ExpressionData

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org.genepattern.data.expr
Class ExpressionData

java.lang.Object
  org.genepattern.data.expr.ExpressionData

All Implemented Interfaces:: IExpressionData

Direct Known Subclasses:: ResExpressionData

public class ExpressionData
extends java.lang.Object
implements IExpressionData

Implementation of IExpressionData interface

Constructor Summary

ExpressionData(DoubleMatrix2D dataset, java.lang.String[] _rowDescriptions, java.lang.String[] _columnDescriptions)


Method Summary

double get(int row, int column)
          Gets a single element

double[][] getArray()
          Gets the underlying double[][] array

int getColumnCount()
          Gets the number of column in the expression data matrix

java.lang.String getColumnDescription(int column)
          Gets the column description at the given column or null if no column description exists.

java.lang.String[] getColumnDescriptions()
          Gets the array containing the column descriptions or null if no column descriptions are set

int getColumnIndex(java.lang.String columnName)
          Gets the column index for the column name .

java.lang.String getColumnName(int column)
          Gets the column name at the given column

java.lang.String[] getColumnNames()
          Allocates a new array contains the column names

DoubleMatrix2D getExpressionMatrix()
          Gets the 2-dimensional matrix that holds the expression values

double[] getRow(int row)
          Gets the underlying array at the given row

int getRowCount()
          Gets the number of rows in the expression data matrix

java.lang.String getRowDescription(int row)
          Gets the row description at the given row or null if no row description exists.

java.lang.String[] getRowDescriptions()
          Gets the array containing the row descriptions or null if no row descriptions are set

int getRowIndex(java.lang.String rowName)
          Gets the row index for the row name .

java.lang.String getRowName(int row)
          Gets the row name at the given row

java.lang.String[] getRowNames()
          Allocates a new array contains the row names

double getValue(int row, int column)
          Gets the expression value at the given row and column.

java.lang.String getValueAsString(int row, int column)
          Gets the value at the given row and column as a string.

void set(int rowIndex, int columnIndex, double value)
          Sets a single element.

void set(java.lang.String rowName, java.lang.String columnName, double value)
          Sets a single element.

void setColumnDescription(int column, java.lang.String description)


void setColumnDescriptions(java.lang.String[] descs)
          Sets the column descriptions

void setColumnName(int column, java.lang.String name)


void setRowDescription(int row, java.lang.String description)


void setRowDescriptions(java.lang.String[] descs)
          Sets the row descriptions

void setRowName(int row, java.lang.String name)


ExpressionData slice(int[] rowIndices, int[] columnIndices)


ExpressionData slice(java.lang.String[] rowNames, java.lang.String[] columnNames)


Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ExpressionData

public ExpressionData(DoubleMatrix2D dataset,
                      java.lang.String[] _rowDescriptions,
                      java.lang.String[] _columnDescriptions)

Method Detail

slice

public ExpressionData slice(java.lang.String[] rowNames,
                            java.lang.String[] columnNames)

slice

public ExpressionData slice(int[] rowIndices,
                            int[] columnIndices)

setRowDescription

public void setRowDescription(int row,
                              java.lang.String description)

setColumnDescription

public void setColumnDescription(int column,
                                 java.lang.String description)

setColumnName

public void setColumnName(int column,
                          java.lang.String name)