Example usage for org.apache.commons.collections.keyvalue MultiKey MultiKey

Introduction

In this page you can find the example usage for org.apache.commons.collections.keyvalue MultiKey MultiKey.

Prototype

public MultiKey(Object[] keys, boolean makeClone) 

Source Link

Document

Constructor taking an array of keys, optionally choosing whether to clone.

Usage

From source file:org.intermine.bio.dataconversion.IdResolver.java

/**
 * For the given id return a set of matching primary identifiers in the given
 * taxonId.  In many cases the set will have just one element. Some will have
 * zero element.// w w  w .  j  a  v  a 2 s  .c  o  m
 * @param taxonId the organism to search within
 * @param clsName go term
 * @param id the identifier to resolve
 * @return a set of matching primary identifiers
 */
public Set<String> resolveId(String taxonId, String clsName, String id) {
    checkTaxonId(taxonId, clsName);
    // if this is a primary identifier, just return it
    if (isPrimaryIdentifier(taxonId, clsName, id)) {
        return Collections.singleton(id);
    }
    if (orgMainMaps.containsKey(new MultiKey(taxonId, clsName))
            && orgMainMaps.get(new MultiKey(taxonId, clsName)).containsKey(id)) {
        return orgMainMaps.get(new MultiKey(taxonId, clsName)).get(id);
    }
    if (orgSynMaps.containsKey(new MultiKey(taxonId, clsName))
            && orgSynMaps.get(new MultiKey(taxonId, clsName)).containsKey(id)) {
        return orgSynMaps.get(new MultiKey(taxonId, clsName)).get(id);
    }
    return Collections.emptySet();
}

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From source file:org.intermine.bio.dataconversion.IdResolver.java

/**
 * For a particular primary identifier fetch a set of synonyms or return
 * null if id is not a primary identifier for the taxonId given.
 * @param taxonId the organism to do a lookup for
 * @param clsName go term//w w w . j  a v a2  s .  c  o m
 * @param id the primary identifier to look up
 * @return a set of synonyms or null if id is not a primary identifier
 */
public Set<String> getSynonyms(String taxonId, String clsName, String primaryIdentifier) {
    checkTaxonId(taxonId, clsName);
    if (!isPrimaryIdentifier(taxonId, clsName, primaryIdentifier)) {
        return null;
    }
    return orgIdMaps.get(new MultiKey(taxonId, clsName)).get(primaryIdentifier);
}

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From source file:org.intermine.bio.dataconversion.IdResolver.java

/**
 * Check if resolver has taxon id and class name
 * @param taxonId taxon id as string/*from ww w . jav  a  2s.co  m*/
 * @param clsName class name as string
 */
public boolean hasTaxonAndClassName(String taxonId, String clsName) {
    return orgIdMaps.keySet().contains(new MultiKey(taxonId, clsName));
}

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From source file:org.intermine.bio.dataconversion.IdResolver.java

/**
 * Check if resolver has a set of keys (taxon id + class name)
 * @param taxonIdAndClsNameMap data structure to hold keys
 * @return boolean value/*from  w  w w . j  a va2  s.  c om*/
 */
public boolean hasTaxonsAndClassNames(Map<String, Set<String>> taxonIdAndClsNameMap) {
    Set<MultiKey> keySet = new HashSet<MultiKey>();
    for (Entry<String, Set<String>> e : taxonIdAndClsNameMap.entrySet()) {
        for (String clsName : e.getValue()) {
            keySet.add(new MultiKey(e.getKey(), clsName));
        }
    }

    return orgIdMaps.keySet().containsAll(keySet);
}

---

From source file:org.intermine.bio.dataconversion.IdResolver.java

/**
 * Add an entry to the IdResolver, a primary identifier and any number of synonyms.
 * @param taxonId the organism of the identifier
 * @param clsName go term/*  w ww . j ava 2s  .c  o m*/
 * @param primaryIdentifier the main identifier
 * @param synonyms a set of synonyms
 * @param mainId if true these are main ids, otherwise synonms
*/
protected void addEntry(String taxonId, String clsName, String primaryIdentifier, Collection<String> ids,
        Boolean mainId) {
    Map<String, Set<String>> idMap = orgIdMaps.get(new MultiKey(taxonId, clsName));
    if (idMap == null) {
        idMap = new LinkedHashMap<String, Set<String>>();
        orgIdMaps.put(new MultiKey(taxonId, clsName), idMap);
    }

    addToMapList(idMap, primaryIdentifier, ids);

