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.CSVPrinter;
  
  import java.io.File;
  import java.io.FileWriter;
  import java.io.IOException;
  import java.util.ArrayList;
  import java.util.List;
  import java.util.Map;
  
  // TODO: move this and TSVParser to an analysis utility class.  No reason for them to live deep in package hierarchies.
  public class TSVWriter<K, V> implements AutoCloseable {
  
    public static final CSVFormat TSV_FORMAT = CSVFormat.newFormat('\t').
        withRecordSeparator('\n').withQuote('"').withIgnoreEmptyLines(true);
    private List<K> header;
    private CSVPrinter printer;
  
    public TSVWriter(List<K> header) {
      this.header = header;
    }
  
    public void open(File f) throws IOException {
      String[] headerStrings = new String[header.size()];
      for (int i = 0; i < header.size(); i++) {
        headerStrings[i] = header.get(i).toString();
      }
      printer = new CSVPrinter(new FileWriter(f), TSV_FORMAT.withHeader(headerStrings));
    }
  
    public void open(File f, Boolean append) throws IOException {
      if (!append) {
        open(f);
      } else {
        printer = new CSVPrinter(new FileWriter(f, true), TSV_FORMAT);
      }
    }
  
    @Override
    public void close() throws IOException {
      if (printer != null) {
        printer.close();
        printer = null;
      }
    }
  
    public void append(Map<K, V> row) throws IOException {
      List<V> vals = new ArrayList<>(header.size());
      for (K field : header) {
        vals.add(row.get(field));
      }
      printer.printRecord(vals);
    }
  
    public void append(List<Map<K, V>> rows) throws IOException {
      for (Map<K, V> row : rows) {
        append(row);
      }
      printer.flush();
    }
  
    public void flush() throws IOException {
      printer.flush();
    }
  }
  