fr.systemsbiology.cyni
Class CyniTable

java.lang.Object
  fr.systemsbiology.cyni.CyniTable

public class CyniTable
extends Object

Field Summary

protected boolean	anyMissing
protected Boolean[]	colHasMissingValue
protected int[]	colMaxValue
protected int[]	colMinValue
protected int[]	colNumStringsDiff
protected cern.colt.matrix.tobject.ObjectMatrix1D	columnLabels
protected cern.colt.matrix.tdouble.DoubleMatrix1D	colWeights
protected cern.colt.matrix.tobject.ObjectMatrix2D	data
protected boolean	ignoreMissing
protected Class<?>[]	indexToTypes
protected org.cytoscape.model.CyTable	internalTable
protected Map<Object,Integer>	mapColLabels
protected Map<Object,Integer>	mapRowLabels
protected Map<Integer,Integer>	mapRowOrder
protected int	nColumns
protected int	nRows
protected Boolean[]	rowHasMissingValue
protected cern.colt.matrix.tobject.ObjectMatrix1D	rowLabels
protected int[]	rowMaxValue
protected int[]	rowMinValue
protected int[]	rowNumStringsDiff
protected cern.colt.matrix.tdouble.DoubleMatrix1D	rowWeights
protected boolean	selectedOnly
protected ArrayList<String>	stringValues
protected boolean	transpose

Constructor Summary

CyniTable(CyniTable duplicate)
Create a cyni table from an existing one.

CyniTable(org.cytoscape.model.CyTable table, String[] attributes, boolean transpose, boolean ignoreMissing, boolean selectedOnly)
Create a Cyni table from the current selected table.

CyniTable(int rows, int cols)
Create an empty Cyni Table with the specified number of columns and rows.

Method Summary

void	changeOrderRowsByColumnValuesOrder(List<Object> colValues) Changes the order of the rows according to the values of a selected column The method supposes that the first value of the input list corresponds to the first element of the column and so on.
void	changeOrderRowsToRandom() Changes the order of the rows in the table randomly
boolean	columnHasMissingValue(int column) Tells if the specified column has a missing value.
double	doubleValue(int row, int column) Returns the double value for the specified row and column combination
ArrayList<String>	getAttributeStringValues() Returns the list of all possible strings values in the table
Integer	getColIndex(Object label) Returns the index column for the specified label.
Object	getColLabel(int col) Returns the label for the specified column.
Object[]	getColLabels() Returns the array with all column labels.
double	getColWeight(int col) Returns the weight for the specified column.
double[]	getColWeights() Returns the array of weights for the columns.
int	getNumPossibleStrings(int index, boolean inRow) Returns the number of possible/different strings stored in the defined column or row
double[]	getRank(int row) Returns an array with a number for each position representing the rank of the value in the whole row
Integer	getRowIndex(Object label) Returns the index row for the specified label.
Object	getRowLabel(int row) Returns the label for the specified row.
Object[]	getRowLabels() Returns the array with all row labels.
double	getRowWeight(int row) Returns the weight for the specified row.
double[]	getRowWeights() Returns the array of weights for the rows.
Class<?>	getType(int row, int column) Returns the type of for the specified row and column combination.
Object	getValue(int row, int column) Returns the value for the specified row and column
boolean	hasAnyMissingValue() Returns if the table has any missing value
boolean	hasValue(int row, int column) Returns if the content of the table for the specified row and column combination has a real value.
int	integerValue(int row, int column) Returns the integer value for the specified row and column combination.
boolean	isMatching(int row, int col, Object value) Checks whether the element in position defined by row and col parameters matches the given value.
boolean	isTransposed() Returns if the table is transposed
int	nColumns() Returns the number of columns in the table.
int	nRows() Returns the number of rows in the table.
void	resetOrderRows() Changes the order to the initial internal state
boolean	rowHasMissingValue(int row) Tells if the specified row has a missing value.
void	setColLabel(int col, Object label) Set the label for the specified column.
void	setColWeight(int col, double value) Set the weight for the specified column.
void	setRowLabel(int row, Object label) Set the label for the specified row.
void	setRowWeight(int row, double value) Set the weight for the specified row.
void	setType(int row, int column, Class<?> type) Allows setting the type of for the specified row and column combination.
void	setUniformWeights() Set the weights to a constant value.
void	setValue(int row, int column, Object value) Set the value for the specified row and column
String	stringValue(int row, int column) Returns the string value for the specified row and column combination.

