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

  • Constructor Details

    • 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 Details

    • 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.

    • getIndex

      public <T> Dataframe.Column<T,T> getIndex(Class<T> indexClass)
      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:

    • 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.

    • getEnumArrayColumn

      public EnumArray getEnumArrayColumn(String columnName)
      Obtain an enum array column.

      This is very similar to getCategoricalColumn(String), but the main difference is that the enumerated value is backed internally by H5 enum data type.

    • 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