Class EmptyExpressionMatrix
- java.lang.Object
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- ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix<Object>
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- ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
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- All Implemented Interfaces:
Serializable
,ExpressionDataMatrix<Object>
public class EmptyExpressionMatrix extends BaseExpressionDataMatrix<Object>
Used to make a 'dummy matrix' that has the column information populated. This is useful for processing where we want the sample information organized,but not the data. Data access operations are not supported.- Author:
- paul
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description EmptyExpressionMatrix(Collection<BioAssayDimension> dims)
EmptyExpressionMatrix(BioAssayDimension ba)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
columns()
Total number of columns.Object
get(int row, int column)
Access a single value of the matrix.Object[][]
get(List<CompositeSequence> designElements, List<BioAssay> bioAssays)
Access a submatrixObject
get(CompositeSequence designElement, BioAssay bioAssay)
Access a single value of the matrix.Object[]
getColumn(Integer column)
Access a single column of the matrix.Object[]
getColumn(BioAssay bioAssay)
Access a single column of the matrix.Object[][]
getColumns(List<BioAssay> bioAssays)
Access a submatrix slice by columnsObject[][]
getRawMatrix()
Access the entire matrix.Object[]
getRow(Integer index)
Access a single row of the matrix, by index.Object[]
getRow(CompositeSequence designElement)
Return a row that 'came from' the given design element.Object[][]
getRows(List<CompositeSequence> designElements)
Access a submatrixboolean
hasMissingValues()
int
rows()
void
set(int row, int column, Object value)
Set a value in the matrix, by indexprotected void
vectorsToMatrix(Collection<? extends DesignElementDataVector> vectors)
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Methods inherited from class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix
columns, getBestBioAssayDimension, getBioAssayDimension, getBioAssaysForColumn, getBioMaterialForColumn, getColumnIndex, getDesignElementForRow, getDesignElements, getExpressionExperiment, getQuantitationTypes, getRowElement, getRowElements, getRowIndex
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Constructor Detail
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EmptyExpressionMatrix
public EmptyExpressionMatrix(BioAssayDimension ba)
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EmptyExpressionMatrix
public EmptyExpressionMatrix(Collection<BioAssayDimension> dims)
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Method Detail
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columns
public int columns()
Description copied from interface:ExpressionDataMatrix
Total number of columns.- Returns:
- int
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get
public Object get(CompositeSequence designElement, BioAssay bioAssay)
Description copied from interface:ExpressionDataMatrix
Access a single value of the matrix. Note that because there can be multiple bioassays per column and multiple designelements per row, it is possible for this method to retrieve a data that does not come from the bioassay and/or designelement arguments.- Parameters:
designElement
- debioAssay
- ba- Returns:
- T t
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get
public Object get(int row, int column)
Description copied from interface:ExpressionDataMatrix
Access a single value of the matrix. This is generally the easiest way to do it.- Parameters:
row
- rowcolumn
- col- Returns:
- t
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get
public Object[][] get(List<CompositeSequence> designElements, List<BioAssay> bioAssays)
Description copied from interface:ExpressionDataMatrix
Access a submatrix- Parameters:
designElements
- debioAssays
- bas- Returns:
- T[][]
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getColumn
public Object[] getColumn(BioAssay bioAssay)
Description copied from interface:ExpressionDataMatrix
Access a single column of the matrix.- Parameters:
bioAssay
- i- Returns:
- T[]
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getColumn
public Object[] getColumn(Integer column)
Description copied from interface:ExpressionDataMatrix
Access a single column of the matrix.- Parameters:
column
- index- Returns:
- T[]
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getColumns
public Object[][] getColumns(List<BioAssay> bioAssays)
Description copied from interface:ExpressionDataMatrix
Access a submatrix slice by columns- Parameters:
bioAssays
- ba- Returns:
- t[][]
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getRawMatrix
public Object[][] getRawMatrix()
Description copied from interface:ExpressionDataMatrix
Access the entire matrix.- Returns:
- T[][]
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getRow
public Object[] getRow(CompositeSequence designElement)
Description copied from interface:ExpressionDataMatrix
Return a row that 'came from' the given design element.- Parameters:
designElement
- de- Returns:
- t
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getRow
public Object[] getRow(Integer index)
Description copied from interface:ExpressionDataMatrix
Access a single row of the matrix, by index. A complete row is returned.- Parameters:
index
- i- Returns:
- t[]
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getRows
public Object[][] getRows(List<CompositeSequence> designElements)
Description copied from interface:ExpressionDataMatrix
Access a submatrix- Parameters:
designElements
- de- Returns:
- T[][]
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hasMissingValues
public boolean hasMissingValues()
- Returns:
- true if any values are null or NaN (for Doubles); all other values are considered non-missing.
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rows
public int rows()
- Returns:
- int
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set
public void set(int row, int column, Object value)
Description copied from interface:ExpressionDataMatrix
Set a value in the matrix, by index- Parameters:
row
- rowcolumn
- colvalue
- val
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vectorsToMatrix
protected void vectorsToMatrix(Collection<? extends DesignElementDataVector> vectors)
- Specified by:
vectorsToMatrix
in classBaseExpressionDataMatrix<Object>
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