Package htsjdk.tribble.index.linear

Class LinearIndex

java.lang.Object

htsjdk.tribble.index.AbstractIndex

htsjdk.tribble.index.linear.LinearIndex

All Implemented Interfaces:

Index, MutableIndex

public class LinearIndex
extends AbstractIndex

Index defined by dividing the genome by chromosome, then each chromosome into bins of fixed width (in genomic coordinates). Features are allocated to bins by start position. The longest feature in each recorded and used to adjust the start position of a query to include all bins that might have a feature that overlaps the query interval. This works well for feature sets of approximately homogeneous length, or whose longest feature is on the order of the bin width or less.

magicNumber integer type integer version integer filename null terminated character array filesize long lastModified long md5 String flags integer

------ LINEAR INDEX nChromosomes integer

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	LinearIndex.ChrIndex	Blocks are organized as a simple flat list:

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

AbstractIndex.BlockStats, AbstractIndex.IndexType

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	enableAdaptiveIndexing
static final int	INDEX_TYPE
static final double	MAX_FEATURES_PER_BIN

Fields inherited from class htsjdk.tribble.index.AbstractIndex

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

Constructor Summary

Constructors

Constructor	Description
LinearIndex(InputStream inputStream)	Load from file.
LinearIndex(String featureFile)	Initialize with default parameters
LinearIndex(Path featurePath)	Initialize with default parameters
LinearIndex(List<LinearIndex.ChrIndex> indices, File featureFile)	Initialize using the specified indices
LinearIndex(List<LinearIndex.ChrIndex> indices, Path featureFile)	Initialize using the specified indices

Method Summary

Modifier and Type	Method	Description
Class	getChrIndexClass()	returns the class for the index type
List<String>	getSequenceNames()
protected int	getType()	get the index type
boolean	isCurrentVersion()	check the current version against the version we read in
Index	optimize()
Index	optimize(double threshold)	Adapative optimization of the linear index
protected final void	setTS(long ts)
void	writeTable(PrintStream out)	Code to convert linear index to a text table for analysis

Methods inherited from class htsjdk.tribble.index.AbstractIndex

addProperties, addProperty, containsChromosome, equalsIgnoreProperties, finalizeIndex, getBlocks, getBlocks, getBlockStats, getFlags, getIndexedFile, getIndexedFileMD5, getIndexedFileSize, getIndexedFileTS, getIndexedPath, getProperties, getVersion, hasFileSize, hasMD5, hasTimestamp, 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

MAX_FEATURES_PER_BIN

public static final double MAX_FEATURES_PER_BIN

INDEX_TYPE

public static final int INDEX_TYPE

enableAdaptiveIndexing

public static boolean enableAdaptiveIndexing

Constructor Details

LinearIndex

public LinearIndex(List<LinearIndex.ChrIndex> indices,
 Path featureFile)

Initialize using the specified indices

Parameters:

indices -

featureFile -

LinearIndex

public LinearIndex(List<LinearIndex.ChrIndex> indices,
 File featureFile)

Initialize using the specified indices

Parameters:

indices -

featureFile -

LinearIndex

public LinearIndex(String featureFile)

Initialize with default parameters

Parameters:

featureFile - File for which this is an index

LinearIndex

public LinearIndex(Path featurePath)

Initialize with default parameters

Parameters:

featurePath - Path for which this is an index

LinearIndex

public LinearIndex(InputStream inputStream)
            throws IOException

Load from file.

Parameters:

inputStream - This method assumes that the input stream is already buffered as appropriate.

Throws:

IOException

Method Details

isCurrentVersion

public boolean isCurrentVersion()

Description copied from class: AbstractIndex

check the current version against the version we read in

Specified by:

isCurrentVersion in interface Index

Overrides:

isCurrentVersion in class AbstractIndex

Returns:

true if we're up to date, false otherwise

getType

protected int getType()

Description copied from class: AbstractIndex

get the index type

Specified by:

getType in class AbstractIndex

Returns:

The index type

getSequenceNames

public List<String> getSequenceNames()

Specified by:

getSequenceNames in interface Index

Overrides:

getSequenceNames in class AbstractIndex

Returns:

a list of the sequence names we've seen during indexing, in order

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

optimize

public Index optimize(double threshold)

Adapative optimization of the linear index

Parameters:

threshold - threshold to use for optimizing each constituent chrIndex

Returns:

The new optimized index

optimize

public Index optimize()

writeTable

public void writeTable(PrintStream out)

Code to convert linear index to a text table for analysis

Parameters:

out - Stream to which to write out table to

setTS

protected final void setTS(long ts)