htsjdk.tribble.index.interval

Class IntervalTreeIndex.ChrIndex

java.lang.Object

htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex

All Implemented Interfaces:

ChrIndex

Enclosing class:

IntervalTreeIndex

public static class IntervalTreeIndex.ChrIndex
extends java.lang.Object
implements ChrIndex

Constructor Summary

Constructors

Constructor and Description
ChrIndex() Default constructor needed for factory methods -- DO NOT REMOVE
ChrIndex(java.lang.String name)

Method Summary

Modifier and Type	Method and Description
java.util.List<Block>	getBlocks()
java.util.List<Block>	getBlocks(int start, int end)
java.lang.String	getName()
void	insert(Interval iv)
void	printTree()
void	read(LittleEndianInputStream dis)
void	write(LittleEndianOutputStream dos)

Methods inherited from class java.lang.Object

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

Constructor Detail

ChrIndex

public ChrIndex()

Default constructor needed for factory methods -- DO NOT REMOVE

ChrIndex

public ChrIndex(java.lang.String name)

Method Detail

getName

public java.lang.String getName()

Specified by:

getName in interface ChrIndex

insert

public void insert(Interval iv)

getBlocks

public java.util.List<Block> getBlocks()

Specified by:

getBlocks in interface ChrIndex

Returns:

all blocks in ChrIndex

getBlocks

public java.util.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 java.io.IOException

Specified by:

write in interface ChrIndex

Throws:

java.io.IOException

read

public void read(LittleEndianInputStream dis)
          throws java.io.IOException

Specified by:

read in interface ChrIndex

Throws:

java.io.IOException