103 lines
3.3 KiB
Java
103 lines
3.3 KiB
Java
/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package edu.mit.broad.picard.util;
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import edu.mit.broad.picard.PicardException;
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import edu.mit.broad.picard.io.IoUtil;
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import edu.mit.broad.sam.util.AsciiLineReader;
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import edu.mit.broad.sam.util.RuntimeIOException;
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import java.io.*;
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import java.util.List;
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import java.util.Arrays;
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import java.util.ArrayList;
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/**
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* TextFileParser which reads a single text file.
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*
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* @author Kathleen Tibbetts
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*/
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public class BasicTextFileParser extends AbstractTextFileParser
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{
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// TODO: Replace this with AsciiStreamReader when Alec creates it.
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private AsciiLineReader reader;
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private final ArrayList<File> files = new ArrayList<File>();
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String currentFileName = null;
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/**
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* Constructor. Opens up a buffered reader and reads the first line.
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*
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* @param files the file(s) to parse, in order
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*/
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public BasicTextFileParser(boolean treatGroupedDelimitersAsOne, File... files) {
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if (files.length == 0) {
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throw new IllegalArgumentException("At least one file must be specified.");
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}
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this.files.addAll(Arrays.asList(files));
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File f = this.files.remove(0);
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currentFileName = f.getAbsolutePath();
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reader = new AsciiLineReader(IoUtil.openFileForReading(f));
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this.setTreatGroupedDelimitersAsOne(treatGroupedDelimitersAsOne);
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}
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/**
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* Constructor. In addition to opening and priming the files, it sets the number of
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* whitespace-separated "words" per line.
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*
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* @param files the file(s) to parse
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* @param wordCount number of whitespace-separated "words" per line
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*/
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public BasicTextFileParser(boolean treatGroupedDelimitersAsOne, int wordCount, File... files) {
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this(treatGroupedDelimitersAsOne, files);
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setWordCount(wordCount);
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}
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/**
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* Workhorse method that reads the next line from the underlying reader
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*
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* @return String or null if there is no next line
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*/
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protected byte[] readNextLine()
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{
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try {
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String line = reader.readLine();
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if (line != null) {
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return line.getBytes();
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}
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if (files.size() > 0) {
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currentFileName = files.get(0).getAbsolutePath();
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reader = new AsciiLineReader(IoUtil.openFileForReading(files.remove(0)));
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return readNextLine();
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}
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return null;
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}
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catch(RuntimeIOException ioe) {
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throw new PicardException("Error reading from file " + currentFileName, ioe);
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}
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}
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/**
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* Closes the underlying stream
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*/
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public void close() {
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if (reader != null) {
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reader.close();
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}
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}
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/**
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* Gets the name of the file being parsed
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*
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* @return the name of the file being parsed
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*/
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protected String getFileName() {
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return this.currentFileName;
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}
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}
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