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A D F G M O R S T V

## A

AbstractDataset - Class in org.broadinstitute.genee.matrix
  Abstract dataset.
AbstractDataset() - Constructor for class org.broadinstitute.genee.matrix.AbstractDataset
add(String, Class<?>) - Method in interface org.broadinstitute.genee.matrix.MetadataModel
  Appends the specified column name to the end of this meta data (optional operation).
addSeries(String, Class<?>) - Method in class org.broadinstitute.genee.matrix.AbstractDataset
addSeries(String, Object[][], Class<?>) - Method in class org.broadinstitute.genee.matrix.FixedSizeAbstractDataset
  Inserts the specified series.

## D

Dataset - Interface in org.broadinstitute.genee.matrix
  The interface for a dataset consisting of a two-dimensional matrix of float values.

## F

FixedSizeAbstractDataset - Class in org.broadinstitute.genee.matrix
  Fixed size abstract dataset.
fromGenee() - Method in class org.broadinstitute.genee.client.GeneeClient
  Returns the selection from GENE-E.

## G

GeneeClient - Class in org.broadinstitute.genee.client
  Class for interacting with GENE-E.
GeneeClient() - Constructor for class org.broadinstitute.genee.client.GeneeClient
  Constructs a client to interact with GENE-E on localhost:9998.
GeneeClient(String, int) - Constructor for class org.broadinstitute.genee.client.GeneeClient
  Constructs a client to interact with GENE-E.
get(int) - Method in interface org.broadinstitute.genee.matrix.MetadataModel
  Returns the vector at the specified metadata index.
get(String) - Method in interface org.broadinstitute.genee.matrix.MetadataModel
  Returns the vector witht the specified name.
getArray() - Method in class org.broadinstitute.genee.matrix.RowMajorArray2DDataset
  Gets the underlying float[][] array
getColumnClass() - Method in interface org.broadinstitute.genee.matrix.Vector
  Returns the most specific superclass for all the values in this vector.
getColumnCount() - Method in interface org.broadinstitute.genee.matrix.Dataset
  Returns the number of columns in the dataset.
getColumnCount() - Method in class org.broadinstitute.genee.matrix.FixedSizeAbstractDataset
getColumnIndex(String) - Method in interface org.broadinstitute.genee.matrix.MetadataModel
  Returns the column index for the given column name or `-1` if the name is not found.
getColumnMetadata() - Method in interface org.broadinstitute.genee.matrix.Dataset
  Gets the column metadata for this dataset.
getColumnMetadata() - Method in class org.broadinstitute.genee.matrix.FixedSizeAbstractDataset
getColumnName(int) - Method in interface org.broadinstitute.genee.matrix.MetadataModel
  Returns the name of the column at `metadataIndex`.
getComparator() - Method in interface org.broadinstitute.genee.matrix.Vector
  Returns the comparator used to compare values in this vector.
getItemCount() - Method in interface org.broadinstitute.genee.matrix.MetadataModel
  Returns the number of items that a vector in this instance contains.
getMetadataCount() - Method in interface org.broadinstitute.genee.matrix.MetadataModel
  Returns the number of columns in this meta data instance.
getName() - Method in class org.broadinstitute.genee.matrix.AbstractDataset
getName() - Method in interface org.broadinstitute.genee.matrix.Dataset
  Returns the name of this dataset.
getName() - Method in interface org.broadinstitute.genee.matrix.Vector
  Returns the name of this vector.
getObjectValue(int, int, int) - Method in class org.broadinstitute.genee.matrix.AbstractDataset
getObjectValue(int, int, int) - Method in interface org.broadinstitute.genee.matrix.Dataset
  Returns the value at the given row and column for the given series.
getProperty(Object) - Method in class org.broadinstitute.genee.matrix.AbstractDataset
getProperty(Object) - Method in interface org.broadinstitute.genee.matrix.Dataset
  Returns the value to which the specified key is mapped, or `null` if this dataset does not contain the specified property.
getProperty(Object) - Method in interface org.broadinstitute.genee.matrix.Vector
  Gets the value for the specified key.
getPropertyKeys() - Method in class org.broadinstitute.genee.matrix.AbstractDataset
getPropertyKeys() - Method in interface org.broadinstitute.genee.matrix.Dataset
  Returns a collection of all the property keys contained in this dataset.
getPropertyKeys() - Method in interface org.broadinstitute.genee.matrix.Vector
  Returns a collection of all property keys in this vector.
getRowCount() - Method in interface org.broadinstitute.genee.matrix.Dataset
  Returns the number of rows in the dataset.
getRowCount() - Method in class org.broadinstitute.genee.matrix.FixedSizeAbstractDataset
getRowMetadata() - Method in interface org.broadinstitute.genee.matrix.Dataset
  Gets the row metadata for this dataset.
getRowMetadata() - Method in class org.broadinstitute.genee.matrix.FixedSizeAbstractDataset
getSeriesClass(int) - Method in class org.broadinstitute.genee.matrix.AbstractDataset
getSeriesClass(int) - Method in interface org.broadinstitute.genee.matrix.Dataset
  Returns the most specific superclass for all the values in the series.
getSeriesCount() - Method in class org.broadinstitute.genee.matrix.AbstractDataset
getSeriesCount() - Method in interface org.broadinstitute.genee.matrix.Dataset
  Returns the number of matrix series, which is always at least 1 (the dataset itself).
getSeriesName(int) - Method in class org.broadinstitute.genee.matrix.AbstractDataset
getSeriesName(int) - Method in interface org.broadinstitute.genee.matrix.Dataset
  Returns the name for the given series.
getValue(int, int, int) - Method in class org.broadinstitute.genee.matrix.AbstractDataset
getValue(int, int) - Method in interface org.broadinstitute.genee.matrix.Dataset
  Returns the value at the given row and column.
getValue(int, int, int) - Method in interface org.broadinstitute.genee.matrix.Dataset
  Returns the value at the given row and column for the given series as a float.
getValue(int, int) - Method in interface org.broadinstitute.genee.matrix.MetadataModel
  Returns the value for the element at `itemIndex` and `metadataIndex`.
getValue(int, String) - Method in interface org.broadinstitute.genee.matrix.MetadataModel
  Returns the value for the element at `metadataIndex` and `columnName`.
getValue(int, int) - Method in class org.broadinstitute.genee.matrix.RowMajorArray2DDataset
getValue(int) - Method in interface org.broadinstitute.genee.matrix.Vector
  Returns the value at the specified index.

