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

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

Source

/*
 * 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.TreeSet;
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 YMDBGateway implements DBGateway {

    private static final String ymdbSeachAddress = "http://www.ymdb.ca/structures/search/compounds/mass?";
    private static final String ymdbEntryAddress = "http://www.ymdb.ca/structures/structures/compounds/";

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

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

        String queryAddress = ymdbSeachAddress + "query_from=" + toleranceRange.lowerEndpoint() + "&query_to="
                + toleranceRange.upperEndpoint();

        URL queryURL = new URL(queryAddress);

        // Submit the query
        String queryResult = InetUtils.retrieveData(queryURL);

        // Organize the IDs as a TreeSet to keep them sorted
        TreeSet<String> results = new TreeSet<String>();

        // Find IDs in the HTML data
        Pattern pat = Pattern.compile("/compounds/(YMDB[0-9]{5})");
        Matcher matcher = pat.matcher(queryResult);
        while (matcher.find()) {
            String ymdbID = matcher.group(1);
            results.add(ymdbID);
        }

        // Remove all except first numOfResults IDs. The reason why we first
        // retrieve all results and then remove those above numOfResults is to
        // keep the lowest YDMB IDs - these may be the most interesting ones.
        while (results.size() > numOfResults) {
            String lastItem = results.last();
            results.remove(lastItem);
        }

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

    }

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

        // We will parse the name and formula from the SDF file, it seems like
        // the easiest way
        URL sdfURL = new URL(ymdbEntryAddress + ID + ".sdf");

        String sdfRecord = InetUtils.retrieveData(sdfURL);
        String lines[] = sdfRecord.split("\n");

        String compoundName = null;
        String compoundFormula = null;
        URL entryURL = new URL(ymdbEntryAddress + ID);
        URL structure2DURL = sdfURL;
        URL structure3DURL = sdfURL;

        for (int i = 0; i < lines.length - 1; i++) {

            if (lines[i].contains("> <GENERIC_NAME>")) {
                compoundName = lines[i + 1];
            }

            if (lines[i].contains("> <JCHEM_FORMULA>")) {
                compoundFormula = lines[i + 1];
            }
        }

        if (compoundName == null) {
            throw (new IOException("Could not parse compound name"));
        }

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

        return newCompound;

    }
}