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Example 1 with EntryReportStats

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

the class EntryGeneReportServiceImpl method reportEntry.

@Cacheable("entry-reports")
@Override
public List<EntryReport> reportEntry(String entryAccession) {
    EntryReportStats ers = entryReportStatsService.reportEntryStats(entryAccession);
    EntryReport report = new EntryReport();
    report.setAccession(entryAccession);
    report.setDescription(ers.getDescription());
    report.setProteinExistence(ers.getProteinExistence());
    report.setPropertyTest(EntryReport.IS_PROTEOMICS, ers.isProteomics());
    report.setPropertyTest(EntryReport.IS_ANTIBODY, ers.isAntibody());
    report.setPropertyTest(EntryReport.IS_3D, ers.is3D());
    report.setPropertyTest(EntryReport.IS_DISEASE, ers.isDisease());
    report.setPropertyCount(EntryReport.ISOFORM_COUNT, ers.countIsoforms());
    report.setPropertyCount(EntryReport.VARIANT_COUNT, ers.countVariants());
    report.setPropertyCount(EntryReport.PTM_COUNT, ers.countPTMs());
    report.setPropertyCount(EntryReport.CURATED_PUBLICATION_COUNT, ers.countCuratedPublications());
    report.setPropertyCount(EntryReport.ADDITIONAL_PUBLICATION_COUNT, ers.countAdditionalPublications());
    report.setPropertyCount(EntryReport.PATENT_COUNT, ers.countPatents());
    report.setPropertyCount(EntryReport.SUBMISSION_COUNT, ers.countSubmissions());
    report.setPropertyCount(EntryReport.WEB_RESOURCE_COUNT, ers.countWebResources());
    return duplicateReportForEachGene(entryAccession, report);
}
Also used : EntryReport(org.nextprot.api.core.domain.EntryReport) EntryReportStats(org.nextprot.api.core.domain.EntryReportStats) Cacheable(org.springframework.cache.annotation.Cacheable)

Example 2 with EntryReportStats

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

the class FilterAndPropertiesFieldsBuilder method init.

@Override
protected void init(Entry entry) {
    EntryReportStats ers = entryReportStatsService.reportEntryStats(entry.getUniqueName());
    // Filters and entry properties
    EntryProperties props = entry.getProperties();
    addField(Fields.ISOFORM_NUM, ers.countIsoforms());
    int cnt;
    cnt = ers.countPTMs();
    if (cnt > 0) {
        addField(Fields.PTM_NUM, cnt);
    }
    cnt = ers.countVariants();
    if (cnt > 0) {
        addField(Fields.VAR_NUM, cnt);
    }
    String filters = "";
    if (props.getFilterstructure())
        filters += "filterstructure ";
    if (props.getFilterdisease())
        filters += "filterdisease ";
    if (props.getFilterexpressionprofile())
        filters += "filterexpressionprofile ";
    if (props.getFiltermutagenesis())
        filters += "filtermutagenesis ";
    if (props.getFilterproteomics())
        filters += "filterproteomics ";
    if (filters.length() > 0) {
        addField(Fields.FILTERS, filters.trim());
    }
    // max length among all isoforms
    addField(Fields.AA_LENGTH, props.getMaxSeqLen());
}
Also used : EntryProperties(org.nextprot.api.core.domain.EntryProperties) EntryReportStats(org.nextprot.api.core.domain.EntryReportStats)

Aggregations

EntryReportStats (org.nextprot.api.core.domain.EntryReportStats)2 EntryProperties (org.nextprot.api.core.domain.EntryProperties)1 EntryReport (org.nextprot.api.core.domain.EntryReport)1 Cacheable (org.springframework.cache.annotation.Cacheable)1