net.maizegenetics.dna.map

Class AbstractTagsOnPhysicalMap

java.lang.Object

net.maizegenetics.dna.tag.AbstractTags

net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap

All Implemented Interfaces:

cern.colt.function.IntComparator, cern.colt.Swapper, TOPMInterface, Tags

Direct Known Subclasses:

TagsOnPhysicalMap, TagsOnPhysicalMapV3, TagsOnPhysMapHDF5

public abstract class AbstractTagsOnPhysicalMap
extends AbstractTags
implements TOPMInterface

Abstract TagsOnPhysicalMap object. Abstract alignment is implemented by two types of TOPM classes TagsOnPhysicalMap and TagsOnPhysMapHDF5. TagsOnPhysicalMap is fully loaded into memory when read, and it can only support one mapping position (the files are either binary or text). TagsOnPhysMapHDF5 can support a large number of mapping position, and only a portion of the data is loaded into memory. In most cases, TagsOnPhysMapHDF5 should be preferred going forward.

Author:

edbuckler

Field Summary

Fields inherited from interface net.maizegenetics.dna.map.TOPMInterface

BYTE_MISSING, INT_MISSING

Constructor Summary

Constructors

Constructor and Description
AbstractTagsOnPhysicalMap()

Method Summary

Modifier and Type	Method and Description
int	getChromosome(int index) Returns chromosome at give tag index.
int	getChromosomeIndex(int intChrName) Finds the index in the myChromosomes[] (length = # of chromosomes) corresponding to the provided int version of the chromosome name
int[]	getChromosomes() Returns an array whose values are the distinct chromosomes in this file, as stored in the chromosome[] array.
Chromosome[]	getLoci() Returns Loci created from getChromosomes().
Chromosome	getLocus(int tagIndex) Get Chromosome representing chromosome for given tag.
int	getMaxNumVariants() Returns maximum number of variants stored per tag.
byte	getMultiMaps(int index)
int	getSize() Returns number of tags.
int	getStartPosition(int index) Returns start position of given tag.
byte	getStrand(int tagIndex) Returns Strand for given tag.
int[]	getUniquePositions(int chromosome) Returns the set of unique positions for the given chromosome
byte[][]	getVariantDef() Returns variant definitions for all tags.
byte	getVariantDef(int tagIndex, int variantIndex) Returns variant definition at given tag and variant index.
byte[]	getVariantDefArray(int tagIndex) Returns an array containing all variant definitions for the tag at the supplied index.
byte[][]	getVariantOff() Returns variant position offsets for all tags.
byte	getVariantPosOff(int tagIndex, int variantIndex) Returns variant position offset from start position at given tag and variant index.
byte[]	getVariantPosOffArray(int tagIndex) Returns an array containing all variant position offsets for the tag at the supplied index.
int[]	mappedTags()
String	printRow(int row)
String	printRow(int row, boolean byPosition)
void	printRows(int numRows)
void	printRows(int numRows, boolean requirePhysPosition, boolean byPosition)
void	printRows(int numRows, boolean requirePhysPosition, int printChr)
static String	printWithMissing(byte b)
static String	printWithMissing(int i)
void	writeBinaryFile(File outFile)
void	writeBinaryFile(File outFile, int minResolution, boolean requirePhysPosition, boolean requireDCOMap, float minDCOP, boolean binary) TODO need to add LocusList to test, whether to include in output, move this to abstract
void	writeBinaryFileForChromosomalRegion(File outFile, int targetChr, int minPos, int maxPos) Outputs a new binary topm containing only tags with start positions that lie within the specified chromosomal region (inclusive).
void	writeTextFile(File outfile)

Methods inherited from class net.maizegenetics.dna.tag.AbstractTags

areTagsEqual, areTagsUnique, compare, compareTags, compareTags, compareTags, getNullTag, getTag, getTagCount, getTagIndex, getTagIndexFirst, getTagIndexSet, getTagLength, getTagLength, getTagSizeInLong, sort, swap

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.maizegenetics.dna.map.TOPMInterface

addVariant, clearVariants, compare, getDcoP, getDivergence, getEndPosition, getMapP, getPositionArray, getReadIndexForPositionIndex, setChromoPosition, setDivergence, setMapP, setMapP, setVariantDef, setVariantPosOff

Methods inherited from interface net.maizegenetics.dna.tag.Tags

areTagsUnique, getNullTag, getTag, getTagCount, getTagIndex, getTagIndexSet, getTagLength, getTagSizeInLong

Methods inherited from interface cern.colt.Swapper

swap

Methods inherited from interface cern.colt.function.IntComparator

equals

Constructor Detail

AbstractTagsOnPhysicalMap

public AbstractTagsOnPhysicalMap()

Method Detail

getMaxNumVariants

public int getMaxNumVariants()

Description copied from interface: TOPMInterface

Returns maximum number of variants stored per tag.

Specified by:

getMaxNumVariants in interface TOPMInterface

Returns:

maximum number of variants

getMultiMaps

public byte getMultiMaps(int index)

Specified by:

getMultiMaps in interface TOPMInterface

getChromosome

public int getChromosome(int index)

Description copied from interface: TOPMInterface

Returns chromosome at give tag index.

Specified by:

getChromosome in interface TOPMInterface

Parameters:

index - tag index

Returns:

chromosome

getSize

public int getSize()

Description copied from interface: TOPMInterface

Returns number of tags.

Specified by:

getSize in interface TOPMInterface

Returns:

number of tags

getStartPosition

public int getStartPosition(int index)

Description copied from interface: TOPMInterface

Returns start position of given tag.

