content: /*************************************************************************
  *                                                                        *
  *  This file is part of the 20n/act project.                             *
  *  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
  *  Copyright (C) 2017 20n Labs, Inc.                                     *
  *                                                                        *
  *  Please direct all queries to act@20n.com.                             *
  *                                                                        *
  *  This program 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 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 General Public License for more details.                          *
  *                                                                        *
  *  You should have received a copy of the GNU General Public License     *
  *  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
  *                                                                        *
  *************************************************************************/
  
  package com.act.lcms;
  
  import javax.xml.parsers.ParserConfigurationException;
  import javax.xml.stream.XMLStreamException;
  import java.io.IOException;
  import java.util.ArrayList;
  import java.util.Iterator;
  import java.util.List;
  
  /**
   * A class that can parse a particular format of LCMS apparatus output.
   */
  public interface LCMSParser {
    /**
     * Returns an iterator over the LCMS time points in the given input file.
     * @param inputFile The LCMS input file to read.
     * @return An iterator over the LCMS time points in that file, represented by LCMSSpectrum objects.
     * @throws ParserConfigurationException
     * @throws IOException
     * @throws XMLStreamException
     */
    Iterator<LCMSSpectrum> getIterator(String inputFile)
        throws ParserConfigurationException, IOException, XMLStreamException;
  
    /**
     * Parses an LCMS file, returning all time points in that file as LCMSSpectra.
     *
     * Note: expect this function to be very memory-intensive.  Use getIterator() instead if possible.
     * @param inputFile The LCMS input file to read.
     * @return The list of all LCMS time points read from that file, represented by LCMSSpectrum objects.
     * @throws ParserConfigurationException
     * @throws IOException
     * @throws XMLStreamException
     */
    List<LCMSSpectrum> parse(String inputFile)
        throws ParserConfigurationException, IOException, XMLStreamException;
  }
  