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;
  
  import org.apache.logging.log4j.LogManager;
  import org.apache.logging.log4j.Logger;
  
  import java.util.ArrayList;
  import java.util.List;
  import java.util.Map;
  import java.util.NavigableMap;
  import java.util.TreeMap;
  import java.util.stream.Collectors;
  
  /**
   * This class holds the API for a {Double mass -> List<RawMetabolite> rawMetabolites} map.
   * Its purpose is to store in memory enumerated lists of structures or formulae and allow for quick lookups.
   * Along with the NavigableMap holding the data structure, an enum defines the expected kind of metabolite.
   * TODO: add support to convert RawMetabolite -> Metabolite once #492 goes through and provide APIs to retrieve
   * Metabolites directly form the map.
   */
  
  public class MassToRawMetaboliteMap {
  
    private static final Logger LOGGER = LogManager.getFormatterLogger(MassToRawMetaboliteMap.class);
  
    // The data structure holding the RawMetabolites.
    // A NaviagableMap has very convenient properties (sorted, API for extracting sub-maps) for our use case.
    private NavigableMap<Double, List<RawMetabolite>> massToRawMetaboliteMap;
    private RawMetaboliteKind kind;
  
    // Sub-class defining the kind of metabolite. Defined at the top-level to avoid storing it in every RawMetabolite.
    public enum RawMetaboliteKind  {
      INCHI, FORMULA
    }
  
    public MassToRawMetaboliteMap(RawMetaboliteKind kind) {
      this.massToRawMetaboliteMap = new TreeMap<>();
      this.kind = kind;
    }
  
    public RawMetaboliteKind getKind() {
      return kind;
    }
  
    /**
     * Add a RawMetabolite to the map
     */
    public void add(RawMetabolite rawMetabolite) {
      Double mass = rawMetabolite.getMonoIsotopicMass();
      List<RawMetabolite> matchingMetabolites = massToRawMetaboliteMap.get(mass);
      if (matchingMetabolites == null) {
        matchingMetabolites = new ArrayList<>();
        massToRawMetaboliteMap.put(mass, matchingMetabolites);
      }
      matchingMetabolites.add(rawMetabolite);
    }
  
    /**
     * Retrieve all the RawMetabolites within a given mono-isotopic mass window
     */
    public Map<Double, List<RawMetabolite>> getMassWindow(Double minMass, Double maxMass, Boolean inclusive) {
      return massToRawMetaboliteMap.subMap(minMass, inclusive, maxMass, inclusive);
    }
  
    /**
     * Retrieve all the RawMetabolites within a given centered mono-isotopic mass window
     */
    public Map<Double, List<RawMetabolite>> getMassCenteredWindow(Double center, Double windowSize) {
      // We default to being inclusive of the query bounds
      return getMassWindow(center - windowSize / 2, center + windowSize / 2, true);
    }
  
    /**
     * Retrieve a sorted list of the RawMetabolites within a given a centered mono-isotopic mass window,
     * ordered by their closeness to the center.
     */
    public List<RawMetabolite> getSortedFromCenter(Double center, Double windowSize) {
      Map<Double, List<RawMetabolite>> subMap =  getMassCenteredWindow(center, windowSize);
      TreeMap<Double, List<RawMetabolite>> newMap = new TreeMap<>();
      subMap.entrySet().stream().forEachOrdered(entry -> newMap.put(Math.abs(entry.getKey() - center), entry.getValue()));
      return newMap.values().stream().flatMap(List::stream).collect(Collectors.toList());
    }
  
    /**
     * The following three methods expose part of the NavigableMap API for easier testing
     */
    Boolean containsKey(Double key) {
      return massToRawMetaboliteMap.containsKey(key);
    }
  
    Double ceilingKey(Double key) {
      return massToRawMetaboliteMap.ceilingKey(key);
    }
  
    List<RawMetabolite> get(Double key) {
      return massToRawMetaboliteMap.get(key);
    }
  
  }
  