htsjdk.tribble.index.linear

Class LinearIndex.ChrIndex

java.lang.Object

htsjdk.tribble.index.linear.LinearIndex.ChrIndex

All Implemented Interfaces:

ChrIndex

Enclosing class:

LinearIndex

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

Blocks are organized as a simple flat list:

Block 0 Block 1 Block 2

There's a constant bin width, so that each block corresponds to a specific interval over the genome based on its index, as in:

Block 0: (0 - binWidth] Block 1: (binWidth - 2 * binWidth] Block 2: (2 * binWidth - 3 * binWidth]

Note that covered regions are open on the left ( and closed on the right ].

In general, if block i is the ith block (starting from 0), then block i contains all records that have starting position > (i * binWidth) and <= ((i + 1) * binWidth))

Constructor Summary

Constructors

Constructor and Description
ChrIndex() Default constructor needed for factory methods -- DO NOT REMOVE

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object obj)
double	getAverageFeatureSize()
java.util.List<Block>	getBlocks()
java.util.List<Block>	getBlocks(int start, int end)
double	getFeaturesPerBlock()
java.lang.String	getName()
int	getNBlocks()
int	getNFeatures()
long	getTotalSize()
void	incrementFeatureCount()
LinearIndex.ChrIndex	optimize(double threshold)
void	read(LittleEndianInputStream dis)
void	updateLongestFeature(int featureLength)
void	write(LittleEndianOutputStream dos)

Methods inherited from class java.lang.Object

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

Constructor Detail

ChrIndex

public ChrIndex()

Default constructor needed for factory methods -- DO NOT REMOVE

Method Detail

getName

public java.lang.String getName()

Specified by:

getName in interface ChrIndex

getNBlocks

public int getNBlocks()

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

updateLongestFeature

public void updateLongestFeature(int featureLength)

getNFeatures

public int getNFeatures()

incrementFeatureCount

public void incrementFeatureCount()

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

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

getTotalSize

public long getTotalSize()

Returns:

Total size of all blocks

getAverageFeatureSize

public double getAverageFeatureSize()

getFeaturesPerBlock

public double getFeaturesPerBlock()

optimize

public LinearIndex.ChrIndex optimize(double threshold)