other fields
continue;
// We also should exclude uninformative category 'sequence conflict'
// if(!category.equals("tissue specificity")) {//These values are
// indexed under other fields
// if(!apiCategory.equals(AnnotationCategory.) {//These values are
// indexed under other fields
String desc = currannot.getDescription();
if (apiCategory.equals(AnnotationCategory.GLYCOSYLATION_SITE)) {
String xref = currannot.getSynonym();
if (xref != null)
// It is actually not a synonym but the carbohydrate id from
// glycosuitedb !
addField(Fields.ANNOTATIONS, xref);
} else if (apiCategory.equals(AnnotationCategory.DNA_BINDING_REGION))
addField(Fields.ANNOTATIONS, category);
else if (apiCategory.equals(AnnotationCategory.VARIANT))
// We need to index them somehow for the GOLD/SILVER tests, or
// do we ? in creates a lot of useless 'variant null' tokens
desc = "Variant " + desc;
if (desc != null) {
// System.err.println(category + ": " + desc);
if (apiCategory.equals(AnnotationCategory.SEQUENCE_CAUTION)) {
int stringpos = 0;
// The sequence
desc = desc.split(":")[1].substring(1);
// AAH70170 differs
// from that shown.
// Reason:
// miscellaneous
// discrepancy
String[] desclevels = desc.split("\\.");
String mainreason = desclevels[0];
if ((stringpos = mainreason.indexOf(" at position")) != -1) {
// truncate the position
mainreason = mainreason.substring(0, stringpos);
}
addField(Fields.ANNOTATIONS, mainreason);
if (desclevels.length > 1) {
if (// mainreason truncated
stringpos > 0)
desc = desc.substring(desc.indexOf(".") + 2);
else {
stringpos = desc.indexOf(mainreason) + mainreason.length();
desc = desc.substring(stringpos + 2);
}
addField(Fields.ANNOTATIONS, desc);
}
}
if (!category.startsWith("go") && desc.length() > 1) {
// description
if (!this.isGold() || quality.equals("GOLD")) {
if (apiCategory.equals(AnnotationCategory.PHENOTYPIC_VARIATION)) {
// Get BED data (also get the notes ? )
Map<String, AnnotationIsoformSpecificity> annotSpecs = currannot.getTargetingIsoformsMap();
for (Map.Entry<String, AnnotationIsoformSpecificity> mapentry : annotSpecs.entrySet()) {
String subjectName = mapentry.getValue().getName();
// update description with the subject for each
// target isofotm
addField(Fields.ANNOTATIONS, subjectName + " " + desc);
// System.err.println("adding: " + subjectName +
// " " + desc);
}
} else
addField(Fields.ANNOTATIONS, desc);
}
}
// in pathway and disease new annotations may appear due to
// transformation of specific xrefs (orphanet...) into
// annotations in the api
}
handleAnnotationTerm(currannot, entry);
if (apiCategory.equals(AnnotationCategory.MATURE_PROTEIN) || apiCategory.equals(AnnotationCategory.MATURATION_PEPTIDE)) {
String chainid = currannot.getSynonym();
if (chainid != null) {
// " synonyms: " + currannot.getAllSynonyms());
if (chainid.contains("-"))
// Uniprot FT id,
addField(Fields.ANNOTATIONS, chainid);
else // like
// PRO_0000019235,
// shouldn't be
// called a
// synonym
{
List<String> chainsynonyms = currannot.getSynonyms();
if (chainsynonyms.size() == 1)
addField(Fields.ANNOTATIONS, StringUtils.getSortedValueFromPipeSeparatedField(desc + " | " + chainid));
else {
chainid = "";
for (String syno : chainsynonyms) {
chainid += syno + " | ";
}
addField(Fields.ANNOTATIONS, StringUtils.getSortedValueFromPipeSeparatedField(chainid));
}
}
}
// else System.err.println("chainid null for: " + desc);
// chainid 's null for the main chain, this is wrong
}
// variant xrefs and identifiers
if (apiCategory.equals(AnnotationCategory.VARIANT)) {
String evidxrefaccs = "";
List<AnnotationEvidence> evidences = currannot.getEvidences();
if (evidences != null)
for (AnnotationEvidence ev : evidences) {
if (ev.isResourceAXref()) {
String db = ev.getResourceDb();
if (db == null)
System.err.println("db is null for evidence in variant annot: " + desc);
else {
if (!evidxrefaccs.isEmpty())
evidxrefaccs += " | ";
if (db.equals("Cosmic"))
evidxrefaccs += db.toLowerCase() + ":" + ev.getResourceAccession();
else if (// Just to allow
db.equals("dbSNP"))
// comparison with
// incoherent
// current solr
// implementation
evidxrefaccs += ev.getResourceAccession();
else
// Uniprot
evidxrefaccs += currannot.getSynonym();
// FT
// id,
// like
// VAR_056577
}
}
}
if (!this.isGold() || quality.equals("GOLD")) {
if (!evidxrefaccs.isEmpty())
addField(Fields.ANNOTATIONS, StringUtils.getSortedValueFromPipeSeparatedField(evidxrefaccs));
Collection<AnnotationProperty> props = currannot.getProperties();
for (AnnotationProperty prop : props) if (prop.getName().equals("mutation AA"))
// eg: p.D1685E, it is unclear why this property
// exists only in cosmic variants
addField(Fields.ANNOTATIONS, prop.getValue());
}
}
}
// Families (why not part of Annotations ?), always GOLD
for (Family family : entry.getOverview().getFamilies()) {
String ac = family.getAccession();
int stringpos = 0;
addField(Fields.ANNOTATIONS, ac);
String famdesc = family.getDescription();
// There is no get_synonyms() method for families -> can't access
// PERVR for FA-04785
addField(Fields.ANNOTATIONS, famdesc);
stringpos = famdesc.indexOf("elongs to ") + 14;
// Skip the 'Belongs to' and
famdesc = famdesc.substring(stringpos);
// what may come before (eg:
// NX_P19021)
// remove
famdesc = famdesc.substring(0, famdesc.length() - 1);
// final dot
addField(Fields.ANNOTATIONS, famdesc);
// are there subfamilies
String[] families = famdesc.split("\\. ");
// ?
