Constructor and Description |
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Bin(int referenceSequence,
int binNumber) |
Modifier and Type | Method and Description |
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void |
addInitialChunk(Chunk newChunk)
Adds the first chunk to the bin
|
int |
compareTo(Bin other)
Compare two bins to see what ordering they should appear in.
|
boolean |
containsChunks()
Returns whether the bin currently contains chunks.
|
boolean |
equals(java.lang.Object other)
See whether two bins are equal.
|
int |
getBinNumber() |
java.util.List<Chunk> |
getChunkList()
Gets the list of chunks associated with this bin.
|
Chunk |
getLastChunk()
Warning: Currently only valid during index building, not when reading existing index,
(AbstractBAMFileIndex.optimizeChunkList doesn't maintain this)
|
protected int |
getReferenceSequence() |
int |
hashCode()
Compute a unique hash code for the given reference sequence and bin number.
|
void |
setChunkList(java.util.List<Chunk> list)
Sets the chunks associated with this bin
|
void |
setLastChunk(Chunk c)
Optimization to keep lastChunk instead of iterating over all chunks repeatedly
|
protected int getReferenceSequence()
public int getBinNumber()
public boolean equals(java.lang.Object other)
equals
in class java.lang.Object
other
- The other Bin to which to compare this.public int hashCode()
hashCode
in class java.lang.Object
public boolean containsChunks()
public int compareTo(Bin other)
compareTo
in interface java.lang.Comparable<Bin>
other
- Other bin to which this bin should be compared.public void addInitialChunk(Chunk newChunk)
public void setChunkList(java.util.List<Chunk> list)
public java.util.List<Chunk> getChunkList()
public void setLastChunk(Chunk c)
public Chunk getLastChunk()