java.lang.Object
- ubic.gemma.core.loader.util.anndata.AnnData

All Implemented Interfaces:: Closeable, AutoCloseable

public class AnnData
extends Object
implements Closeable

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
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 Detail
  - 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

Class AnnData

Method Summary

Methods inherited from class java.lang.Object

Method Detail

open

getObs

getObs

getVar

getVar

getX

getLayers

getLayer

getRawX

getRawVar

getRawVar

getUns

close

toString