Package htsjdk.tribble.index.interval

Class IntervalTreeIndex

java.lang.Object

htsjdk.tribble.index.AbstractIndex

htsjdk.tribble.index.interval.IntervalTreeIndex

All Implemented Interfaces:

Index, MutableIndex

public class IntervalTreeIndex
extends AbstractIndex

Index based on an interval tree

See Also:

• IntervalTree

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	IntervalTreeIndex.ChrIndex

Nested classes/interfaces inherited from class htsjdk.tribble.index.AbstractIndex

AbstractIndex.BlockStats, AbstractIndex.IndexType

Field Summary

Fields

Modifier and Type	Field	Description
static final int	INDEX_TYPE

Fields inherited from class htsjdk.tribble.index.AbstractIndex

chrIndices, flags, indexedFileMD5, indexedFileSize, indexedFileTS, indexedPath, logger, MAGIC_NUMBER, version, VERSION

Constructor Summary

Constructors

Constructor	Description
IntervalTreeIndex(InputStream inputStream)	Load from file.
IntervalTreeIndex(String featureFile)	Prepare to build an index.
IntervalTreeIndex(Path featureFile)	Prepare to build an index.

Method Summary

Modifier and Type	Method	Description
Class	getChrIndexClass()	returns the class for the index type
protected int	getType()	get the index type
void	insert(String chr, Interval interval)	Add a new interval to this index
void	printTree()
protected void	setChrIndex(List<IntervalTreeIndex.ChrIndex> indicies)

Methods inherited from class htsjdk.tribble.index.AbstractIndex

addProperties, addProperty, containsChromosome, equalsIgnoreProperties, finalizeIndex, getBlocks, getBlocks, getBlockStats, getFlags, getIndexedFile, getIndexedFileMD5, getIndexedFileSize, getIndexedFileTS, getIndexedPath, getProperties, getSequenceNames, getVersion, hasFileSize, hasMD5, hasTimestamp, isCurrentVersion, printIndexInfo, read, setMD5, statsSummary, validateIndexHeader, write, write, writeBasedOnFeaturePath

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.tribble.index.Index

write, writeBasedOnFeatureFile

Field Details

INDEX_TYPE

public static final int INDEX_TYPE

Constructor Details

IntervalTreeIndex

public IntervalTreeIndex(InputStream inputStream)
                  throws IOException

Load from file.

Parameters:

inputStream - This method assumes that the input stream is already buffered as appropriate. Caller should close after this object is constructed.

Throws:

IOException

IntervalTreeIndex

public IntervalTreeIndex(Path featureFile)

Prepare to build an index.

Parameters:

featureFile - File which we are indexing

IntervalTreeIndex

public IntervalTreeIndex(String featureFile)

Prepare to build an index.

Parameters:

featureFile - File which we are indexing

Method Details

getChrIndexClass

public Class getChrIndexClass()

Description copied from class: AbstractIndex

returns the class for the index type

Specified by:

getChrIndexClass in class AbstractIndex

Returns:

a Class, from which a new instance can be created

getType

protected int getType()

Description copied from class: AbstractIndex

get the index type

Specified by:

getType in class AbstractIndex

Returns:

The index type

insert

public void insert(String chr,
 Interval interval)

Add a new interval to this index

Parameters:

chr - Chromosome

interval -

setChrIndex

protected void setChrIndex(List<IntervalTreeIndex.ChrIndex> indicies)

printTree

public void printTree()