Constructor Detail

• ChrIndex

  public ChrIndex()

  Default constructor needed for factory methods -- DO NOT REMOVE

• ChrIndex

  public ChrIndex(String name)

Method Detail

• getName

  public String getName()

  Specified by:

  getName in interface ChrIndex

• insert

  public void insert(Interval iv)

• getBlocks

  public List<Block> getBlocks()

  Specified by:

  getBlocks in interface ChrIndex

  Returns:

  all blocks in ChrIndex

• getBlocks

  public List<Block> getBlocks(int start,
                               int end)

  Specified by:

  getBlocks in interface ChrIndex

  Parameters:

  start - the start position, one based

  end - the end position, one based

  Returns:

  a list of blocks that include the region defined from start to stop. Can never return null

• printTree

  public void printTree()

• write

  public void write(LittleEndianOutputStream dos)
             throws IOException

  Specified by:

  write in interface ChrIndex

  Throws:

  IOException

• read

  public void read(LittleEndianInputStream dis)
            throws IOException

  Specified by:

  read in interface ChrIndex

  Throws:

  IOException