Methods inherited from class java.lang.Object

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

Field Detail

nRows

protected int nRows

nColumns

protected int nColumns

data

protected cern.colt.matrix.tobject.ObjectMatrix2D data

internalTable

protected org.cytoscape.model.CyTable internalTable

colWeights

protected cern.colt.matrix.tdouble.DoubleMatrix1D colWeights

rowWeights

protected cern.colt.matrix.tdouble.DoubleMatrix1D rowWeights

rowLabels

protected cern.colt.matrix.tobject.ObjectMatrix1D rowLabels

columnLabels

protected cern.colt.matrix.tobject.ObjectMatrix1D columnLabels

transpose

protected boolean transpose

anyMissing

protected boolean anyMissing

ignoreMissing

protected boolean ignoreMissing

selectedOnly

protected boolean selectedOnly

indexToTypes

protected Class<?>[] indexToTypes

stringValues

protected ArrayList<String> stringValues

colHasMissingValue

protected Boolean[] colHasMissingValue

rowHasMissingValue

protected Boolean[] rowHasMissingValue

mapRowLabels

protected Map<Object,Integer> mapRowLabels

mapColLabels

protected Map<Object,Integer> mapColLabels

mapRowOrder

protected Map<Integer,Integer> mapRowOrder

colNumStringsDiff

protected int[] colNumStringsDiff

rowNumStringsDiff

protected int[] rowNumStringsDiff

colMaxValue

protected int[] colMaxValue

colMinValue

protected int[] colMinValue

rowMaxValue

protected int[] rowMaxValue

rowMinValue

protected int[] rowMinValue

Constructor Detail

CyniTable

public CyniTable(org.cytoscape.model.CyTable table,
                 String[] attributes,
                 boolean transpose,
                 boolean ignoreMissing,
                 boolean selectedOnly)

Create a Cyni table from the current selected table. The Cyni Table will contain the columns of the CyTable that are defined in the attributes variable

Parameters:

attribute - name of the columns to store

table - CyTable

transpose - true if we are transposing this table

ignoreMissing - true if the new table will not have any row with missing values

selectedOnly - true if the new table will only contains rows that correspond to selected nodes

CyniTable

public CyniTable(CyniTable duplicate)

Create a cyni table from an existing one.

Parameters:

duplicate - The cyni table to duplicate

CyniTable

public CyniTable(int rows,
                 int cols)

Create an empty Cyni Table with the specified number of columns and rows.

Parameters:

rows - number of rows

cols - number of cols

Method Detail

isTransposed

public boolean isTransposed()

Returns if the table is transposed

Returns:

True if the table is transposed

hasAnyMissingValue

public boolean hasAnyMissingValue()

Returns if the table has any missing value

Returns:

True if the table has any missing value

nRows

public int nRows()

Returns the number of rows in the table.

Returns:

The number of rows in the table.

nColumns

public int nColumns()

Returns the number of columns in the table.

Returns:

The number of columns in the table

getValue

public Object getValue(int row,
                       int column)

Returns the value for the specified row and column

Parameters:

row - The number of the row.

column - The number of the column.

Returns:

The value for the column and row

setValue

public void setValue(int row,
                     int column,
                     Object value)

Set the value for the specified row and column

Parameters:

row - The number of the row.

column - The number of the column.

value - The value for the column and row

getAttributeStringValues

public ArrayList<String> getAttributeStringValues()

Returns the list of all possible strings values in the table

Returns:

The list of all possible strings values in the table

doubleValue

public double doubleValue(int row,
                          int column)

Returns the double value for the specified row and column combination

Parameters:

row - The number of the row.

column - The number of the column.

Returns:

The double value, if the content is not a number, it returns a not a number value

integerValue

public int integerValue(int row,
                        int column)

Returns the integer value for the specified row and column combination.

Parameters:

row - The number of the row.

column - The number of the column.

Returns:

The integer value, if the content is not a number, it returns a zero value.

stringValue

public String stringValue(int row,
                          int column)

Returns the string value for the specified row and column combination.

Parameters:

row - The number of the row.

column - The number of the column.

Returns:

The string value, if the content is not a string, it returns an empty string.

hasValue

public boolean hasValue(int row,
                        int column)

Returns if the content of the table for the specified row and column combination has a real value.

Parameters:

row - The number of the row.

column - The number of the column.

