/*************************************************************************
* *
* 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;
}