picard.util

Class BasicInputParser

java.lang.Object

htsjdk.samtools.util.AbstractIterator<java.lang.String[]>

picard.util.AbstractInputParser

picard.util.BasicInputParser

All Implemented Interfaces:

htsjdk.samtools.util.CloseableIterator<java.lang.String[]>, java.io.Closeable, java.lang.AutoCloseable, java.lang.Iterable<java.lang.String[]>, java.util.Iterator<java.lang.String[]>

Direct Known Subclasses:

CsvInputParser, TabbedInputParser

public class BasicInputParser
extends AbstractInputParser

TextFileParser which reads a single text file.

Author:

Kathleen Tibbetts

Field Summary

Fields inherited from class htsjdk.samtools.util.AbstractIterator

next

Constructor Summary

Constructors

Constructor and Description
BasicInputParser(boolean treatGroupedDelimitersAsOne, java.io.File... files) Constructor.
BasicInputParser(boolean treatGroupedDelimitersAsOne, java.io.InputStream... inputStreams) Constructor.
BasicInputParser(boolean treatGroupedDelimitersAsOne, int wordCount, java.io.File... files) Constructor.
BasicInputParser(boolean treatGroupedDelimitersAsOne, int wordCount, java.io.InputStream... inputStreams)

Method Summary

Modifier and Type	Method and Description
protected void	advanceFile()
void	close() Closes the underlying stream
java.lang.String	getCurrentLine() Provides access to the current (just parsed) line in pre-parsed format.
int	getCurrentLineNumber() NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the next line, not the most recent line returned by next().
java.lang.String	getFileName() Gets the name of the file being parsed
protected byte[]	readNextLine() Workhorse method that reads the next line from the underlying reader

Methods inherited from class picard.util.AbstractInputParser

advance, calculateWordCount, getWordCount, isBlank, isComment, isDelimiter, isSkipBlankLines, isTreatGroupedDelimitersAsOne, iterator, setSkipBlankLines, setTreatGroupedDelimitersAsOne, setWordCount

Methods inherited from class htsjdk.samtools.util.AbstractIterator

hasNext, isIterating, next, peek, remove

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining, hasNext, next, remove

Constructor Detail

BasicInputParser

public BasicInputParser(boolean treatGroupedDelimitersAsOne,
                        java.io.InputStream... inputStreams)

Constructor. Opens up a buffered reader and reads the first line.

Parameters:

inputStreams - the file(s) to parse, in order

BasicInputParser

public BasicInputParser(boolean treatGroupedDelimitersAsOne,
                        int wordCount,
                        java.io.InputStream... inputStreams)

BasicInputParser

public BasicInputParser(boolean treatGroupedDelimitersAsOne,
                        java.io.File... files)

Constructor. Opens up a buffered reader and reads the first line.

Parameters:

files - the file(s) to parse, in order

BasicInputParser

public BasicInputParser(boolean treatGroupedDelimitersAsOne,
                        int wordCount,
                        java.io.File... files)

Constructor. In addition to opening and priming the files, it sets the number of whitespace-separated "words" per line.

Parameters:

files - the file(s) to parse

wordCount - number of whitespace-separated "words" per line

Method Detail

readNextLine

protected byte[] readNextLine()

Workhorse method that reads the next line from the underlying reader

Specified by:

readNextLine in class AbstractInputParser

Returns:

String or null if there is no next line

advanceFile

protected void advanceFile()

close

public void close()

Closes the underlying stream

Specified by:

close in interface htsjdk.samtools.util.CloseableIterator<java.lang.String[]>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in class AbstractInputParser

getFileName

public java.lang.String getFileName()

Gets the name of the file being parsed

Specified by:

getFileName in class AbstractInputParser

Returns:

the name of the file being parsed

getCurrentLine

public java.lang.String getCurrentLine()

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().

getCurrentLineNumber

public int getCurrentLineNumber()

NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the next line, not the most recent line returned by next().