## M

MetadataModel - Interface in org.broadinstitute.genee.matrix
  Stores annotations for the rows or columns of a dataset.

## O

org.broadinstitute.genee.client - package org.broadinstitute.genee.client
  Provides facilities for interacting with GENE-E.
org.broadinstitute.genee.matrix - package org.broadinstitute.genee.matrix
  Provides matrix classes and interfaces.

## R

remove(int) - Method in interface org.broadinstitute.genee.matrix.MetadataModel
  Removes the column at the specified position in this meta data instance (optional operation).
removeSeries(int) - Method in class org.broadinstitute.genee.matrix.AbstractDataset
RowMajorArray2DDataset - Class in org.broadinstitute.genee.matrix
  Dataset implementation using two-dimensional float array.
RowMajorArray2DDataset(String, float[][]) - Constructor for class org.broadinstitute.genee.matrix.RowMajorArray2DDataset
  Creates a new dataset with the specified name and array.
RowMajorArray2DDataset(String, int, int) - Constructor for class org.broadinstitute.genee.matrix.RowMajorArray2DDataset
  Creates a new dataset

## S

setArray(float[][]) - Method in class org.broadinstitute.genee.matrix.RowMajorArray2DDataset
  Sets the underlying float[][] array
setColumnClass(Class<?>) - Method in interface org.broadinstitute.genee.matrix.Vector
  Sets the most specific superclass for all the values in this vector.
setColumnMetadata(MetadataModel) - Method in class org.broadinstitute.genee.matrix.FixedSizeAbstractDataset
setComparator(Comparator<Object>) - Method in interface org.broadinstitute.genee.matrix.Vector
  Sets the comparator used to compare values in this vector.
setName(String) - Method in class org.broadinstitute.genee.matrix.AbstractDataset
setName(String) - Method in interface org.broadinstitute.genee.matrix.Dataset
  Sets the name of this dataset.
setObjectValue(int, int, Object, int) - Method in class org.broadinstitute.genee.matrix.AbstractDataset
  Sets the value at the given row and column.
setProperty(Object, Object) - Method in class org.broadinstitute.genee.matrix.AbstractDataset
setProperty(Object, Object) - Method in interface org.broadinstitute.genee.matrix.Dataset
  Sets the property for the specified key.
setProperty(Object, Object) - Method in interface org.broadinstitute.genee.matrix.Vector
  Sets the property for the specified key.
setRowMetadata(MetadataModel) - Method in class org.broadinstitute.genee.matrix.FixedSizeAbstractDataset
setValue(int, int, float) - Method in interface org.broadinstitute.genee.matrix.Dataset
  Sets the value at the given row and column indices.
setValue(int, int, Object) - Method in interface org.broadinstitute.genee.matrix.MetadataModel
  Sets the value in the cell at `columnName` and `itemIndex` to `aValue`.
setValue(int, String, Object) - Method in interface org.broadinstitute.genee.matrix.MetadataModel
  Sets the value in the cell at `columnName` and `itemIndex` to `aValue`.
setValue(int, int, float) - Method in class org.broadinstitute.genee.matrix.RowMajorArray2DDataset
setValue(int, Object) - Method in interface org.broadinstitute.genee.matrix.Vector
  Sets the value at the specified index.
size() - Method in interface org.broadinstitute.genee.matrix.Vector
  Returns the number of elements in this vector.

## T

toGenee(Dataset) - Method in class org.broadinstitute.genee.client.GeneeClient
  Views the given dataset in GENE-E.

## V

Vector - Interface in org.broadinstitute.genee.matrix
  A collection of values of the same type.

A D F G M O R S T V

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