htsjdk.samtools.util

Class AbstractLocusInfo<E extends AbstractRecordAndOffset>

java.lang.Object

htsjdk.samtools.util.AbstractLocusInfo<E>

All Implemented Interfaces:

Locus

Direct Known Subclasses:

SamLocusIterator.LocusInfo

public class AbstractLocusInfo<E extends AbstractRecordAndOffset>
extends java.lang.Object
implements Locus

The unit of iteration for AbstractLocusIterator. Holds information about the locus (the SAMSequenceRecord and 1-based position on the reference), plus list of AbstractRecordAndOffset objects, If RecordAndOffset class is used, one object represents one aligned read that overlaps the locus. If TypedRecordAndOffset class is used, one object represents one aligned read, that starts or ends at the locus.

Constructor Summary

Constructors

Constructor and Description
AbstractLocusInfo(SAMSequenceRecord referenceSequence, int position)

Method Summary

Modifier and Type	Method and Description
void	add(E recordAndOffset) Accumulates info for one read aligned to the locus.
int	getPosition()
java.util.List<E>	getRecordAndOffsets()
java.util.List<E>	getRecordAndPositions() Deprecated. since name of the method can be confusing, new implementation should be used getRecordAndOffsets()
int	getSequenceIndex()
int	getSequenceLength()
java.lang.String	getSequenceName()
boolean	isEmpty()
int	size()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractLocusInfo

public AbstractLocusInfo(SAMSequenceRecord referenceSequence,
                         int position)

Parameters:

referenceSequence - reference sequence to which the reads are aligned

position - position in the sequence to which the reads are aligned

Method Detail

add

public void add(E recordAndOffset)

Accumulates info for one read aligned to the locus. Method doesn't check, that recordAndOffset is really aligned to current reference position, so it must have valid reference sequence and position or further processing can go wrong.

Parameters:

recordAndOffset - object to add to current locus

getSequenceIndex

public int getSequenceIndex()

Specified by:

getSequenceIndex in interface Locus

Returns:

the index of reference sequence

getPosition

public int getPosition()

Specified by:

getPosition in interface Locus

Returns:

1-based reference position

getRecordAndPositions

@Deprecated
public java.util.List<E> getRecordAndPositions()

Deprecated. since name of the method can be confusing, new implementation should be used getRecordAndOffsets()

Returns:

unmodifiable list of aligned to the reference position recordsAndOffsets

getRecordAndOffsets

public java.util.List<E> getRecordAndOffsets()

Returns:

unmodifiable list of aligned to the reference position recordsAndOffsets

getSequenceName

public java.lang.String getSequenceName()

Returns:

the name of reference sequence

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getSequenceLength

public int getSequenceLength()

Returns:

the length of reference sequence

size

public int size()

Returns:

the number of records overlapping the position

isEmpty

public boolean isEmpty()

Returns:

true if RecordAndOffset list is empty;