Examples with AnnotationProperty org.nextprot.api.core.domain.annotation.AnnotationProperty used on opensource projects

Example 6 with AnnotationProperty

use of org.nextprot.api.core.domain.annotation.AnnotationProperty in project nextprot-api by calipho-sib.

the class AnnotationUtilsUnconfirmedPE1Test method createPeptideMappingAnnot.

private Annotation createPeptideMappingAnnot(int id, String pepname, Integer p1, Integer p2, boolean proteotypic) {
    Annotation a = new Annotation();
    a.setAnnotationCategory(AnnotationCategory.PEPTIDE_MAPPING);
    a.setAnnotationId(id);
    AnnotationProperty p = new AnnotationProperty();
    p.setName("is proteotypic");
    p.setValue(proteotypic ? "Y" : "N");
    a.addProperty(p);
    if (pepname != null) {
        p = new AnnotationProperty();
        p.setName("peptide name");
        p.setValue(pepname);
        a.addProperty(p);
    }
    AnnotationIsoformSpecificity spec1 = new AnnotationIsoformSpecificity();
    spec1.setIsoformAccession("NX_P10000-1");
    spec1.setFirstPosition(p1);
    spec1.setLastPosition(p2);
    AnnotationIsoformSpecificity spec2 = new AnnotationIsoformSpecificity();
    spec2.setIsoformAccession("NX_P10000-2");
    spec2.setFirstPosition(p1 == null ? null : p1 + 10);
    spec2.setLastPosition(p2 == null ? null : p2 + 10);
    List<AnnotationIsoformSpecificity> specs = new ArrayList<>();
    specs.add(spec1);
    specs.add(spec2);
    a.addTargetingIsoforms(specs);
    return a;
}

Example 7 with AnnotationProperty

use of org.nextprot.api.core.domain.annotation.AnnotationProperty in project nextprot-api by calipho-sib.

the class AnnotationDAOImplTest method testSetMutationPropertyNameValue.

@Test
public void testSetMutationPropertyNameValue() throws Exception {
    AnnotationProperty property = new AnnotationProperty();
    AnnotationDAOImpl.setPropertyNameValue(property, "mutation AA", "p.R54C");
    Assert.assertNotEquals("p.R54C", property.getValue());
}

Example 8 with AnnotationProperty

use of org.nextprot.api.core.domain.annotation.AnnotationProperty in project nextprot-api by calipho-sib.

the class PepXServiceImpl method buildAnnotationProperty.

private static AnnotationProperty buildAnnotationProperty(String name, String value) {
    AnnotationProperty result = new AnnotationProperty();
    result.setName(name);
    result.setValue(value);
    return result;
}

Example 9 with AnnotationProperty

use of org.nextprot.api.core.domain.annotation.AnnotationProperty 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());
    }
}

Example 10 with AnnotationProperty

use of org.nextprot.api.core.domain.annotation.AnnotationProperty in project nextprot-api by calipho-sib.

the class AnnotationUtils method convertRelativeEvidenceToProperty.

private static List<AnnotationEvidence> convertRelativeEvidenceToProperty(Annotation annot, String propertyName) {
    List<AnnotationEvidence> toRemove = new ArrayList<>();
    for (AnnotationEvidence evi : annot.getEvidences()) {
        if ("relative".equals(evi.getResourceAssociationType())) {
            AnnotationProperty p = new AnnotationProperty();
            p.setAnnotationId(annot.getAnnotationId());
            p.setAccession(evi.getResourceAccession());
            p.setName(propertyName);
            p.setValue(Long.toString(evi.getResourceId()));
            p.setValueType(PropertyApiModel.VALUE_TYPE_RIF);
            annot.addProperties(Arrays.asList(p));
            toRemove.add(evi);
        }
    }
    return toRemove;
}