    Map<String, Set<String>> lookupMap = null;
    Map<String, Set<String>> reverseMap = null;
    if (mainId.booleanValue()) {
        lookupMap = orgMainMaps.get(new MultiKey(taxonId, clsName));
        if (lookupMap == null) {
            lookupMap = new HashMap<String, Set<String>>();
            orgMainMaps.put(new MultiKey(taxonId, clsName), lookupMap);
        }

        reverseMap = orgIdMainMaps.get(new MultiKey(taxonId, clsName));
        if (reverseMap == null) {
            reverseMap = new LinkedHashMap<String, Set<String>>();
            orgIdMainMaps.put(new MultiKey(taxonId, clsName), reverseMap);
        }
    } else {
        // these ids are synonyms
        lookupMap = orgSynMaps.get(new MultiKey(taxonId, clsName));
        if (lookupMap == null) {
            lookupMap = new LinkedHashMap<String, Set<String>>();
            orgSynMaps.put(new MultiKey(taxonId, clsName), lookupMap);
        }

        reverseMap = orgIdSynMaps.get(new MultiKey(taxonId, clsName));
        if (reverseMap == null) {
            reverseMap = new LinkedHashMap<String, Set<String>>();
            orgIdSynMaps.put(new MultiKey(taxonId, clsName), reverseMap);
        }
    }

    // map from primaryId back to main/synonym ids
    addToMapList(reverseMap, primaryIdentifier, ids);

    for (String id : ids) {
        addToMapList(lookupMap, id, Collections.singleton(primaryIdentifier));
    }
}

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From source file:org.intermine.bio.dataconversion.OrthodbConverter.java

private String getGene(String geneId, String taxonId) throws ObjectStoreException {
    String identifierType = config.get(taxonId);

    {/*  ww  w . ja  v a  2 s.c  o  m*/
        /**
         * !!! Ugly Code Ahead
         * OrthoDB use secondaryIdentifier for worm gene, in wormbase-identifiers, gene
         * WBGene00006756 (ZC416.8, unc-17) and WBGene00000481 (ZC416.8, cha-1) have the same
         * secondaryIdentifier ZC416.8, but OrthoDB points to cha-1 in term of the protein id
         * ZC416.8b. To fix the issue, set symbol as another key to filter the duplication.
         * Same for Y105E8A.7 and B0564.1
         *
         * For a better fix, load uniprot data, set key to secondaryIdentifier, protein and
         * organism. But MasterMine does not load protein data.
         */

        if ("ZC416.8".equals(geneId)) {
            geneId = "cha-1";
            identifierType = "symbol";
        }

        if ("Y105E8A.7".equals(geneId)) {
            geneId = "lev-10";
            identifierType = "symbol";
        }

        if ("B0564.1".equals(geneId)) {
            geneId = "exos-4.1";
            identifierType = "symbol";
        }
    }

    // Resolver always returns primaryIdentifier, this behaviour could adjust in id resolver.
    String resolvedGenePid = resolveGene(taxonId, geneId);
    if (resolvedGenePid == null) {
        return null;
    }

    // Id resolver always resolve ids to pids.
    String refId = identifiersToGenes.get(new MultiKey(taxonId, resolvedGenePid));
    if (refId == null) {
        Item gene = createItem("Gene");
        gene.setAttribute(DEFAULT_IDENTIFIER_TYPE, resolvedGenePid);

        if (!StringUtils.isEmpty(identifierType)) {
            if (!identifierType.equals(DEFAULT_IDENTIFIER_TYPE)) {
                if ("crossReferences".equals(identifierType)) {
                    gene.addToCollection(identifierType,
                            createCrossReference(gene.getIdentifier(), geneId, DATA_SOURCE_NAME, true));
                } else {
                    gene.setAttribute(identifierType, geneId);
                }
            }
        }

        gene.setReference("organism", getOrganism(taxonId));
        refId = gene.getIdentifier();
        identifiersToGenes.put(new MultiKey(taxonId, resolvedGenePid), refId);
        store(gene);
    }
    return refId;
}

---

From source file:org.intermine.bio.dataconversion.PantherConverter.java

private String getGene(String geneId, String taxonId) throws ObjectStoreException {
    String identifierType = config.get(taxonId);
    if (StringUtils.isEmpty(identifierType)) {
        identifierType = DEFAULT_IDENTIFIER_TYPE;
    }//w  ww  .  ja va 2  s  .  c  o m

    geneId = parseIdentifier(geneId);
    String resolvedGenePid = resolveGene(taxonId, geneId);
    if (resolvedGenePid == null) {
        return null;
    }

    String refId = identifiersToGenes.get(new MultiKey(taxonId, resolvedGenePid));
    if (refId == null) {
        Item gene = createItem("Gene");
        gene.setAttribute(DEFAULT_IDENTIFIER_TYPE, resolvedGenePid);

        if (geneIdPolymorphism.containsKey(taxonId)) {
            Map<String, String> patternMap = geneIdPolymorphism.get(taxonId);
            for (String key : patternMap.keySet()) {
                if (geneId.startsWith(key)) {
                    identifierType = patternMap.get(key);
                    if (!identifierType.equals(DEFAULT_IDENTIFIER_TYPE)) {
                        if ("crossReferences".equals(identifierType)) {
                            gene.addToCollection(identifierType,
                                    createCrossReference(gene.getIdentifier(), geneId, DATA_SOURCE_NAME, true));
                        } else {
                            gene.setAttribute(identifierType, geneId);
                        }
                    }
                }
            }
        } else {
            if (!identifierType.equals(DEFAULT_IDENTIFIER_TYPE)) {
                if ("crossReferences".equals(identifierType)) {
                    gene.addToCollection(identifierType,
                            createCrossReference(gene.getIdentifier(), geneId, DATA_SOURCE_NAME, true));
                } else {
                    gene.setAttribute(identifierType, geneId);
                }
            }
        }

        gene.setReference("organism", getOrganism(taxonId));
        refId = gene.getIdentifier();
        identifiersToGenes.put(new MultiKey(taxonId, resolvedGenePid), refId);
        store(gene);
    }
    return refId;
}

