de.unijena.bioinf.ChemistryBase.chem.utils.IsotopicDistributionJSONFile.java Source code

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Here is the source code for de.unijena.bioinf.ChemistryBase.chem.utils.IsotopicDistributionJSONFile.java

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/*
 *  This file is part of the SIRIUS library for analyzing MS and MS/MS data
 *
 *  Copyright (C) 2013-2015 Kai Dhrkop
 *
 *  This library 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 2.1 of the License, or (at your option) any later version.
 *
 *  This library 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 General Public License along with SIRIUS.  If not, see <http://www.gnu.org/licenses/>.
 */
package de.unijena.bioinf.ChemistryBase.chem.utils;

import de.unijena.bioinf.ChemistryBase.chem.Isotopes;
import de.unijena.bioinf.ChemistryBase.chem.PeriodicTable;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.Reader;
import java.util.Iterator;

public class IsotopicDistributionJSONFile extends DistributionReader {

    public IsotopicDistribution read(Reader json) throws IOException {
        final IsotopicDistribution dist = new IsotopicDistribution(PeriodicTable.getInstance());
        final BufferedReader reader = new BufferedReader(json);
        final StringBuilder buffer = new StringBuilder();
        while (reader.ready()) {
            buffer.append(reader.readLine()).append("\n");
        }
        JSONObject obj;
        try {
            obj = new JSONObject(buffer.toString());
            for (Iterator<?> keys = obj.keys(); keys.hasNext();) {
                final String key = keys.next().toString();
                final Isotopes prev = PeriodicTable.getInstance().getDistribution().getIsotopesFor(key);
                //final JSONObject element = (JSONObject)obj.get(key);
                //final JSONArray jmasses = (JSONArray)obj.get("masses");
                final JSONArray jabundances = (JSONArray) obj.get(key);
                final String elementSymbol = key;
                final double[] abundances = new double[jabundances.length()];
                final double[] masses = new double[jabundances.length()];
                for (int i = 0; i < prev.getNumberOfIsotopes(); ++i) { // TODO: fix!!!
                    abundances[i] = jabundances.getDouble(i);
                    masses[i] = prev.getMass(i);
                }
                dist.addIsotope(key, masses, abundances);
            }
        } catch (JSONException e) {
            throw new IOException("Can't parse json file. Invalid JSON syntax");
        }
        return dist;
    }
}