Package htsjdk.samtools

Class Bin

java.lang.Object
htsjdk.samtools.Bin
All Implemented Interfaces:
Comparable<Bin>
Direct Known Subclasses:
BinWithOffset
public class Bin extends Object implements Comparable<Bin>
An individual bin in a BAM file.

  • Constructor Summary

    Constructors
    Constructor
    Description
    Bin(int referenceSequence, int binNumber)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addChunk(Chunk newChunk)
    Adds a chunk to the bin (may be the first chunk or a later one).
    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(Object other)
    See whether two bins are equal.
    int
    getBinNumber()
     
    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(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

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • Bin

      public Bin(int referenceSequence, int binNumber)

  • Method Details

    • getReferenceSequence

      protected int getReferenceSequence()

    • getBinNumber

      public int getBinNumber()

    • equals

      public boolean equals(Object other)
      See whether two bins are equal. If the ref seq and the bin number are equal, assume equality of the chunk list.
      Overrides:
      equals in class Object
      Parameters:
      other - The other Bin to which to compare this.
      Returns:
      True if the two bins are equal. False otherwise.

    • hashCode

      public int hashCode()
      Compute a unique hash code for the given reference sequence and bin number.
      Overrides:
      hashCode in class Object
      Returns:
      A unique hash code.

    • containsChunks

      public boolean containsChunks()
      Returns whether the bin currently contains chunks.
      Returns:
      True if the bin has chunks, false otherwise.

    • compareTo

      public int compareTo(Bin other)
      Compare two bins to see what ordering they should appear in.
      Specified by:
      compareTo in interface Comparable<Bin>
      Parameters:
      other - Other bin to which this bin should be compared.
      Returns:
      -1 if this < other, 0 if this == other, 1 if this > other.

    • addInitialChunk

      public void addInitialChunk(Chunk newChunk)
      Adds the first chunk to the bin

    • addChunk

      public void addChunk(Chunk newChunk)
      Adds a chunk to the bin (may be the first chunk or a later one).
      Parameters:
      newChunk - the chunk to add

    • setChunkList

      public void setChunkList(List<Chunk> list)
      Sets the chunks associated with this bin

    • getChunkList

      public List<Chunk> getChunkList()
      Gets the list of chunks associated with this bin.
      Returns:
      the chunks in this bin. If no chunks are associated, an empty list will be returned.

    • setLastChunk

      public void setLastChunk(Chunk c)
      Optimization to keep lastChunk instead of iterating over all chunks repeatedly

    • getLastChunk

      public Chunk getLastChunk()
      Warning: Currently only valid during index building, not when reading existing index, (AbstractBAMFileIndex.optimizeChunkList doesn't maintain this)
      Returns:
      the last Chunk of the chunkList