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/*
* The MIT License
*
* Copyright (c) 2011 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.util;
import htsjdk.samtools.util.BufferedLineReader;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.RuntimeIOException;
import picard.PicardException;
import java.io.File;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Arrays;
/**
* TextFileParser which reads a single text file.
*
* @author Kathleen Tibbetts
*/
public class BasicInputParser extends AbstractInputParser
{
private BufferedLineReader reader;
private final ArrayList inputs = new ArrayList();
private final ArrayList fileNames = new ArrayList();
String currentFileName = null;
private String currentLine = null;
private String nextLine = null;
private int currentLineNumber = 0;
private int nextLineNumber = 0;
/**
* Constructor. Opens up a buffered reader and reads the first line.
*
* @param inputStreams the file(s) to parse, in order
*/
public BasicInputParser(final boolean treatGroupedDelimitersAsOne, final InputStream... inputStreams) {
if (inputStreams.length == 0) {
throw new IllegalArgumentException("At least one input must be specified.");
}
this.inputs.addAll(Arrays.asList(inputStreams));
reader = new BufferedLineReader(this.inputs.remove(0));
this.setTreatGroupedDelimitersAsOne(treatGroupedDelimitersAsOne);
}
public BasicInputParser(final boolean treatGroupedDelimitersAsOne, final int wordCount, final InputStream... inputStreams) {
this(treatGroupedDelimitersAsOne, inputStreams);
setWordCount(wordCount);
}
/**
* Constructor. Opens up a buffered reader and reads the first line.
*
* @param files the file(s) to parse, in order
*/
public BasicInputParser(final boolean treatGroupedDelimitersAsOne, final File... files) {
this(treatGroupedDelimitersAsOne, filesToInputStreams(files));
for (File f : files) fileNames.add(f.getAbsolutePath());
this.currentFileName = fileNames.remove(0);
}
/**
* Constructor. In addition to opening and priming the files, it sets the number of
* whitespace-separated "words" per line.
*
* @param files the file(s) to parse
* @param wordCount number of whitespace-separated "words" per line
*/
public BasicInputParser(final boolean treatGroupedDelimitersAsOne, final int wordCount, final File... files) {
this(treatGroupedDelimitersAsOne, files);
setWordCount(wordCount);
}
/**
* Workhorse method that reads the next line from the underlying reader
*
* @return String or null if there is no next line
*/
protected byte[] readNextLine()
{
try {
final String line = reader.readLine();
if (nextLine != null && !isComment(nextLine.getBytes())) {
currentLineNumber = nextLineNumber;
currentLine = nextLine;
}
if (line != null) {
nextLineNumber++;
nextLine = line;
return line.getBytes();
}
if (!inputs.isEmpty()) {
advanceFile();
return readNextLine();
}
return null;
}
catch(RuntimeIOException ioe) {
throw new PicardException("Error reading from file " + currentFileName, ioe);
}
}
protected void advanceFile() {
currentFileName = !fileNames.isEmpty() ? fileNames.remove(0) : null;
nextLineNumber = 0;
nextLine = null;
reader = new BufferedLineReader(inputs.remove(0));
}
/**
* Closes the underlying stream
*/
public void close() {
if (reader != null) {
reader.close();
}
for(final InputStream stream : inputs){
CloserUtil.close(stream);
}
}
/**
* Gets the name of the file being parsed
*
* @return the name of the file being parsed
*/
public String getFileName() {
return this.currentFileName != null ? this.currentFileName : "(file name unavailable)";
}
/**
* Provides access to the current (just parsed) line in pre-parsed format.
* NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the
* next line, not the most recent line returned by next().
*/
public String getCurrentLine() {
return this.currentLine;
}
/**
* NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the
* next line, not the most recent line returned by next().
*/
public int getCurrentLineNumber() {
return currentLineNumber;
}
private static InputStream[] filesToInputStreams(final File[] files) {
final InputStream[] result = new InputStream[files.length];
for (int i = 0; i < files.length; i++) {
result[i] = IOUtil.openFileForReading(files[i]);
}
return result;
}
}