if (families.length > 1) {
// Always GOLD
for (int i = 0; i < families.length; i++) {
addField(Fields.ANNOTATIONS, families[i]);
if (families[i].contains(") superfamily")) {
// index one
// more time
// without
// parenthesis
famdesc = families[i].substring(0, families[i].indexOf("(")) + "superfamily";
addField(Fields.ANNOTATIONS, famdesc);
}
}
}
// Sonetimes these synonymes are wrong eg: NX_Q6NUT3 -> Major
// facilitator (TC 2.A.1) superfamily
List<String> famsynonyms = this.terminologyservice.findCvTermByAccession(ac).getSynonyms();
if (famsynonyms != null)
for (String famsynonym : famsynonyms) addField(Fields.ANNOTATIONS, famsynonym.trim());
}
}
use of org.nextprot.api.commons.constants.AnnotationCategory in project nextprot-api by calipho-sib.
the class SchemaDaoImpl method findAllAnnotation.
@Override
public List<OWLAnnotation> findAllAnnotation() {
// get description for annotations that exist in db
AnnotationCategory[] cats = AnnotationCategory.values();
List<Long> typeIds = new ArrayList<Long>();
for (AnnotationCategory cat : cats) typeIds.add(new Long(cat.getDbId()));
SqlParameterSource params = new MapSqlParameterSource("typeIds", typeIds);
List<NameDescr> nds = new NamedParameterJdbcTemplate(dsLocator.getDataSource()).query(sqlDictionary.getSQLQuery("schema-instantiated-annotation-list"), params, new ParameterizedRowMapper<NameDescr>() {
@Override
public NameDescr mapRow(ResultSet rs, int row) throws SQLException {
NameDescr nd = new NameDescr(rs.getString("cv_name"), rs.getString("description"));
// System.out.println("rs.cv_name=" + nd.name + " description="+ nd.descr);
return nd;
}
});
// inject descriptions found in db into the OWLAnnotationCategory enum values
for (NameDescr nd : nds) {
AnnotationCategory m = AnnotationCategory.getByDbAnnotationTypeName(nd.name);
// System.out.println("before descr: " + m.toString());
m.setDescription(nd.descr);
// System.out.println("after descr: " + m.toString());
// AnnotationCategory.getByDbAnnotationTypeName(nd.name).setDescription(nd.descr);
}
// encapsulate OWLAnnotationCategory into OWLAnnotation to be compatible with the rest
List<OWLAnnotation> annotations = new ArrayList<OWLAnnotation>();
for (AnnotationCategory cat : AnnotationCategory.values()) {
annotations.add(new OWLAnnotation(cat));
}
return annotations;
}
use of org.nextprot.api.commons.constants.AnnotationCategory in project nextprot-api by calipho-sib.
the class SequenceFeatureBase method newFeature.
public static SequenceFeature newFeature(SingleFeatureQuery query) throws FeatureQueryException {
// throw exception if invalid query
query.checkFeatureQuery();
AnnotationCategory annotationCategory = AnnotationCategory.getDecamelizedAnnotationTypeName(query.getFeatureType());
try {
switch(annotationCategory) {
case MUTAGENESIS:
case VARIANT:
return new SequenceVariant(query.getFeature());
case GENERIC_PTM:
return new SequenceModification(query.getFeature());
default:
throw new InvalidFeatureQueryTypeException(query);
}
} catch (ParseException e) {
throw new InvalidFeatureQueryFormatException(query, e);
}
}
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