Specified by:

getStartPosition in interface TOPMInterface

Parameters:

index - tag index

Returns:

start position

getStrand

public byte getStrand(int tagIndex)

Description copied from interface: TOPMInterface

Returns Strand for given tag.

Specified by:

getStrand in interface TOPMInterface

Parameters:

tagIndex - tag index

Returns:

1 = same sense as reference FASTA file. -1 = opposite sense. unknown = Byte.MIN_VALUE

getVariantDef

public byte[][] getVariantDef()

Description copied from interface: TOPMInterface

Returns variant definitions for all tags. First index of result is tag and second is variant.

Specified by:

getVariantDef in interface TOPMInterface

Returns:

all variant definitions

getVariantDef

public byte getVariantDef(int tagIndex,
                          int variantIndex)

Description copied from interface: TOPMInterface

Returns variant definition at given tag and variant index.

Specified by:

getVariantDef in interface TOPMInterface

Parameters:

tagIndex - tag index

variantIndex - variant index

Returns:

variant definition (see addVariant())

getVariantDefArray

public byte[] getVariantDefArray(int tagIndex)

Returns an array containing all variant definitions for the tag at the supplied index.

Specified by:

getVariantDefArray in interface TOPMInterface

Parameters:

tagIndex - tag index

Returns:

variant definitions for tag

getVariantOff

public byte[][] getVariantOff()

Description copied from interface: TOPMInterface

Returns variant position offsets for all tags. First index of result is tag and second is variant.

Specified by:

getVariantOff in interface TOPMInterface

Returns:

all variant position offsets

getVariantPosOff

public byte getVariantPosOff(int tagIndex,
                             int variantIndex)

Description copied from interface: TOPMInterface

Returns variant position offset from start position at given tag and variant index.

Specified by:

getVariantPosOff in interface TOPMInterface

Parameters:

tagIndex - tag index

variantIndex - variant index

Returns:

variant position offset

getVariantPosOffArray

public byte[] getVariantPosOffArray(int tagIndex)

Returns an array containing all variant position offsets for the tag at the supplied index.

Specified by:

getVariantPosOffArray in interface TOPMInterface

Parameters:

tagIndex - tag index

Returns:

variant position offsets for tag

printRow

public String printRow(int row)

printWithMissing

public static String printWithMissing(byte b)

printWithMissing

public static String printWithMissing(int i)

writeTextFile

public void writeTextFile(File outfile)

Specified by:

writeTextFile in interface TOPMInterface

getChromosomes

public int[] getChromosomes()

Description copied from interface: TOPMInterface

Returns an array whose values are the distinct chromosomes in this file, as stored in the chromosome[] array. The indices are arbitrary.

Specified by:

getChromosomes in interface TOPMInterface

Returns:

list of distinct chromosomes

getChromosomeIndex

public int getChromosomeIndex(int intChrName)

Description copied from interface: TOPMInterface

Finds the index in the myChromosomes[] (length = # of chromosomes) corresponding to the provided int version of the chromosome name

Specified by:

getChromosomeIndex in interface TOPMInterface

Returns:

int index of that chromosome if present (Integer.MIN_VALUE otherwise)

getUniquePositions

public int[] getUniquePositions(int chromosome)

Description copied from interface: TOPMInterface

Returns the set of unique positions for the given chromosome

Specified by:

getUniquePositions in interface TOPMInterface

Returns:

unique positions on chromosome

getLoci

public Chromosome[] getLoci()

Description copied from interface: TOPMInterface

Returns Loci created from getChromosomes().

Specified by:

getLoci in interface TOPMInterface

Returns:

Loci

getLocus

public Chromosome getLocus(int tagIndex)

Description copied from interface: TOPMInterface

Get Chromosome representing chromosome for given tag.

Specified by:

getLocus in interface TOPMInterface

Parameters:

tagIndex - tag index

Returns:

Chromosome

writeBinaryFile

public void writeBinaryFile(File outFile)

writeBinaryFile

public void writeBinaryFile(File outFile,
                            int minResolution,
                            boolean requirePhysPosition,
                            boolean requireDCOMap,
                            float minDCOP,
                            boolean binary)

TODO need to add LocusList to test, whether to include in output, move this to abstract

Parameters:

outFile -

minResolution -

requirePhysPosition -

requireDCOMap -

minDCOP -

binary -

writeBinaryFileForChromosomalRegion

public void writeBinaryFileForChromosomalRegion(File outFile,
                                                int targetChr,
                                                int minPos,
                                                int maxPos)

Outputs a new binary topm containing only tags with start positions that lie within the specified chromosomal region (inclusive). To obtain the whole chromosome, set minPos to Integer.MIN_VALUE and maxPos to Integer.MAX_VALUE TODO : generalize to other types of topm (HDF5, text)?

Parameters:

outFile - : use the suffix .topm

targetChr -

minPos - : set to Integer.MIN_VALUE for no cutoff

maxPos - : set to Integer.MAX_VALUE for no cutoff

mappedTags

public int[] mappedTags()

Returns:

An int[] result where : result[0] = The number of tags with a unique physical positions in this file (i.e. , tags for which the bestChr number is known). result[1] = The number of tags which align to multiple positions (i.e., where multimaps[tagIndex] > 0)

printRows

public void printRows(int numRows)

printRow

public String printRow(int row,
                       boolean byPosition)

printRows

public void printRows(int numRows,
                      boolean requirePhysPosition,
                      boolean byPosition)

printRows

public void printRows(int numRows,
                      boolean requirePhysPosition,
                      int printChr)