Class BulkExpressionDataIntMatrix
java.lang.Object
ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix<Integer>
ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix<Integer>
ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix
- All Implemented Interfaces:
BulkExpressionDataMatrix<Integer>,BulkExpressionDataPrimitiveIntMatrix,ExpressionDataMatrix<Integer>,ExpressionDataPrimitiveIntMatrix
public class BulkExpressionDataIntMatrix
extends AbstractBulkExpressionDataMatrix<Integer>
implements BulkExpressionDataPrimitiveIntMatrix
A bulk expression data matrix that can be efficiently accessed as a primitive int matrix.
- Author:
- poirigui
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected Stringformat(int i, int j) Format a matrix entry at a particular row/column.get(int row, int column) Access a single value of the matrix by row and column.intgetAsInt(int row, int column) Retrieve the value at the given row and column without boxing.Integer[]getColumn(int column) Access a single column of the matrix.int[]getColumnAsInts(int column) Retrieve the given column without boxing.int[]getColumnAsInts(BioAssay bioAssay) Retrieve the given column without boxing.Integer[][]Access the entire matrix.int[][]Obtain the raw matrix as a int array.Integer[]getRow(int index) Access a single row of the matrix, by index.int[]getRowAsInts(int index) Retrieve a row without boxing.int[]getRowAsInts(CompositeSequence designElement) Retrieve the row for the given design element without boxing.booleansliceColumns(List<BioMaterial> bioMaterials) Slice the requested samples (columns) from this matrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension) Slice the requested samples (columns) from this matrix.sliceRows(List<CompositeSequence> designElements) Slice the given design elements (rows) from the matrix.Methods inherited from class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix
columns, get, getBioAssayDimension, getBioAssayForColumn, getBioMaterialForColumn, getBioMaterials, getColumn, getColumnIndex, getColumnIndex, getColumnLabel, getDesignElementForRow, getDesignElements, getExpressionExperiment, getQuantitationType, getRow, getRowElement, getRowElements, getRowIndex, getRowIndices, getRowLabel, rowsMethods inherited from class ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix
format, format, formatRepresentation, toStringMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitMethods inherited from interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix
get, getBioAssayDimension, getBioAssayForColumn, getBioMaterialForColumn, getBioMaterials, getColumn, getColumnIndex, getColumnIndexMethods inherited from interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
columns, getDesignElementForRow, getDesignElements, getExpressionExperiment, getQuantitationType, getRow, getRowElement, getRowElements, getRowIndex, getRowIndices, rows
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Constructor Details
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BulkExpressionDataIntMatrix
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Method Details
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hasMissingValues
public boolean hasMissingValues()- Specified by:
hasMissingValuesin interfaceBulkExpressionDataMatrix<Integer>- Returns:
- true if any values are null or NaN (for doubles and floats); any other value that is considered missing.
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getRawMatrix
Description copied from interface:BulkExpressionDataMatrixAccess the entire matrix.- Specified by:
getRawMatrixin interfaceBulkExpressionDataMatrix<Integer>- Returns:
- T[][]
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sliceColumns
Description copied from interface:BulkExpressionDataMatrixSlice the requested samples (columns) from this matrix.Dimensions will be altered to reflect only the selected samples.
- Specified by:
sliceColumnsin interfaceBulkExpressionDataMatrix<Integer>- Parameters:
bioMaterials- samples to select from the matrix
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sliceColumns
public BulkExpressionDataIntMatrix sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension) Description copied from interface:BulkExpressionDataMatrixSlice the requested samples (columns) from this matrix.This also allows specifying a new dimension for the columns that will be used for every design element (rows).
- Specified by:
sliceColumnsin interfaceBulkExpressionDataMatrix<Integer>- Parameters:
bioMaterials- samples to select from the matrixdimension- the dimension to use
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getRawMatrixAsInts
public int[][] getRawMatrixAsInts()Description copied from interface:BulkExpressionDataPrimitiveIntMatrixObtain the raw matrix as a int array.- Specified by:
getRawMatrixAsIntsin interfaceBulkExpressionDataPrimitiveIntMatrix- See Also:
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getColumn
Description copied from interface:ExpressionDataMatrixAccess a single column of the matrix.- Specified by:
getColumnin interfaceExpressionDataMatrix<Integer>- Parameters:
column- index- Returns:
- T[]
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getColumnAsInts
public int[] getColumnAsInts(int column) Description copied from interface:ExpressionDataPrimitiveIntMatrixRetrieve the given column without boxing.- Specified by:
getColumnAsIntsin interfaceExpressionDataPrimitiveIntMatrix- See Also:
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getColumnAsInts
Description copied from interface:BulkExpressionDataPrimitiveIntMatrixRetrieve the given column without boxing.- Specified by:
getColumnAsIntsin interfaceBulkExpressionDataPrimitiveIntMatrix- See Also:
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getRow
Description copied from interface:ExpressionDataMatrixAccess a single row of the matrix, by index. A complete row is returned.- Specified by:
getRowin interfaceExpressionDataMatrix<Integer>- Parameters:
index- i- Returns:
- t[]
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sliceRows
Description copied from interface:ExpressionDataMatrixSlice the given design elements (rows) from the matrix.- Specified by:
sliceRowsin interfaceExpressionDataMatrix<Integer>
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getRowAsInts
public int[] getRowAsInts(int index) Description copied from interface:ExpressionDataPrimitiveIntMatrixRetrieve a row without boxing.- Specified by:
getRowAsIntsin interfaceExpressionDataPrimitiveIntMatrix- See Also:
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getRowAsInts
Description copied from interface:ExpressionDataPrimitiveIntMatrixRetrieve the row for the given design element without boxing.- Specified by:
getRowAsIntsin interfaceExpressionDataPrimitiveIntMatrix- See Also:
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get
Description copied from interface:ExpressionDataMatrixAccess a single value of the matrix by row and column.- Specified by:
getin interfaceExpressionDataMatrix<Integer>
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getAsInt
public int getAsInt(int row, int column) Description copied from interface:ExpressionDataPrimitiveIntMatrixRetrieve the value at the given row and column without boxing.- Specified by:
getAsIntin interfaceExpressionDataPrimitiveIntMatrix- See Also:
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format
Description copied from class:AbstractExpressionDataMatrixFormat a matrix entry at a particular row/column.- Specified by:
formatin classAbstractExpressionDataMatrix<Integer>
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