Returns:

False if the content of the table for that cell is null or it doesn't exist

rowHasMissingValue

public boolean rowHasMissingValue(int row)

Tells if the specified row has a missing value.

Parameters:

row - The number of the row.

Returns:

False if the content of that row is null for one of its values or the specified row doesn't exist

columnHasMissingValue

public boolean columnHasMissingValue(int column)

Tells if the specified column has a missing value.

Parameters:

column - The number of the column.

Returns:

False if the content of that column is null for one of its values or the specified column doesn't exist

getType

public Class<?> getType(int row,
                        int column)

Returns the type of for the specified row and column combination.

Parameters:

row - The number of the row.

column - The number of the column.

Returns:

The type of that table content

setType

public void setType(int row,
                    int column,
                    Class<?> type)

Allows setting the type of for the specified row and column combination.

Parameters:

row - The number of the row.

column - The number of the column.

type - The type of that table content

getNumPossibleStrings

public int getNumPossibleStrings(int index,
                                 boolean inRow)

Returns the number of possible/different strings stored in the defined column or row

Parameters:

index - The index of the row or column.

inRow - True if the index corresponds to a row index, false if it is for a column

Returns:

The number of different strings stored in the selected row or column or 0 if the row or column does not contain strings

setUniformWeights

public void setUniformWeights()

Set the weights to a constant value.

getRowWeights

public double[] getRowWeights()

Returns the array of weights for the rows.

Returns:

The array of weights for the rows.

getRowWeight

public double getRowWeight(int row)

Returns the weight for the specified row.

Parameters:

row - The number of the row.

Returns:

The weight for the specified row.

getColWeights

public double[] getColWeights()

Returns the array of weights for the columns.

Returns:

The array of weights for the columns.

getColWeight

public double getColWeight(int col)

Returns the weight for the specified column.

Parameters:

col - The number of the column.

Returns:

The weight for the specified column.

setRowWeight

public void setRowWeight(int row,
                         double value)

Set the weight for the specified row.

Parameters:

row - The number of the row.

value - The weight

setColWeight

public void setColWeight(int col,
                         double value)

Set the weight for the specified column.

Parameters:

col - The number of the column.

value - The weight

getColLabels

public Object[] getColLabels()

Returns the array with all column labels.

Returns:

The array with all column labels.

getColLabel

public Object getColLabel(int col)

Returns the label for the specified column.

Parameters:

col - The number of the column.

Returns:

The label for the specified column.

setColLabel

public void setColLabel(int col,
                        Object label)

Set the label for the specified column.

Parameters:

col - The number of the column.

label - The label.

getColIndex

public Integer getColIndex(Object label)

Returns the index column for the specified label.

Parameters:

label - The label object.

Returns:

The index column for the specified label or -1 if the label does not exist.

getRowLabels

public Object[] getRowLabels()

Returns the array with all row labels.

Returns:

The array with all row labels.

getRowLabel

public Object getRowLabel(int row)

Returns the label for the specified row.

Parameters:

row - The number of the row.

Returns:

The label for the specified row.

getRowIndex

public Integer getRowIndex(Object label)

Returns the index row for the specified label.

Parameters:

label - The label object.

Returns:

The index row for the specified label or -1 if the label does not exist.

setRowLabel

public void setRowLabel(int row,
                        Object label)

Set the label for the specified row.

Parameters:

row - The number of the row.

label - The label.

isMatching

public boolean isMatching(int row,
                          int col,
                          Object value)

Checks whether the element in position defined by row and col parameters matches the given value.

Parameters:

row - The row index.

col - The col index.

value - The object value to check.

Returns:

True if the value matches the element in position(row,col) or false otherwise.

changeOrderRowsToRandom

public void changeOrderRowsToRandom()

Changes the order of the rows in the table randomly

resetOrderRows

public void resetOrderRows()

Changes the order to the initial internal state

changeOrderRowsByColumnValuesOrder

public void changeOrderRowsByColumnValuesOrder(List<Object> colValues)

Changes the order of the rows according to the values of a selected column The method supposes that the first value of the input list corresponds to the first element of the column and so on. If the list of column values has different size than the number of rows of the table, the change of order will not proceed.

Parameters:

colValues - The list of values for the selected column

getRank

public double[] getRank(int row)

Returns an array with a number for each position representing the rank of the value in the whole row

Parameters:

row - The number of the row.

Returns:

The array with the ranks