com.pacbio.secondary.vis.io.hdf.data

Class AlignmentIndexTable

java.lang.Object

com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray

com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable

public class AlignmentIndexTable
extends UIntMatrixArray

Simple extension class to store Alignement Index table data. Uses base UIntMatrixArray class to handle conversion of unsigned integers to long

Author:

mmilletti

Field Summary

Fields

Modifier and Type	Field and Description
static int	CMPH5_AIDX_ALIGNMENT_READ_START
static int	CMPH5_AIDX_STROBE_NUMBER

Fields inherited from class com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray

data, num_columns, num_rows

Constructor Summary

Constructors

Constructor and Description
AlignmentIndexTable(long num_rows, long num_columns, java.lang.Object data_in) Public constructor

Method Summary

Methods

Modifier and Type	Method and Description
long	getAlignmentReadEnd(int row) Returns sub-read end on alignment sequence
long	getAlignmentReadStart(int row) Returns sub-read start on alignment sequence
long	getHoleNumber(int row) Returns hole number
long	getMapQV(int row) Returns Map QV for specific row
long	getMoleculeID(int row) Returns molecule id
int	getMovieID(int row) Returns movie id
long	getNumDel(int row) Returns num deletions for specific row
long	getNumIns(int row) Returns num insertions for specific row
long	getNumMM(int row) Returns num mismatches for specific row
long	getRawReadEnd(int row) Returns index of raw read end in alignindex
long	getRawReadStart(int row) Returns index of raw read start in alignindex
int	getReadGroupID(int row) Returns read group id
long	getRefEnd(int row) Returns mapped reference end
long	getRefSeqID(int row) Returns mapped reference id
long	getRefStart(int row) Returns mapped reference start
long	getRefStrand(int row) Returns mapped reference strand
long	getSetNumber(int row) Returns set number
long	getStrobeNumber(int row) Returns strobe number

Methods inherited from class com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray

get, get, getData, getNumColumns, getNumRows, toString

Methods inherited from class java.lang.Object

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

Field Detail

CMPH5_AIDX_STROBE_NUMBER

public static final int CMPH5_AIDX_STROBE_NUMBER

See Also:

Constant Field Values

CMPH5_AIDX_ALIGNMENT_READ_START

public static final int CMPH5_AIDX_ALIGNMENT_READ_START

See Also:

Constant Field Values

Constructor Detail

AlignmentIndexTable

public AlignmentIndexTable(long num_rows,
                   long num_columns,
                   java.lang.Object data_in)

Public constructor

Parameters:

num_rows - total rows

num_columns - total columns

data_in - array of data

Method Detail

getReadGroupID

public int getReadGroupID(int row)

Returns read group id

Parameters:

row -

Returns:

getMovieID

public int getMovieID(int row)

Returns movie id

Parameters:

row -

Returns:

getRefSeqID

public long getRefSeqID(int row)

Returns mapped reference id

Parameters:

row -

Returns:

getRefStrand

public long getRefStrand(int row)

Returns mapped reference strand

Parameters:

row -

Returns:

getRefStart

public long getRefStart(int row)

Returns mapped reference start

Parameters:

row -

Returns:

getRefEnd

public long getRefEnd(int row)

Returns mapped reference end

Parameters:

row -

Returns:

getHoleNumber

public long getHoleNumber(int row)

Returns hole number

Parameters:

row -

Returns:

getStrobeNumber

public long getStrobeNumber(int row)

Returns strobe number

Parameters:

row -

Returns:

getMoleculeID

public long getMoleculeID(int row)

Returns molecule id

Parameters:

row -

Returns:

getSetNumber

public long getSetNumber(int row)

Returns set number

Parameters:

row -

Returns:

getAlignmentReadStart

public long getAlignmentReadStart(int row)

Returns sub-read start on alignment sequence

Parameters:

row -

Returns:

getAlignmentReadEnd

public long getAlignmentReadEnd(int row)

Returns sub-read end on alignment sequence

Parameters:

row -

Returns:

getRawReadStart

public long getRawReadStart(int row)

Returns index of raw read start in alignindex

Parameters:

row -

Returns:

getRawReadEnd

public long getRawReadEnd(int row)

Returns index of raw read end in alignindex

Parameters:

row -

Returns:

getNumMM

public long getNumMM(int row)

Returns num mismatches for specific row

Parameters:

row -

Returns:

getNumIns

public long getNumIns(int row)

Returns num insertions for specific row

Parameters:

row -

Returns:

getNumDel

public long getNumDel(int row)

Returns num deletions for specific row

Parameters:

row -

Returns:

getMapQV

public long getMapQV(int row)

Returns Map QV for specific row

Parameters:

row -

Returns: