htsjdk.tribble.index

Class AbstractIndex

java.lang.Object

htsjdk.tribble.index.AbstractIndex

All Implemented Interfaces:

Index, MutableIndex

Direct Known Subclasses:

IntervalTreeIndex, LinearIndex

public abstract class AbstractIndex
extends java.lang.Object
implements MutableIndex

An abstract implementation of the index class. This class takes care of the basics that are common to all of the current indexing classes; including the version information, common header properties, and reading and writing the header to disk.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	AbstractIndex.BlockStats
static class	AbstractIndex.IndexType

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.LinkedHashMap<java.lang.String,ChrIndex>	chrIndices the map of our chromosome bins
protected int	flags
protected java.io.File	indexedFile
protected java.lang.String	indexedFileMD5
protected long	indexedFileSize
protected long	indexedFileTS
static int	MAGIC_NUMBER
protected int	version
static int	VERSION

Constructor Summary

Constructors

Constructor and Description
AbstractIndex() create an abstract index, with defaults for the version value, and empty properties and chromosome lists
AbstractIndex(AbstractIndex parent)
AbstractIndex(java.io.File featureFile)
AbstractIndex(java.lang.String featureFile) create an index file from the target feature file

Method Summary

Methods

Modifier and Type	Method and Description
void	addProperties(java.util.Map<java.lang.String,java.lang.String> properties)
void	addProperty(java.lang.String key, java.lang.String value)
boolean	containsChromosome(java.lang.String chr)
boolean	equalsIgnoreProperties(java.lang.Object obj) Returns true if this and obj are 'effectively' equivalent indices.
void	finalizeIndex()
java.util.List<Block>	getBlocks(java.lang.String chr)
java.util.List<Block>	getBlocks(java.lang.String chr, int start, int end) Query the index.
protected AbstractIndex.BlockStats	getBlockStats(boolean logDetails)
abstract java.lang.Class	getChrIndexClass() returns the class for the index type
int	getFlags()
java.io.File	getIndexedFile()
java.lang.String	getIndexedFileMD5()
long	getIndexedFileSize()
long	getIndexedFileTS()
java.util.Map<java.lang.String,java.lang.String>	getProperties() return a mapping of name to property value
java.util.List<java.lang.String>	getSequenceNames()
protected abstract int	getType() get the index type
int	getVersion()
boolean	hasFileSize()
boolean	hasMD5()
boolean	hasTimestamp()
boolean	isCurrentVersion() check the current version against the version we read in
protected void	printIndexInfo()
void	read(LittleEndianInputStream dis)
void	setMD5(java.lang.String md5)
protected java.lang.String	statsSummary()
protected void	validateIndexHeader(int indexType, LittleEndianInputStream dis)
void	write(LittleEndianOutputStream stream) all indexes are writable to disk
void	writeBasedOnFeatureFile(java.io.File featureFile) Write an appropriately named and located Index file based on the name and location of the featureFile.

Methods inherited from class java.lang.Object

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

Field Detail

VERSION

public static final int VERSION

See Also:

Constant Field Values

MAGIC_NUMBER

public static final int MAGIC_NUMBER

See Also:

Constant Field Values

version

protected int version

indexedFile

protected java.io.File indexedFile

indexedFileSize

protected long indexedFileSize

indexedFileTS

protected long indexedFileTS

indexedFileMD5

protected java.lang.String indexedFileMD5

flags

protected int flags

chrIndices

protected java.util.LinkedHashMap<java.lang.String,ChrIndex> chrIndices

the map of our chromosome bins

Constructor Detail

AbstractIndex

public AbstractIndex()

create an abstract index, with defaults for the version value, and empty properties and chromosome lists

AbstractIndex

public AbstractIndex(java.lang.String featureFile)

create an index file from the target feature file

Parameters:

featureFile - the feature file to create an index from

AbstractIndex

public AbstractIndex(java.io.File featureFile)

AbstractIndex

public AbstractIndex(AbstractIndex parent)

Method Detail

hasFileSize

public boolean hasFileSize()

hasTimestamp

public boolean hasTimestamp()

hasMD5

public boolean hasMD5()

equalsIgnoreProperties

public boolean equalsIgnoreProperties(java.lang.Object obj)

Description copied from interface: Index

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

Specified by:

equalsIgnoreProperties in interface Index

Parameters:

obj -

Returns:

true if this and obj are 'effectively' equivalent data structures.

validateIndexHeader

protected void validateIndexHeader(int indexType,
                       LittleEndianInputStream dis)
                            throws java.io.IOException

Throws:

java.io.IOException

isCurrentVersion

public boolean isCurrentVersion()

check the current version against the version we read in

Specified by:

isCurrentVersion in interface Index

Returns:

true if we're up to date, false otherwise

getIndexedFile

public java.io.File getIndexedFile()

getIndexedFileSize

public long getIndexedFileSize()

getIndexedFileTS

public long getIndexedFileTS()

getIndexedFileMD5

public java.lang.String getIndexedFileMD5()

getFlags

public int getFlags()

getVersion

public int getVersion()

setMD5

public void setMD5(java.lang.String md5)

containsChromosome

public boolean containsChromosome(java.lang.String chr)

Specified by:

containsChromosome in interface Index

Parameters:

chr - the chromosome (or contig) name

Returns:

true if we have an entry; false otherwise

finalizeIndex

public void finalizeIndex()

getSequenceNames

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

Specified by:

getSequenceNames in interface Index

Returns:

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

getBlocks

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

Description copied from interface: Index

Query the index.

Specified by:

getBlocks in interface 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

getBlocks

public java.util.List<Block> getBlocks(java.lang.String chr)

write

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

Description copied from interface: Index

all indexes are writable to disk

Specified by:

write in interface Index

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

writeBasedOnFeatureFile

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

Description copied from interface: Index

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.

Specified by:

writeBasedOnFeatureFile in interface Index

Throws:

java.io.IOException

read

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

Throws:

java.io.IOException

printIndexInfo

protected void printIndexInfo()

getBlockStats

protected AbstractIndex.BlockStats getBlockStats(boolean logDetails)

statsSummary

protected java.lang.String statsSummary()

addProperty

public void addProperty(java.lang.String key,
               java.lang.String value)

Specified by:

addProperty in interface MutableIndex

addProperties

public void addProperties(java.util.Map<java.lang.String,java.lang.String> properties)

Specified by:

addProperties in interface MutableIndex

getProperties

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

return a mapping of name to property value

Specified by:

getProperties in interface Index

Returns:

the mapping of values as an unmodifiable map

getType

protected abstract int getType()

get the index type

Returns:

The index type

getChrIndexClass

public abstract java.lang.Class getChrIndexClass()

returns the class for the index type

Returns:

a Class, from which a new instance can be created