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.utils;
  
  import org.apache.commons.csv.CSVFormat;
  import org.apache.commons.csv.CSVParser;
  import org.apache.commons.csv.CSVRecord;
  
  import java.io.File;
  import java.io.FileInputStream;
  import java.io.FileReader;
  import java.io.IOException;
  import java.io.InputStream;
  import java.io.InputStreamReader;
  import java.util.ArrayList;
  import java.util.Iterator;
  import java.util.List;
  import java.util.Map;
  
  public class TSVParser {
    private List<Map<String, String>> results = null;
    Map<String, Integer> headerMap = null;
  
    public static final CSVFormat TSV_FORMAT = CSVFormat.newFormat('\t').
        withRecordSeparator('\n').withQuote('"').withIgnoreEmptyLines(true).withHeader();
  
  
    public void parse(File file) throws IOException {
      parse(new FileInputStream(file));
    }
  
    public void parse(InputStream inStream) throws IOException {
      List<Map<String, String>> results = new ArrayList<>();
      try (CSVParser parser = new CSVParser(new InputStreamReader(inStream), TSV_FORMAT)) {
        headerMap = parser.getHeaderMap();
        Iterator<CSVRecord> iter = parser.iterator();
        while (iter.hasNext()) {
          CSVRecord r = iter.next();
          results.add(r.toMap());
        }
      }
      this.results = results;
    }
  
    public List<Map<String, String>> getResults() {
      return this.results;
    }
  
    public Map<String, Integer> getHeaderMap() { return this.headerMap; }
  
    public List<String> getHeader() {
      List<String> header = new ArrayList<>(this.headerMap.size());
      for (Map.Entry<String, Integer> entry : headerMap.entrySet()) {
        header.add(entry.getValue(), entry.getKey());
      }
      return header;
    }
  }
  