Package vcf

Class RefIt

java.lang.Object

vcf.RefIt

All Implemented Interfaces:

FileIt<RefGTRec>, SampleFileIt<RefGTRec>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<RefGTRec>

public class RefIt
extends java.lang.Object
implements SampleFileIt<RefGTRec>

Class RefIt represents an iterator whose next() method returns an object storing data from a VCF record with phased, non-missing genotypes.

Instances of class RefIt are not thread-safe.

Methods of this class will terminate the Java Virtual Machine with an error message if an I/O error or file format error is detected.

Field Summary

Fields

Modifier and Type	Field	Description
static int	MAX_EM_BUFFER_SIZE	The default number of GTRec objects that are stored in a buffer.

Method Summary

Modifier and Type	Method	Description
void	close()	Terminates the iteration and releases any system resources that are held by this object.
static RefIt	create(FileIt<java.lang.String> strIt)	Create and returns a new RefIt instance from the specified iterator.
static RefIt	create(FileIt<java.lang.String> strIt, Filter<java.lang.String> sampleFilter, Filter<Marker> markerFilter, int bufferSize)	Create and returns a new RefIt instance from the specified objects.
java.io.File	file()	Returns the file from which the data are read, or null if the data are read from standard input or are computed data.
boolean	hasNext()	Returns true if the iteration has more elements, and returns false otherwise.
RefGTRec	next()	Returns the next element in the iteration.
static RefGTRec	recodeIfLowFreq(RefGTRec rec)
void	remove()	The remove method is not supported by this iterator.
Samples	samples()	Returns the list of samples.
java.lang.String	toString()	Returns a string representation of this.

Methods inherited from interface java.util.Iterator

forEachRemaining

Methods inherited from class java.lang.Object

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

Field Detail

MAX_EM_BUFFER_SIZE

public static final int MAX_EM_BUFFER_SIZE

The default number of GTRec objects that are stored in a buffer.

See Also:

Constant Field Values

Method Detail

create

public static RefIt create(FileIt<java.lang.String> strIt)

Create and returns a new RefIt instance from the specified iterator.

Parameters:

strIt - an iterator that returns lines of a VCF file

Returns:

a new RefIt instance

Throws:

java.lang.IllegalArgumentException - if a format error is detected in a line of a VCF file returned by strIt

java.lang.NullPointerException - if strIt == null

create

public static RefIt create(FileIt<java.lang.String> strIt,
                           Filter<java.lang.String> sampleFilter,
                           Filter<Marker> markerFilter,
                           int bufferSize)

Create and returns a new RefIt instance from the specified objects.

Parameters:

strIt - an iterator that returns lines of a VCF file

sampleFilter - a sample filter or null

markerFilter - a marker filter or null

bufferSize - the buffer size

Returns:

a new RefIt instance

Throws:

java.lang.IllegalArgumentException - if a format error is detected in a line of a VCF file returned by strItt

java.lang.IllegalArgumentException - if bufferSize < 1

java.lang.NullPointerException - if strIt == null

close

public void close()

Description copied from interface: FileIt

Terminates the iteration and releases any system resources that are held by this object. After invoking close(), further invocations of close() have no effect.

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface FileIt<RefGTRec>

hasNext

public boolean hasNext()

Returns true if the iteration has more elements, and returns false otherwise.

Specified by:

hasNext in interface java.util.Iterator<RefGTRec>

Returns:

true if the iteration has more elements

next

public RefGTRec next()

Returns the next element in the iteration.

Specified by:

next in interface java.util.Iterator<RefGTRec>

Returns:

the next element in the iteration

Throws:

java.util.NoSuchElementException - if the iteration has no more elements

remove

public void remove()

The remove method is not supported by this iterator.

Specified by:

remove in interface java.util.Iterator<RefGTRec>

Throws:

java.lang.UnsupportedOperationException - if this method is invoked

file

public java.io.File file()

Description copied from interface: FileIt

Returns the file from which the data are read, or null if the data are read from standard input or are computed data.

Specified by:

file in interface FileIt<RefGTRec>

Returns:

the file from which the data are read, or null if the data are read from standard input or are computed data

samples

public Samples samples()

Description copied from interface: SampleFileIt

Returns the list of samples.

Specified by:

samples in interface SampleFileIt<RefGTRec>

Returns:

the list of samples

toString

public java.lang.String toString()

Description copied from interface: FileIt

Returns a string representation of this. The exact details of the representation are unspecified and subject to change.

Specified by:

toString in interface FileIt<RefGTRec>

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this

recodeIfLowFreq

public static RefGTRec recodeIfLowFreq(RefGTRec rec)