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.v2;
  
  /**
   * An interface for representing detected LCMS peaks
   */
  public interface DetectedPeak {
    /**
     * Return the estimated peak m/z value
     */
    Double getMz();
  
    /**
     * Return the estimated peak retention time (in sec)
     */
    Double getRetentionTime();
  
    /**
     * Return the estimated peak intensity
     */
    Double getIntensity();
  
    /**
     * Return the id of the source scan file
     */
    String getSourceScanFileId();
  
    /**
     * Return the peak confidence (likelihood that the detected peak is actually a real peak)
     * The value would typically reflect the confidence of the peak detection algorithm that it found a peak at
     * that location
     */
    Double getConfidence();
  
    /**
     * Test whether an input m/z value matches with a detected peak at a certain confidence level.
     * @param mz input m/z value
     * @param confidenceLevel input confidence level, unrelated to the above peak confidence
     *                        given the peak true value distribution, this value indicates how conservative
     *                        the matching will be
     * @return result of the test, true if the m/z value matches with the peak
     */
    Boolean matchesMz(Double mz, Double confidenceLevel);
  
    /**
     * Test whether an input m/z value and retention time matches with a detected peak at a certain confidence level.
     * @param mz input m/z value
     * @param retentionTime input retention time
     * @param confidenceLevel input confidence level, unrelated to the above peak confidence
     *                        given the peak true value distribution, this value indicates how conservative
     *                        the matching will be
     * @return result of the test, true if the m/z value matches with the peak
     */
    Boolean matchesMzTime(Double mz, Double retentionTime, Double confidenceLevel);
  }
  