Package picard.illumina.parser
Class ReadStructure.Substructure
- java.lang.Object
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- picard.illumina.parser.ReadStructure.Substructure
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- All Implemented Interfaces:
Iterable<ReadDescriptor>
- Enclosing class:
- ReadStructure
public class ReadStructure.Substructure extends Object implements 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
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Constructor Summary
Constructors Constructor Description Substructure(List<Integer> descriptorIndices, 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)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description ReadDescriptor
get(int index)
Range[]
getCycleIndexRanges()
int[]
getCycles()
int[]
getDescriptorLengths()
int[]
getIndices()
int
getTotalCycles()
boolean
isEmpty()
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
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Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Detail
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Substructure
public Substructure(List<Integer> descriptorIndices, 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 ReadStructureallRanges
- A list of ranges for all reads (not just those in this substructure) in the same order as ReadStructure.descriptors
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Method Detail
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get
public ReadDescriptor get(int index)
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isEmpty
public boolean isEmpty()
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length
public int length()
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getTotalCycles
public int getTotalCycles()
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getIndices
public int[] getIndices()
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getDescriptorLengths
public int[] getDescriptorLengths()
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getCycleIndexRanges
public Range[] getCycleIndexRanges()
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iterator
public Iterator<ReadDescriptor> iterator()
- Specified by:
iterator
in interfaceIterable<ReadDescriptor>
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getCycles
public int[] getCycles()
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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
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