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SOMA Blockwise Read Iterator Base Class

Source: R/BlockwiseIter.R
BlockwiseReadIterBase.Rd

Virtual base class that allows for blockwise read iteration of SOMA reads.

See also

Derived classes: BlockwiseTableReadIter, BlockwiseSparseReadIter

Super class

tiledbsoma::ReadIter -> BlockwiseReadIterBase

Active bindings

array

The underlying SOMA array.

axis

The axis to iterate over in a blockwise fashion.

axes_to_reindex

The axes to re-index.

coords

A list of CoordsStrider objects.

coords_axis

The CoordsStrider for axis.

reindex_disable_on_axis

Additional axes that will not be re-indexed.

reindexable

Shorthand to see if this iterator is poised to be re-indexed or not.

Methods

Public methods

Inherited methods

Method new()

Create.

Usage

BlockwiseReadIterBase$new(
  sr,
  array,
  coords,
  axis,
  ...,
  reindex_disable_on_axis = NA
)

Arguments

sr

SOMA read pointer

array

Underlying SOMASparseNDArray

coords

Named list of CoordsStrider objects; must be named after array$dimnames()

axis

Axis to iterate over in a blockwise manner

...

Ignored

reindex_disable_on_axis

Additional axes that will not be re-indexed; the following values may be used as shorthands for common settings:

  • “TRUE”: disable re-indexing on all axes

  • “NA”: re-index only on axis, disable re-indexing on all others

  • “FALSE”: re-index on all axes, do not disable re-indexing

Method read_complete()

Check if the iterated read is complete or not.

Usage

BlockwiseReadIterBase$read_complete()

Returns

TRUE if read is complete, otherwise FALSE.

Method read_next()

Read the next chunk of the iterated read. If read is complete, throws an iterationCompleteWarning warning and returns NULL.

Usage

BlockwiseReadIterBase$read_next()

Returns

NULL or the next blockwise chunk of the iterated read.

Method clone()

The objects of this class are cloneable with this method.

Usage

BlockwiseReadIterBase$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.