public class BinningIndexContent
extends java.lang.Object
Modifier and Type | Class and Description |
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static class |
BinningIndexContent.BinList
This class is used to encapsulate the list of Bins store in the BAMIndexContent
While it is currently represented as an array, we may decide to change it to an ArrayList or other structure
|
Constructor and Description |
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BinningIndexContent(int referenceSequence,
BinningIndexContent.BinList binList,
LinearIndex linearIndex) |
Modifier and Type | Method and Description |
---|---|
boolean |
containsBin(Bin bin)
Does this content have anything in this bin?
|
boolean |
equals(java.lang.Object o) |
java.util.List<Chunk> |
getAllChunks() |
BinningIndexContent.BinList |
getBins() |
java.util.List<Chunk> |
getChunksOverlapping(int startPos,
int endPos) |
LinearIndex |
getLinearIndex() |
int |
getReferenceSequence()
Reference for this Content
|
int |
hashCode() |
public BinningIndexContent(int referenceSequence, BinningIndexContent.BinList binList, LinearIndex linearIndex)
referenceSequence
- Content corresponds to this reference.binList
- Array of bins represented by this content, possibly sparselinearIndex
- Additional index used to optimize queriespublic int getReferenceSequence()
public boolean containsBin(Bin bin)
public BinningIndexContent.BinList getBins()
public java.util.List<Chunk> getAllChunks()
public LinearIndex getLinearIndex()
public java.util.List<Chunk> getChunksOverlapping(int startPos, int endPos)
startPos
- 1-based, inclusiveendPos
- 1-based, inclusivepublic boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object