picard.illumina.parser

Class ReadStructure.Substructure

java.lang.Object

picard.illumina.parser.ReadStructure.Substructure

All Implemented Interfaces:

java.lang.Iterable<ReadDescriptor>

Enclosing class:

ReadStructure

public class ReadStructure.Substructure
extends java.lang.Object
implements java.lang.Iterable<ReadDescriptor>

Represents a subset of ReadDescriptors in the containing ReadStructure, they ARE NOT necessarily contiguous in the containing ReadStructure but they ARE in the order they appear in the containing ReadStructure

Constructor Summary

Constructors

Constructor and Description
Substructure(java.util.List<java.lang.Integer> descriptorIndices, java.util.List<Range> allRanges) Indices into the ReadStructure.descriptors for this specific substructure, indices must be in the order they appear in the descriptors list (but the indices do NOT have to be continuous)

Method Summary

Modifier and Type	Method and Description
ReadDescriptor	get(int index)
Range[]	getCycleIndexRanges()
int[]	getCycles()
int[]	getDescriptorLengths()
int[]	getIndices()
int	getTotalCycles()
boolean	isEmpty()
java.util.Iterator<ReadDescriptor>	iterator()
int	length()
ReadStructure	toReadStructure() Create a ReadStructure from this substructure composed of only the descriptors contained in this substructure, Any ReadDescriptors not in this substructure are treated as if they don't exist (e.g.

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

Constructor Detail

Substructure

public Substructure(java.util.List<java.lang.Integer> descriptorIndices,
                    java.util.List<Range> allRanges)

Indices into the ReadStructure.descriptors for this specific substructure, indices must be in the order they appear in the descriptors list (but the indices do NOT have to be continuous)

Parameters:

descriptorIndices - A list of indices into ReadStructure.descriptors of the enclosing ReadStructure

allRanges - A list of ranges for all reads (not just those in this substructure) in the same order as ReadStructure.descriptors

Method Detail

get

public ReadDescriptor get(int index)

isEmpty

public boolean isEmpty()

length

public int length()

getTotalCycles

public int getTotalCycles()

getIndices

public int[] getIndices()

getDescriptorLengths

public int[] getDescriptorLengths()

getCycleIndexRanges

public Range[] getCycleIndexRanges()

iterator

public java.util.Iterator<ReadDescriptor> iterator()

Specified by:

iterator in interface java.lang.Iterable<ReadDescriptor>

getCycles

public int[] getCycles()

toReadStructure

public ReadStructure toReadStructure()

Create a ReadStructure from this substructure composed of only the descriptors contained in this substructure, Any ReadDescriptors not in this substructure are treated as if they don't exist (e.g. if you have a readStructure (36T8S8B36T) and this substructure consists of all the non-skipped reads than toReadStructure would return (36T8B36T) in ReadStructure form