/*
* #%L
* org.gitools.utils
* %%
* Copyright (C) 2013 - 2014 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* 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/gpl-3.0.html>.
* #L%
*/
/**
Copyright 2005 Bytecode Pty Ltd.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/
package org.gitools.utils.readers.text;
import java.io.BufferedReader;
import java.io.Closeable;
import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
import java.util.List;
/**
* A very simple CSV reader released under a commercial-friendly license.
*
* @author Glen Smith
* @noinspection ALL
*/
public class CSVReader implements Closeable {
private final BufferedReader br;
private boolean hasNext = true;
private final CSVParser parser;
private final int skipLines;
private final char commentchar;
private boolean linesSkiped;
private int lineNumber;
/**
* The default line to start reading.
*/
public static final int DEFAULT_SKIP_LINES = 0;
/*
* The default comment character. All lines that start with this
* character will be skipped.
*
*/
public static final char DEFAULT_COMMENT_CHARACTER = '#';
/**
* Constructs CSVReader using a comma for the separator.
*
* @param reader the reader to an underlying CSV source.
*/
public CSVReader(Reader reader) {
this(reader, CSVParser.DEFAULT_SEPARATOR, CSVParser.DEFAULT_QUOTE_CHARACTER, CSVParser.DEFAULT_ESCAPE_CHARACTER);
}
/**
* Constructs CSVReader with supplied separator.
*
* @param reader the reader to an underlying CSV source.
* @param separator the delimiter to use for separating entries.
*/
public CSVReader(Reader reader, char separator) {
this(reader, separator, CSVParser.DEFAULT_QUOTE_CHARACTER, CSVParser.DEFAULT_ESCAPE_CHARACTER);
}
/**
* Constructs CSVReader with supplied separator and quote char.
*
* @param reader the reader to an underlying CSV source.
* @param separator the delimiter to use for separating entries
* @param quotechar the character to use for quoted elements
*/
public CSVReader(Reader reader, char separator, char quotechar) {
this(reader, separator, quotechar, CSVParser.DEFAULT_ESCAPE_CHARACTER, DEFAULT_SKIP_LINES, CSVParser.DEFAULT_STRICT_QUOTES);
}
/**
* Constructs CSVReader with supplied separator, quote char and quote handling
* behavior.
*
* @param reader the reader to an underlying CSV source.
* @param separator the delimiter to use for separating entries
* @param quotechar the character to use for quoted elements
* @param strictQuotes sets if characters outside the quotes are ignored
*/
public CSVReader(Reader reader, char separator, char quotechar, boolean strictQuotes) {
this(reader, separator, quotechar, CSVParser.DEFAULT_ESCAPE_CHARACTER, DEFAULT_SKIP_LINES, strictQuotes);
}
/**
* Constructs CSVReader with supplied separator and quote char.
*
* @param reader the reader to an underlying CSV source.
* @param separator the delimiter to use for separating entries
* @param quotechar the character to use for quoted elements
* @param escape the character to use for escaping a separator or quote
*/
private CSVReader(Reader reader, char separator, char quotechar, char escape) {
this(reader, separator, quotechar, escape, DEFAULT_SKIP_LINES, CSVParser.DEFAULT_STRICT_QUOTES);
}
/**
* Constructs CSVReader with supplied separator and quote char.
*
* @param reader the reader to an underlying CSV source.
* @param separator the delimiter to use for separating entries
* @param quotechar the character to use for quoted elements
* @param line the line number to skip for start reading
*/
public CSVReader(Reader reader, char separator, char quotechar, int line) {
this(reader, separator, quotechar, CSVParser.DEFAULT_ESCAPE_CHARACTER, line, CSVParser.DEFAULT_STRICT_QUOTES);
}
/**
* Constructs CSVReader with supplied separator and quote char.
*
* @param reader the reader to an underlying CSV source.
