/*************************************************************************
* *
* 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();
}
}