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