htsjdk.tribble.index

Interface Index

All Known Subinterfaces:

MutableIndex

All Known Implementing Classes:

AbstractIndex, IntervalTreeIndex, LinearIndex, TabixIndex

public interface Index

Interface for all index implementations. An index file is used for efficient lookup of features from a feature file; and Index represents that index file.

Method Summary

Modifier and Type	Method and Description
boolean	containsChromosome(java.lang.String chr)
boolean	equalsIgnoreProperties(java.lang.Object obj) Returns true if this and obj are 'effectively' equivalent indices.
java.util.List<Block>	getBlocks(java.lang.String chr, int start, int end) Query the index.
java.util.Map<java.lang.String,java.lang.String>	getProperties()
java.util.List<java.lang.String>	getSequenceNames()
boolean	isCurrentVersion()
default void	write(java.io.File idxFile) Writes the index into a file.
void	write(LittleEndianOutputStream stream) all indexes are writable to disk
void	write(java.nio.file.Path indexPath) Writes the index into a path.
default void	writeBasedOnFeatureFile(java.io.File featureFile) Write an appropriately named and located Index file based on the name and location of the featureFile.
void	writeBasedOnFeaturePath(java.nio.file.Path featurePath) Write an appropriately named and located Index file based on the name and location of the featureFile.

Method Detail

getBlocks

java.util.List<Block> getBlocks(java.lang.String chr,
                                int start,
                                int end)

Query the index.

Parameters:

chr - the chromosome

start - the start position

end - the end position

Returns:

a list of blocks that contain the specified interval. Can never return null

Throws:

java.lang.IllegalArgumentException - of chr isn't part of this index

isCurrentVersion

boolean isCurrentVersion()

Returns:

true if the index is up to date, false otherwise

getSequenceNames

java.util.List<java.lang.String> getSequenceNames()

Returns:

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

containsChromosome

boolean containsChromosome(java.lang.String chr)

Parameters:

chr - the chromosome (or contig) name

Returns:

true if we have an entry; false otherwise

write

void write(LittleEndianOutputStream stream)
    throws java.io.IOException

all indexes are writable to disk

Parameters:

stream - the stream to write the index to. Caller must close after invocation.

Throws:

java.io.IOException - if the index is unable to write to the specified location

write

default void write(java.io.File idxFile)
            throws java.io.IOException

Writes the index into a file. Default implementation delegates to write(Path)

Parameters:

idxFile - Where to write the index.

Throws:

java.io.IOException - if the index is unable to write to the specified file

write

void write(java.nio.file.Path indexPath)
    throws java.io.IOException

Writes the index into a path.

Parameters:

indexPath - Where to write the index.

Throws:

java.io.IOException - if the index is unable to write to the specified path.

writeBasedOnFeatureFile

default void writeBasedOnFeatureFile(java.io.File featureFile)
                              throws java.io.IOException

Write an appropriately named and located Index file based on the name and location of the featureFile. Default implementation delegates to writeBasedOnFeaturePath(Path)

Parameters:

featureFile -

Throws:

java.io.IOException - if featureFile is not a normal file.

writeBasedOnFeaturePath

void writeBasedOnFeaturePath(java.nio.file.Path featurePath)
                      throws java.io.IOException

Write an appropriately named and located Index file based on the name and location of the featureFile. If featureFile is not a normal file, the index will silently not be written.

Parameters:

featurePath -

Throws:

java.io.IOException - if featureFile is not a normal file.

getProperties

java.util.Map<java.lang.String,java.lang.String> getProperties()

Returns:

get the list of properties for this index. Returns null if no properties.

equalsIgnoreProperties

boolean equalsIgnoreProperties(java.lang.Object obj)

Returns true if this and obj are 'effectively' equivalent indices. Ignores the time stamp on the file, as this may not be the same for even identical indices

Parameters:

obj -

Returns: