picard.util

Class SequenceDictionaryUtils.SamSequenceRecordsIterator

java.lang.Object

picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator

All Implemented Interfaces:

java.util.Iterator<htsjdk.samtools.SAMSequenceRecord>

Enclosing class:

SequenceDictionaryUtils

public static class SequenceDictionaryUtils.SamSequenceRecordsIterator
extends java.lang.Object
implements java.util.Iterator<htsjdk.samtools.SAMSequenceRecord>

Constructor Summary

Constructors

Constructor and Description
SamSequenceRecordsIterator(java.io.File referenceSequence, boolean truncateNamesAtWhitespace)

Method Summary

Modifier and Type	Method and Description
boolean	hasNext()
htsjdk.samtools.SAMSequenceRecord	next()
void	setGenomeAssembly(java.lang.String genomeAssembly)
void	setSpecies(java.lang.String species)
void	setUri(java.lang.String uri)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining, remove

Constructor Detail

SamSequenceRecordsIterator

public SamSequenceRecordsIterator(java.io.File referenceSequence,
                                  boolean truncateNamesAtWhitespace)

Method Detail

setGenomeAssembly

public void setGenomeAssembly(java.lang.String genomeAssembly)

setUri

public void setUri(java.lang.String uri)

setSpecies

public void setSpecies(java.lang.String species)

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<htsjdk.samtools.SAMSequenceRecord>

next

public htsjdk.samtools.SAMSequenceRecord next()

Specified by:

next in interface java.util.Iterator<htsjdk.samtools.SAMSequenceRecord>