analyses.result

Class ReacAnalysisResult

java.lang.Object

analyses.result.AnalysisResult

analyses.result.ReacAnalysisResult

public class ReacAnalysisResult
extends AnalysisResult

Class representing the result of an analysis with a varying flux.

Author:

lmarmiesse 18 avr. 2013

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private class	ReacAnalysisResult.MyRenderer Class used to set the right colors and sized for the plot.

Field Summary

Fields

Modifier and Type	Field and Description
static java.awt.Color[]	COLORLIST
private PhenotypicPhaseComparator	comparator Comparator between phenotype phases.
(package private) double	deltaF Parameters of the varying variable.
(package private) double	end Parameters of the varying variable.
private java.util.Map<java.lang.Double,java.util.List<java.lang.Double>>	expValues Experimental values.
private java.util.List<java.lang.Double>	fluxValues All flux values.
private java.util.Map<java.lang.Double,java.lang.Integer>	groupIndex Map to get the group index of a shadow-price value.
(package private) double	init Parameters of the varying variable.
(package private) int	minGrpsSize Minimal group size to consider it is a phenotype phase.
private java.lang.String	objName
private java.util.Map<java.lang.Double,java.lang.Integer>	pointIndex Map to get the group index of a point.
private java.lang.String	reacName
private java.util.Map<java.lang.Double,java.lang.Double>	resultValues results.
private double	score
private java.util.Map<java.lang.Double,java.util.List<java.lang.Double>>	shadowPriceGroups phenotype phases sorted by shadow-price value.

Constructor Summary

Constructors

Constructor and Description
ReacAnalysisResult(java.lang.String objName, java.lang.String reacName, java.util.List<java.lang.Double> fluxValues, java.util.Map<java.lang.Double,java.lang.Double> resultValues, int minGrpsSize, double init, double end, double deltaF)

Method Summary

Methods

Modifier and Type	Method and Description
void	addExpValue(double a, double b) Adds an experimental value.
void	addValue(double value, double res) Adds a value to the results.
void	calculateScore() Adds up all the distance of the experimental values to the calculated line.
java.util.Map<java.lang.Double,java.lang.Integer>	getGroupIndex()
double	getScore()
java.util.Map<java.lang.Double,java.util.List<java.lang.Double>>	getShadowPriceGroups()
void	normalizeValues(double xLB, double xUB, boolean invertX, double yLB, double yUB, boolean invertY) Normalizes the values.
void	plot() Plots the results.
void	setComparator(PhenotypicPhaseComparator comparator)
void	setShadowPriceGroups(java.util.Map<java.lang.Double,java.util.List<java.lang.Double>> shadowPriceGroups) Orders the phenotype phases.
void	writeToFile(java.lang.String path) Writes the results to a file.

Methods inherited from class java.lang.Object

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

Field Detail

minGrpsSize

int minGrpsSize

Minimal group size to consider it is a phenotype phase.

init

double init

Parameters of the varying variable.

end

double end

Parameters of the varying variable.

deltaF

double deltaF

Parameters of the varying variable.

COLORLIST

public static final java.awt.Color[] COLORLIST

resultValues

private java.util.Map<java.lang.Double,java.lang.Double> resultValues

results.

fluxValues

private java.util.List<java.lang.Double> fluxValues

All flux values.

reacName

private java.lang.String reacName

objName

private java.lang.String objName

shadowPriceGroups

private java.util.Map<java.lang.Double,java.util.List<java.lang.Double>> shadowPriceGroups

phenotype phases sorted by shadow-price value.

pointIndex

private java.util.Map<java.lang.Double,java.lang.Integer> pointIndex

Map to get the group index of a point.

groupIndex

private java.util.Map<java.lang.Double,java.lang.Integer> groupIndex

Map to get the group index of a shadow-price value.

comparator

private PhenotypicPhaseComparator comparator

Comparator between phenotype phases.

expValues

private java.util.Map<java.lang.Double,java.util.List<java.lang.Double>> expValues

Experimental values. Used for pareto analysis, not for phenotype phase.

score

private double score

Constructor Detail

ReacAnalysisResult

public ReacAnalysisResult(java.lang.String objName,
                  java.lang.String reacName,
                  java.util.List<java.lang.Double> fluxValues,
                  java.util.Map<java.lang.Double,java.lang.Double> resultValues,
                  int minGrpsSize,
                  double init,
                  double end,
                  double deltaF)

Method Detail

setShadowPriceGroups

public void setShadowPriceGroups(java.util.Map<java.lang.Double,java.util.List<java.lang.Double>> shadowPriceGroups)

Orders the phenotype phases.

getShadowPriceGroups

public java.util.Map<java.lang.Double,java.util.List<java.lang.Double>> getShadowPriceGroups()

getGroupIndex

public java.util.Map<java.lang.Double,java.lang.Integer> getGroupIndex()

setComparator

public void setComparator(PhenotypicPhaseComparator comparator)

writeToFile

public void writeToFile(java.lang.String path)

Description copied from class: AnalysisResult

Writes the results to a file.

Specified by:

writeToFile in class AnalysisResult

Parameters:

path - Path to the file to write the results.

plot

public void plot()

Description copied from class: AnalysisResult

Plots the results.

Specified by:

plot in class AnalysisResult

addValue

public void addValue(double value,
            double res)

Adds a value to the results.

Parameters:

value - The flux value.

res - The objective value.

normalizeValues

public void normalizeValues(double xLB,
                   double xUB,
                   boolean invertX,
                   double yLB,
                   double yUB,
                   boolean invertY)

Normalizes the values. Used for pareto analysis, not for phenotype phase.

Parameters:

xLB - Lower bound of X.

xUB - Upper bound of X.

invertX - True if X is minimized in the objective.

yLB - Lower bound of Y.

yUB - Upper bound of Y.

invertY - True if Y is minimized in the objective.

addExpValue

public void addExpValue(double a,
               double b)

Adds an experimental value. Used for pareto analysis, not for phenotype phase.

Parameters:

a - The experimental value for X.

b - The experimental value for Y.

calculateScore

public void calculateScore()

Adds up all the distance of the experimental values to the calculated line. The distance is the distance between the experimental value and the closest point on the pareto line. Used for pareto analysis, not for phenotype phase.

getScore

public double getScore()

Returns:

The score.