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

Class AnnData

java.lang.Object

ubic.gemma.core.loader.util.anndata.AnnData

All Implemented Interfaces:

Closeable, AutoCloseable

public class AnnData
extends Object
implements Closeable

Method Summary

Modifier and Type	Method	Description
void	close()
Layer	getLayer(String layerName)	Obtain a layer by name.
List<String>	getLayers()	Obtain all the layer names under layers/ path.
Dataframe<?>	getObs()
<K> Dataframe<K>	getObs(Class<K> indexClass)
Dataframe<?>	getRawVar()	Obtain the raw var dataframe if this AnnData object has been filtered.
<K> Dataframe<K>	getRawVar(Class<K> indexClass)	Obtain the raw var dataframe if this AnnData object has been filtered.
Layer	getRawX()	Obtain the raw X layer if this AnnData object has been filtered.
Mapping	getUns()	Obtain additional free-form data stored under uns.
Dataframe<?>	getVar()
<K> Dataframe<K>	getVar(Class<K> indexClass)
Layer	getX()	Obtain the main layer named X.
static AnnData	open(Path path)
String	toString()

Methods inherited from class java.lang.Object

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

Method Details

open

public static AnnData open(Path path)
                    throws IOException

Throws:

IOException

getObs

public Dataframe<?> getObs()

getObs

public <K> Dataframe<K> getObs(Class<K> indexClass)

getVar

public Dataframe<?> getVar()

getVar

public <K> Dataframe<K> getVar(Class<K> indexClass)

getX

@Nullable
public Layer getX()

Obtain the main layer named X.

getLayers

public List<String> getLayers()

Obtain all the layer names under layers/ path.

getLayer

public Layer getLayer(String layerName)

Obtain a layer by name.

getRawX

@Nullable
public Layer getRawX()

Obtain the raw X layer if this AnnData object has been filtered.

This, along getRawVar() are not part of the on-disk specification, but will be included if the AnnData object has been sliced/filtered. Note that since this is filtered, getRawVar() should be used to refer to the relevant column annotations.

getRawVar

@Nullable
public Dataframe<?> getRawVar()

Obtain the raw var dataframe if this AnnData object has been filtered.

getRawVar

@Nullable
public <K> Dataframe<K> getRawVar(Class<K> indexClass)

Obtain the raw var dataframe if this AnnData object has been filtered.

getUns

@Nullable
public Mapping getUns()

Obtain additional free-form data stored under uns.

close

public void close()
           throws IOException

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Throws:

IOException

toString

public String toString()

Overrides:

toString in class Object