---

From source file:org.intermine.bio.dataconversion.SgdConverter.java

private Item getInteractionItem(String refId, String gene2RefId) throws ObjectStoreException {
    MultiKey key = new MultiKey(refId, gene2RefId);
    Item interaction = interactionsnew.get(key);
    if (interaction == null) {
        interaction = createItem("Interaction");
        interaction.setReference("participant1", refId); //gene1
        interaction.setReference("participant2", gene2RefId); //gene2
    }/*from   ww w . ja v a  2 s . co m*/
    return interaction;
}

---

From source file:org.intermine.bio.util.OrganismRepository.java

/**
 * Return an OrganismRepository created from a properties file in the class path.
 * @return the OrganismRepository/*from   ww  w. ja  v  a 2s .co  m*/
 */
@SuppressWarnings("unchecked")
public static OrganismRepository getOrganismRepository() {
    if (or == null) {
        Properties props = new Properties();
        try {
            InputStream propsResource = OrganismRepository.class.getClassLoader()
                    .getResourceAsStream(PROP_FILE);
            if (propsResource == null) {
                throw new RuntimeException("can't find " + PROP_FILE + " in class path");
            }
            props.load(propsResource);

        } catch (IOException e) {
            throw new RuntimeException("Problem loading properties '" + PROP_FILE + "'", e);
        }

        or = new OrganismRepository();

        Enumeration<String> propNames = (Enumeration<String>) props.propertyNames();

        Pattern pattern = Pattern.compile(REGULAR_EXPRESSION);

        while (propNames.hasMoreElements()) {
            String name = propNames.nextElement();
            if (name.startsWith(PREFIX)) {
                Matcher matcher = pattern.matcher(name);
                if (matcher.matches()) {
                    String taxonIdString = matcher.group(1);
                    int taxonId = Integer.valueOf(taxonIdString).intValue();
                    String fieldName = matcher.group(2);
                    OrganismData od = or.getOrganismDataByTaxonInternal(taxonId);
                    final String attributeValue = props.getProperty(name);
                    if (fieldName.equals(ABBREVIATION)) {
                        od.setAbbreviation(attributeValue);
                        or.abbreviationMap.put(attributeValue.toLowerCase(), od);
                    } else if (fieldName.equals(STRAINS)) {
                        String[] strains = attributeValue.split(" ");
                        for (String strain : strains) {
                            try {
                                or.strains.put(Integer.valueOf(strain), od);
                                or.organismsWithStrains.put(taxonIdString, strain);
                            } catch (NumberFormatException e) {
                                throw new NumberFormatException("taxon ID must be a number");
                            }
                        }
                    } else if (fieldName.equals(ENSEMBL)) {
                        od.setEnsemblPrefix(attributeValue);
                    } else if (fieldName.equals(UNIPROT)) {
                        od.setUniprot(attributeValue);
                        uniprotToTaxon.put(attributeValue, od);
                    } else {
                        if (fieldName.equals(SPECIES)) {
                            od.setSpecies(attributeValue);
                        } else {
                            if (fieldName.equals(GENUS)) {
                                od.setGenus(attributeValue);
                            } else {
                                throw new RuntimeException("internal error didn't match: " + fieldName);
                            }
                        }
                    }
                } else {
                    throw new RuntimeException("unable to parse organism property key: " + name);
                }
            } else {
                throw new RuntimeException("properties in " + PROP_FILE + " must start with " + PREFIX + ".");
            }
        }

        for (OrganismData od : or.taxonMap.values()) {
            or.genusSpeciesMap.put(new MultiKey(od.getGenus(), od.getSpecies()), od);
            // we have some organisms from uniprot that don't have a short name
            if (od.getShortName() != null) {
                or.shortNameMap.put(od.getShortName(), od);
            }
        }
    }

    return or;
}

---

From source file:org.intermine.bio.util.OrganismRepository.java

/**
 * Look up OrganismData objects by genus and species - both must match.  Returns null if there
 * is no OrganismData in this OrganismRepository that matches.
 * @param genus the genus//from w ww .  java2 s  .c o m
 * @param species the species
 * @return the OrganismData
 */
public OrganismData getOrganismDataByGenusSpecies(String genus, String species) {
    MultiKey key = new MultiKey(genus, species);
    return genusSpeciesMap.get(key);
}

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