/*************************************************************************
* *
* 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;
}
}