net.sf.mzmine.modules.peaklistmethods.identification.onlinedbsearch.databases.KEGGGateway.java Source code

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Here is the source code for net.sf.mzmine.modules.peaklistmethods.identification.onlinedbsearch.databases.KEGGGateway.java

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/*
 * Copyright 2006-2015 The MZmine 2 Development Team
 * 
 * This file is part of MZmine 2.
 * 
 * MZmine 2 is free software; you can redistribute it and/or modify it under the
 * terms of the GNU General Public License as published by the Free Software
 * Foundation; either version 2 of the License, or (at your option) any later
 * version.
 * 
 * MZmine 2 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 General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with
 * MZmine 2; if not, write to the Free Software Foundation, Inc., 51 Franklin St,
 * Fifth Floor, Boston, MA 02110-1301 USA
 */

package net.sf.mzmine.modules.peaklistmethods.identification.onlinedbsearch.databases;

import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import net.sf.mzmine.modules.peaklistmethods.identification.onlinedbsearch.DBCompound;
import net.sf.mzmine.modules.peaklistmethods.identification.onlinedbsearch.DBGateway;
import net.sf.mzmine.modules.peaklistmethods.identification.onlinedbsearch.OnlineDatabase;
import net.sf.mzmine.parameters.ParameterSet;
import net.sf.mzmine.parameters.parametertypes.tolerances.MZTolerance;
import net.sf.mzmine.util.InetUtils;

import com.google.common.collect.Range;

public class KEGGGateway implements DBGateway {

    private static final String keggFindAddress1 = "http://rest.kegg.jp/find/compound/";
    private static final String keggFindAddress2 = "/exact_mass";
    private static final String keggGetAddress = "http://rest.kegg.jp/get/";
    private static final String keggEntryAddress = "http://www.kegg.jp/entry/";

    private static final String kegg2DStructureAddress = "http://www.genome.jp/dbget-bin/www_bget?-f+m+";
    private static final String met3DStructureAddress1 = "http://www.3dmet.dna.affrc.go.jp/pdb/";
    private static final String met3DStructureAddress2 = ".pdb";

    public String[] findCompounds(double mass, MZTolerance mzTolerance, int numOfResults, ParameterSet parameters)
            throws IOException {

        Range<Double> toleranceRange = mzTolerance.getToleranceRange(mass);

        String queryAddress = keggFindAddress1 + toleranceRange.lowerEndpoint() + "-"
                + toleranceRange.upperEndpoint() + keggFindAddress2;

        URL queryURL = new URL(queryAddress);

        String queryResult = InetUtils.retrieveData(queryURL);

        ArrayList<String> results = new ArrayList<String>();

        Pattern pat = Pattern.compile("cpd:(C[0-9]+)");
        Matcher matcher = pat.matcher(queryResult);
        while (matcher.find()) {
            String keggID = matcher.group(1);
            results.add(keggID);
        }

        return results.toArray(new String[0]);

    }

    /**
     * This method retrieves the details about a KEGG compound
     * 
     */
    public DBCompound getCompound(String ID, ParameterSet parameters) throws IOException {

        String queryAddress = keggGetAddress + ID;

        URL queryURL = new URL(queryAddress);

        String compoundData = InetUtils.retrieveData(queryURL);

        String dataLines[] = compoundData.split("\n");

        String compoundName = null, compoundFormula = null, ID3DMet = null;

        for (String line : dataLines) {
            if (line.startsWith("NAME")) {
                compoundName = line.substring(12);
                if (compoundName.endsWith(";")) {
                    compoundName = compoundName.substring(0, compoundName.length() - 1);
                }
            }

            if (line.startsWith("FORMULA")) {
                compoundFormula = line.substring(12);
            }

            // 3DMET id is last 6 characters on the line
            if (line.contains("3DMET")) {
                ID3DMet = line.substring(line.length() - 6);
            }

        }

        if ((compoundName == null) || (compoundFormula == null)) {
            throw (new IOException("Could not obtain compound name and formula"));
        }

        URL entryURL = new URL(keggEntryAddress + ID);
        URL structure2DURL = new URL(kegg2DStructureAddress + ID);

        URL structure3DURL = null;

        if (ID3DMet != null) {
            structure3DURL = new URL(met3DStructureAddress1 + ID3DMet + met3DStructureAddress2);
        }

        DBCompound newCompound = new DBCompound(OnlineDatabase.KEGG, ID, compoundName, compoundFormula, entryURL,
                structure2DURL, structure3DURL);

        return newCompound;

    }

}