Package ubic.gemma.core.loader.util.anndata

Class Dataframe<K>

java.lang.Object

ubic.gemma.core.loader.util.anndata.Dataframe<K>

Type Parameters:

K - the type of index being used

All Implemented Interfaces:

AutoCloseable, Iterable<Dataframe.Column<K,?>>

public class Dataframe<K>
extends Object
implements Iterable<Dataframe.Column<K,?>>, AutoCloseable

Represents an AnnData dataframe.

Author:

poirigui

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	Dataframe.Column<K,T>

Constructor Summary

Constructors

Constructor	Description
Dataframe(H5Group group, Class<K> indexClass)	Create a new dataframe from an H5 group.

Method Summary

Modifier and Type	Method	Description
void	close()
H5Dataset	getArrayColumn(String columnName)	Obtain an array column as a H5 dataset.
CategoricalArray<?>	getCategoricalColumn(String columnName)	Obtain a categorical column.
<T> CategoricalArray<T>	getCategoricalColumn(String columnName, Class<T> categoryType)	Obtain a categorical column.
Dataframe.Column<K,?>	getColumn(String columnName)	Obtain a column, the element type is guessed as per getColumnType(String)
<T> Dataframe.Column<K,T>	getColumn(String columnName, Class<T> clazz)	Obtain a column of the given element type.
String	getColumnEncodingType(String columnName)	Obtain the encoding type of a column.
List<String>	getColumns()	Obtain all the columns defined in the dataframe.
Class<?>	getColumnType(String columnName)	Guess the type of a given column.
Dataframe.Column<K,K>	getIndex()	Obtain the index column.
String	getIndexColumn()	Obtain the name of the column used as an index.
Boolean[]	getNullableBooleanArrayColumn(String columnName)	Obtain a nullable boolean array column.
Integer[]	getNullableIntegerArrayColumn(String columnName)	Obtain a nullable integer array column.
String[]	getStringArrayColumn(String columnName)	Obtain a string-array column.
Iterator<Dataframe.Column<K,?>>	iterator()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

Dataframe

public Dataframe(H5Group group,
                 @Nullable
                 Class<K> indexClass)

Create a new dataframe from an H5 group.

Parameters:

group - an H5 group that contains a dataset

indexClass - the type of index to use, or null to ignore. If left unset, indexing will not be possible via Dataframe.Column.get(Object).

Method Detail

getIndexColumn

public String getIndexColumn()

Obtain the name of the column used as an index.

getColumns

public List<String> getColumns()

Obtain all the columns defined in the dataframe.

Unsupported encoding types are ignored.

getColumnEncodingType

public String getColumnEncodingType(String columnName)

Obtain the encoding type of a column.

This is usually one of string-array, categorical or array, but many other encodings are possible.

getIndex

public Dataframe.Column<K,K> getIndex()

Obtain the index column.

getColumnType

public Class<?> getColumnType(String columnName)

Guess the type of a given column.

getColumn

public Dataframe.Column<K,?> getColumn(String columnName)

Obtain a column, the element type is guessed as per getColumnType(String)

See Also:

getColumnType(String), getColumn(String, Class)

getColumn

public <T> Dataframe.Column<K,T> getColumn(String columnName,
                                                 Class<T> clazz)

Obtain a column of the given element type.

getArrayColumn

public H5Dataset getArrayColumn(String columnName)

Obtain an array column as a H5 dataset.

getCategoricalColumn

public <T> CategoricalArray<T> getCategoricalColumn(String columnName,
                                                    Class<T> categoryType)

Obtain a categorical column.

getCategoricalColumn

public CategoricalArray<?> getCategoricalColumn(String columnName)

Obtain a categorical column.

getStringArrayColumn

public String[] getStringArrayColumn(String columnName)

Obtain a string-array column.

getNullableIntegerArrayColumn

public Integer[] getNullableIntegerArrayColumn(String columnName)

Obtain a nullable integer array column.

getNullableBooleanArrayColumn

public Boolean[] getNullableBooleanArrayColumn(String columnName)

Obtain a nullable boolean array column.

iterator

@Nonnull
public Iterator<Dataframe.Column<K,?>> iterator()

Specified by:

iterator in interface Iterable<K>

close

public void close()

Specified by:

close in interface AutoCloseable