uk.ac.ebi.metabolomes.webservices.util.EntryDecider.java Source code

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Here is the source code for uk.ac.ebi.metabolomes.webservices.util.EntryDecider.java

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/*
 * Copyright (C) 2013 Pablo Moreno <pablacious at users.sf.net>
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
package uk.ac.ebi.metabolomes.webservices.util;

import org.apache.commons.lang.StringUtils;

import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
 *
 * @author pmoreno
 */
public class EntryDecider {

    private Pattern prefixPattern;

    /**
     * 
     * @param query
     * @param candidates
     * @return
     * @deprecated {@see getOrderedCandidates(String, Map<String , String> candidates)} This uses a list and thus does not colapse entries with duplicate
     */
    @Deprecated
    public Set<CandidateEntry> decideBestCandidate(String query, Map<String, String> candidates) {

        Set<CandidateEntry> orderedCand = new TreeSet<CandidateEntry>();
        for (String identifier : candidates.keySet()) {
            CandidateEntry candidateT = new CandidateEntry();
            candidateT.setId(identifier);
            candidateT.setDesc(candidates.get(identifier));
            String prefix = this.identiferPrefix(identifier);
            if (prefix != null && candidateT.getDesc().contains(prefix)) {
                candidateT.setDesc(candidateT.getDesc().replace(prefix, ""));
            }
            candidateT.setDistance(StringUtils.getLevenshteinDistance(query.toLowerCase().trim(),
                    candidateT.getDesc().toLowerCase().trim()));

            orderedCand.add(candidateT);
        }

        return orderedCand;
    }

    public List<CandidateEntry> getOrderedCandidates(String query, Map<String, String> candidates) {

        List<CandidateEntry> orderedCand = new ArrayList<CandidateEntry>();
        for (String identifier : candidates.keySet()) {
            CandidateEntry candidateT = new CandidateEntry();
            candidateT.setId(identifier);
            candidateT.setDesc(candidates.get(identifier));
            String prefix = this.identiferPrefix(identifier);
            if (prefix != null && candidateT.getDesc().contains(prefix)) {
                candidateT.setDesc(candidateT.getDesc().replace(prefix, ""));
            }
            candidateT.setDistance(StringUtils.getLevenshteinDistance(query.toLowerCase().trim(),
                    candidateT.getDesc().toLowerCase().trim()));

            orderedCand.add(candidateT);
        }

        Collections.sort(orderedCand);

        return orderedCand;
    }

    /**
     *
     * @param query
     * @param candidates
     * @return
     * @deprecated {@see getOrderedCandidates(String, Collection<String>)} This uses a list and thus does not colapse entries with duplicate
     */
    @Deprecated
    public Set<CandidateEntry> decideBestCandidate(String query, Collection<String> candidates) {
        Set<CandidateEntry> orderedCand = new TreeSet<CandidateEntry>();
        for (String candidate : candidates) {
            CandidateEntry candidateT = new CandidateEntry();
            //candidateT.setId(candidate);
            candidateT.setDesc(candidate);
            String prefix = this.identiferPrefix(candidate);
            if (prefix != null && candidateT.getDesc().contains(prefix)) {
                candidateT.setDesc(candidateT.getDesc().replace(prefix, ""));
            }
            candidateT.setDistance(StringUtils.getLevenshteinDistance(query.toLowerCase().trim(),
                    candidateT.getDesc().toLowerCase().trim()));

            orderedCand.add(candidateT);
        }

        return orderedCand;
    }

    public List<CandidateEntry> getOrderedCandidates(String query, Collection<String> candidates) {

        String formatedQuery = query.toLowerCase(Locale.ENGLISH).trim();

        List<CandidateEntry> orderedCand = new ArrayList<CandidateEntry>();

        for (String candidate : candidates) {

            String description = removePrefix(candidate);
            Integer distance = StringUtils.getLevenshteinDistance(formatedQuery,
                    description.toLowerCase(Locale.ENGLISH).trim());
            orderedCand.add(new CandidateEntry("", description, distance, ""));
        }

        Collections.sort(orderedCand);

        return orderedCand;
    }

    private String removePrefix(String description) {
        String prefix = this.identiferPrefix(description);
        if (prefix != null && description.contains(prefix)) {
            return description.replace(prefix, "");
        }
        return description;
    }

    public EntryDecider() {
        this.prefixPattern = Pattern.compile("([A-Z]+:)\\d");
    }

    private String identiferPrefix(String identifer) {
        Matcher prefixMatcher = this.prefixPattern.matcher(identifer);
        if (prefixMatcher.find()) {
            return prefixMatcher.group(1);
        } else {
            return null;
        }
    }
}