net.maizegenetics.dna.tag

Class AbstractTagsHDF5

AbstractTags

net.maizegenetics.dna.tag.AbstractTagsHDF5

All Implemented Interfaces:

Tags

Direct Known Subclasses:

TagGWASMap

public class AbstractTagsHDF5
extends AbstractTags

Basic implementations of HDF5 tags. This is designed to annotate tags with a bunch of attributes, to solve the memory issues

Field Detail

h5

protected ch.systemsx.cisd.hdf5.IHDF5Writer h5

currentBlockIndex

protected int currentBlockIndex

currentIndex

protected int currentIndex

Method Detail

getBlockSize

public int getBlockSize()

Returns the size of HDF5 block

Returns:

org.jetbrains.dokka.NodeRenderContent@2a5a9f96:

getBlockNum

public int getBlockNum()

Returns the number of block

Returns:

org.jetbrains.dokka.NodeRenderContent@51ceea68:

getBlockIndex

public int getBlockIndex(int tagIndex)

Returns the block index based on the tag index in a full list

Parameters:

tagIndex - as the query tag index in the full list

Returns:

org.jetbrains.dokka.NodeRenderContent@7e0ceb8:

getCurrentBlockIndex

public int getCurrentBlockIndex()

Returns current block index

Returns:

org.jetbrains.dokka.NodeRenderContent@67f7b292:

getCurrentIndex

public int getCurrentIndex()

Returns current index

Returns:

org.jetbrains.dokka.NodeRenderContent@19af37d5:

getCurrentIndexWithinBlock

public int getCurrentIndexWithinBlock()

Returns current index relative to current block

Returns:

org.jetbrains.dokka.NodeRenderContent@3f141322:

initializeMatrix

protected void initializeMatrix(int tagCount,
                                int tagLengthInLong)

Initialize tag matrix

Parameters:

tagCount -

tagLengthInLong -

isInCurrentBlock

public boolean isInCurrentBlock(int queryIndex)

Return boolean value if an index belongs to current block

Parameters:

queryIndex -

Returns:

org.jetbrains.dokka.NodeRenderContent@3e009f76:

getIntStorageFeatures

public ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures getIntStorageFeatures()

Returns default deflation level of boolean, byte, short, int, long, Enum See class Tassel5HDF5Constants

Returns:

org.jetbrains.dokka.NodeRenderContent@64b9d906:

See Also:

class Tassel5HDF5Constants

getGenericStorageFeatures

public ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures getGenericStorageFeatures()

Returns default deflation level of String and Class See class Tassel5HDF5Constants

Returns:

org.jetbrains.dokka.NodeRenderContent@4484bdb:

See Also:

class Tassel5HDF5Constants

getFloatStorageFeatures

public ch.systemsx.cisd.hdf5.HDF5FloatStorageFeatures getFloatStorageFeatures()

Returns default deflation level of float and double See class Tassel5HDF5Constants

Returns:

org.jetbrains.dokka.NodeRenderContent@1bdac573:

See Also:

class Tassel5HDF5Constants

sort

public void sort()

swap

public void swap(int index1,
                 int index2)

writeToFasta

public void writeToFasta(java.lang.String outfileS)

initializeHDF5

public void initializeHDF5(java.lang.String inputFileS)

Initialize a HDF5 file

Parameters:

inputFileS -

readHDF5

public void readHDF5(java.lang.String hdf5FileS)

Read in HDF5 file

Parameters:

hdf5FileS -

populateBlock

public void populateBlock(int blockIndex)

Populate a block in memory with default values, update current block index at the same time

Parameters:

blockIndex -

readBlock

public void readBlock(int blockIndex)

Read in a block from HDF5 file

Parameters:

blockIndex -

writeBlock

public void writeBlock(int blockIndex)

Write current block to HDF5 file

Parameters:

blockIndex -