* @param separator the delimiter to use for separating entries
* @param quotechar the character to use for quoted elements
* @param escape the character to use for escaping a separator or quote
* @param line the line number to skip for start reading
*/
public CSVReader(Reader reader, char separator, char quotechar, char escape, int line) {
this(reader, separator, quotechar, escape, line, CSVParser.DEFAULT_STRICT_QUOTES);
}
/**
* Constructs CSVReader with supplied separator and quote char.
*
* @param reader the reader to an underlying CSV source.
* @param separator the delimiter to use for separating entries
* @param quotechar the character to use for quoted elements
* @param escape the character to use for escaping a separator or quote
* @param line the line number to skip for start reading
* @param strictQuotes sets if characters outside the quotes are ignored
*/
private CSVReader(Reader reader, char separator, char quotechar, char escape, int line, boolean strictQuotes) {
this(reader, separator, quotechar, escape, DEFAULT_COMMENT_CHARACTER, line, strictQuotes, CSVParser.DEFAULT_IGNORE_LEADING_WHITESPACE);
}
/**
* Constructs CSVReader with supplied separator and quote char.
*
* @param reader the reader to an underlying CSV source.
* @param separator the delimiter to use for separating entries
* @param quotechar the character to use for quoted elements
* @param escape the character to use for escaping a separator or quote
* @param commentchar the comment char, all lines that start with this char will be skipped.
* @param line the line number to skip for start reading
* @param strictQuotes sets if characters outside the quotes are ignored
* @param ignoreLeadingWhiteSpace it true, parser should ignore white space before a quote in a field
*/
public CSVReader(Reader reader, char separator, char quotechar, char escape, char commentchar, int line, boolean strictQuotes, boolean ignoreLeadingWhiteSpace) {
this.br = new BufferedReader(reader);
this.parser = new CSVParser(separator, quotechar, escape, strictQuotes, ignoreLeadingWhiteSpace);
this.skipLines = line;
this.commentchar = commentchar;
this.lineNumber = 0;
}
/**
* Reads the entire file into a List with each element being a String[] of
* tokens.
*
* @return a List of String[], with each String[] representing a line of the
* file.
* @throws IOException if bad things happen during the read
*/
public List<String[]> readAll() throws IOException {
List<String[]> allElements = new ArrayList<String[]>();
while (hasNext) {
String[] nextLineAsTokens = readNext();
if (nextLineAsTokens != null) {
allElements.add(nextLineAsTokens);
}
}
return allElements;
}
/**
* Reads the next line from the buffer and converts to a string array.
*
* @return a string array with each comma-separated element as a separate
* entry.
* @throws IOException if bad things happen during the read
*/
public String[] readNext() throws IOException {
String[] result = null;
do {
String nextLine = getNextLine();
if (!hasNext) {
return result; // should throw if still pending?
}
String[] r = parser.parseLineMulti(nextLine);
if (r.length > 0) {
if (result == null) {
result = r;
} else {
String[] t = new String[result.length + r.length];
System.arraycopy(result, 0, t, 0, result.length);
System.arraycopy(r, 0, t, result.length, r.length);
result = t;
}
}
} while (parser.isPending());
return result;
}
/**
* Reads the next line from the file.
*
* @return the next line from the file without trailing newline
* @throws IOException if bad things happen during the read
*/
private String getNextLine() throws IOException {
if (!this.linesSkiped) {
for (int i = 0; i < skipLines; i++) {
br.readLine();
lineNumber++;
}
this.linesSkiped = true;
}
String nextLine = br.readLine();
lineNumber++;
// Skip comments & empty lines
while (nextLine != null && (nextLine.isEmpty() || nextLine.charAt(0) == commentchar)) {
nextLine = br.readLine();
lineNumber++;
}
if (nextLine == null) {
hasNext = false;
}
return hasNext ? nextLine : null;
}
/**
* Closes the underlying reader.
*
* @throws IOException if the close fails
*/
public void close() throws IOException {
br.close();
}
public int getLineNumber() {
return lineNumber;
}
}