Examples with PeptideUnicityService org.nextprot.api.core.service.PeptideUnicityService used on opensource projects

Example 1 with PeptideUnicityService

use of org.nextprot.api.core.service.PeptideUnicityService in project nextprot-api by calipho-sib.

the class PepXServiceImpl method computePeptideUnicityStatus.

/**
 * Computes a unicity value for each peptide: UNIQUE, PSEUDO_UNIQUE, NON_UNIQUE
 * based on the response returned by pepx (a list of peptide - isoform matches)
 * by using the PeptideUnicityService
 * @param entries
 * @param withVariants
 * @return a map with key = peptide sequence, value = unicity value
 */
private Map<String, PeptideUnicity> computePeptideUnicityStatus(List<Entry> entries, boolean withVariants) {
    Map<String, Set<String>> pepIsoSetMap = new HashMap<>();
    entries.forEach(e -> {
        e.getAnnotationsByCategory(AnnotationCategory.PEPX_VIRTUAL_ANNOTATION).stream().filter(a -> a.getVariant() == null || withVariants).forEach(a -> {
            String pep = a.getCvTermName();
            if (!pepIsoSetMap.containsKey(pep))
                pepIsoSetMap.put(pep, new TreeSet<String>());
            a.getTargetingIsoformsMap().values().forEach(i -> {
                pepIsoSetMap.get(pep).add(i.getIsoformAccession());
            });
        });
    });
    Map<String, PeptideUnicity> pepUnicityMap = new HashMap<>();
    pepIsoSetMap.entrySet().forEach(e -> {
        String pep = e.getKey();
        PeptideUnicity pu = peptideUnicityService.getPeptideUnicityFromMappingIsoforms(e.getValue());
        pepUnicityMap.put(pep, pu);
    });
    return pepUnicityMap;
}