picard.util

Class AbstractInputParser

java.lang.Object

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

picard.util.AbstractInputParser

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:

BasicInputParser

public abstract class AbstractInputParser
extends htsjdk.samtools.util.AbstractIterator<java.lang.String[]>
implements java.lang.Iterable<java.lang.String[]>, htsjdk.samtools.util.CloseableIterator<java.lang.String[]>

Class for parsing text files where each line consists of fields separated by whitespace. Code is abstracted into this class so that we can optimize its performance over time. This class assumes that every line will have the same number of whitespace-separated "words" and that lines that start with "#" are comments and should be ignored. Classes that extend this parser can do so simply by implementing their own constructors and the readNextLine(), close(), and getFileName() methods.

Field Summary

Fields inherited from class htsjdk.samtools.util.AbstractIterator

next

Constructor Summary

Constructors

Constructor and Description
AbstractInputParser()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	advance()
protected void	calculateWordCount(byte[] line) Calculates the number of delimiter-separated "words" in a line and sets the value of wordCount
abstract void	close() Closes this stream and releases any system resources associated with it.
abstract java.lang.String	getFileName()
protected int	getWordCount()
protected boolean	isBlank(byte[] line) Determines whether a given line is a comment
protected boolean	isComment(byte[] line) Determines whether a given line is a comment
protected boolean	isDelimiter(byte b) Determines whether a given character is a delimiter
protected boolean	isSkipBlankLines()
protected boolean	isTreatGroupedDelimitersAsOne()
java.util.Iterator<java.lang.String[]>	iterator()
protected abstract byte[]	readNextLine()
protected void	setSkipBlankLines(boolean skipBlankLines)
protected void	setTreatGroupedDelimitersAsOne(boolean treatGroupedDelimitersAsOne)
protected void	setWordCount(int wordCount)

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

AbstractInputParser

public AbstractInputParser()

Method Detail

close

public abstract void close()

Closes this stream and releases any system resources associated with it.

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

readNextLine

protected abstract byte[] readNextLine()

Returns:

the next line of text from the underlying stream(s) or null if there is no next line

getFileName

public abstract java.lang.String getFileName()

Returns:

the name(s) of the file(s) being parsed, or null if no name is available

iterator

public java.util.Iterator<java.lang.String[]> iterator()

Specified by:

iterator in interface java.lang.Iterable<java.lang.String[]>

Returns:

an iterator over a set of elements of type String[]

advance

protected java.lang.String[] advance()

Specified by:

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

calculateWordCount

protected void calculateWordCount(byte[] line)

Calculates the number of delimiter-separated "words" in a line and sets the value of wordCount

Parameters:

line - representative line from the file

isComment

protected boolean isComment(byte[] line)

Determines whether a given line is a comment

Parameters:

line - the line to evaluate

Returns:

true if the line is a comment (and should be ignored) otherwise false

isBlank

protected boolean isBlank(byte[] line)

Determines whether a given line is a comment

Parameters:

line - the line to evaluate

Returns:

true if the line is a comment (and should be ignored) otherwise false

isDelimiter

protected boolean isDelimiter(byte b)

Determines whether a given character is a delimiter

Parameters:

b - the character to evaluate

Returns:

true if b is a delimiter; otherwise false

getWordCount

protected int getWordCount()

setWordCount

protected void setWordCount(int wordCount)

isTreatGroupedDelimitersAsOne

protected boolean isTreatGroupedDelimitersAsOne()

setTreatGroupedDelimitersAsOne

protected void setTreatGroupedDelimitersAsOne(boolean treatGroupedDelimitersAsOne)

isSkipBlankLines

protected boolean isSkipBlankLines()

setSkipBlankLines

protected void setSkipBlankLines(boolean skipBlankLines)