Package gov.nih.mipav.model.algorithms

Class StochasticForests.Data

java.lang.Object

gov.nih.mipav.model.algorithms.StochasticForests.Data

Direct Known Subclasses:

StochasticForests.DataChar, StochasticForests.DataDouble, StochasticForests.DataFloat, StochasticForests.DataSparse

Enclosing class:

StochasticForests

private abstract class StochasticForests.Data
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	externalData
(package private) int	i
protected int[]	index_data
protected java.util.Vector<java.lang.Boolean>	is_ordered_variable
protected int	max_num_unique_values
protected java.util.Vector<java.lang.Integer>	no_split_variables
protected int	num_cols
protected int	num_cols_no_snp
protected int	num_rows
protected int	num_rows_rounded
protected java.util.Vector<java.lang.Integer>	permuted_sampleIDs
protected char[]	snp_data
protected java.util.Vector<java.util.Vector<java.lang.Double>>	unique_data_values
protected java.util.Vector<java.lang.String>	variable_names

Constructor Summary

Constructors

Constructor	Description
Data()
Data(java.util.Vector<java.lang.String> variable_names, int num_rows, int num_cols)

Method Summary

Modifier and Type	Method	Description
void	addNoSplitVariable(int varID)
void	addSnpData(char[] snp_data, int num_cols_snp)
void	dispose()
abstract double	get(int row, int column)
void	getAllValues(java.util.Vector<java.lang.Double> all_values, java.util.Vector<java.lang.Integer> sampleIDs, int varID)
int	getIndex(int row, int col)
java.util.Vector<java.lang.Boolean>	getIsOrderedVariable()
int	getMaxNumUniqueValues()
void	getMinMaxValues(double[] min, double[] max, java.util.Vector<java.lang.Integer> sampleIDs, int varID)
java.util.Vector<java.lang.Integer>	getNoSplitVariables()
int	getNumCols()
int	getNumRows()
int	getNumUniqueDataValues(int varID)
int	getPermutedSampleID(int sampleID)
double	getUniqueDataValue(int varID, int index)
int	getUnpermutedVarID(int varID)
int	getVariableID(java.lang.String variable_name)
java.util.Vector<java.lang.String>	getVariableNames()
boolean	isOrderedVariable(int varID)
boolean	loadFromFile(java.lang.String filename)
boolean	loadFromFileOther(java.io.BufferedReader input_file, java.lang.String header_line, java.lang.String separator)
void	permuteSampleIDs(java.util.Random random)
abstract void	reserveMemory()
abstract void	set(int col, int row, double value, boolean[] error)
void	setIsOrderedVariable(java.util.Vector<java.lang.Boolean> is_ordered_variable)
void	setIsOrderedVariableString(java.util.Vector<java.lang.String> unordered_variable_names)
void	sort()

Methods inherited from class java.lang.Object

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

Field Detail

variable_names

protected java.util.Vector<java.lang.String> variable_names

num_rows

protected int num_rows

num_rows_rounded

protected int num_rows_rounded

num_cols

protected int num_cols

snp_data

protected char[] snp_data

num_cols_no_snp

protected int num_cols_no_snp

externalData

protected boolean externalData

index_data

protected int[] index_data

unique_data_values

protected java.util.Vector<java.util.Vector<java.lang.Double>> unique_data_values

max_num_unique_values

protected int max_num_unique_values

i

int i

no_split_variables

protected java.util.Vector<java.lang.Integer> no_split_variables

is_ordered_variable

protected java.util.Vector<java.lang.Boolean> is_ordered_variable

permuted_sampleIDs

protected java.util.Vector<java.lang.Integer> permuted_sampleIDs

Constructor Detail

Data

public Data()

Data

public Data(java.util.Vector<java.lang.String> variable_names,
            int num_rows,
            int num_cols)

Method Detail

dispose

public void dispose()

get

public abstract double get(int row,
                           int column)

getVariableID

public int getVariableID(java.lang.String variable_name)

addSnpData

public void addSnpData(char[] snp_data,
                       int num_cols_snp)

loadFromFile

public boolean loadFromFile(java.lang.String filename)

loadFromFileOther

public boolean loadFromFileOther(java.io.BufferedReader input_file,
                                 java.lang.String header_line,
                                 java.lang.String separator)

getAllValues

public void getAllValues(java.util.Vector<java.lang.Double> all_values,
                         java.util.Vector<java.lang.Integer> sampleIDs,
                         int varID)

getMinMaxValues

public void getMinMaxValues(double[] min,
                            double[] max,
                            java.util.Vector<java.lang.Integer> sampleIDs,
                            int varID)

sort

public void sort()

reserveMemory

public abstract void reserveMemory()

set

public abstract void set(int col,
                         int row,
                         double value,
                         boolean[] error)

getUnpermutedVarID

public int getUnpermutedVarID(int varID)

getPermutedSampleID

public int getPermutedSampleID(int sampleID)

getIndex

public int getIndex(int row,
                    int col)

getUniqueDataValue

public double getUniqueDataValue(int varID,
                                 int index)

getNumUniqueDataValues

public int getNumUniqueDataValues(int varID)

getVariableNames

public java.util.Vector<java.lang.String> getVariableNames()

getNumCols

public int getNumCols()

getNumRows

public int getNumRows()

getMaxNumUniqueValues

public int getMaxNumUniqueValues()

getNoSplitVariables

public java.util.Vector<java.lang.Integer> getNoSplitVariables()

addNoSplitVariable

public void addNoSplitVariable(int varID)

getIsOrderedVariable

public java.util.Vector<java.lang.Boolean> getIsOrderedVariable()

setIsOrderedVariableString

public void setIsOrderedVariableString(java.util.Vector<java.lang.String> unordered_variable_names)

setIsOrderedVariable

public void setIsOrderedVariable(java.util.Vector<java.lang.Boolean> is_ordered_variable)

isOrderedVariable

public boolean isOrderedVariable(int varID)

permuteSampleIDs

public void permuteSampleIDs(java.util.Random random)