analyses.result

Class TwoReacsAnalysisResult

java.lang.Object

analyses.result.AnalysisResult

analyses.result.TwoReacsAnalysisResult

public class TwoReacsAnalysisResult
extends AnalysisResult

Class representing the result of an analysis with two varying fluxes.

Author:

lmarmiesse 18 avr. 2013

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	TwoReacsAnalysisResult.MyPlot Class to create a personalized grid 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 variables.
(package private) double	deltaF2 Parameters of the varying variables.
(package private) double	end Parameters of the varying variables.
(package private) double	end2 Parameters of the varying variables.
private java.util.Map<java.lang.Double,java.util.List<double[]>>	expValues Experimental values.
(package 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 variables.
(package private) double	init2 Parameters of the varying variables.
(package private) int	minGrpsSize Minimal group size to consider it is a phenotype phase.
private java.lang.String	objName
(package private) java.util.Map<double[],java.lang.Integer>	pointIndex Map to get the group index of a point.
private java.lang.String	reacName
private java.lang.String	reacName2
private java.util.List<double[]>	results Each double[] is a point x,y,z with x : reac1 flux value, y = reac2 flux value and z = objective value.
private double	score
(package private) java.util.Map<java.lang.Double,java.util.List<double[]>>	shadowPriceGroups phenotype phases sorted by shadow-price value.

Constructor Summary

Constructors

Constructor and Description
TwoReacsAnalysisResult(java.lang.String objName, java.lang.String reacName, java.lang.String reacName2, int minGrpsSize, double init, double end, double deltaF, double init2, double end2, double deltaF2)

Method Summary

Methods

Modifier and Type	Method and Description
void	addExpValue(double val1, double val2, double val3) Adds an experimental value.
void	addValue(double[] value)
void	calculateScore() Adds up all the distance of the experimental values to the calculated surface.
void	drawGridPlot(org.math.plot.Plot3DPanel plot, java.lang.String name, double[] x, double[] y, double[] z) Draws a 3D Grid plot
java.util.Map<java.lang.Double,java.lang.Integer>	getGroupIndex()
protected java.awt.Color	getNewColor(org.math.plot.canvas.PlotCanvas plotCanvas)
java.lang.Double	getScore() Adds up all the distance of the experimental values to the calculated line.
java.util.Map<java.lang.Double,java.util.List<double[]>>	getShadowPriceGroups()
void	normalizeValues(double xLB, double xUB, boolean invertX, double yLB, double yUB, boolean invertY, double zLB, double zUB, boolean invertZ) Normalizes the values.
void	plot() Plots the results.
void	savePng(org.math.plot.Plot3DPanel panel, java.io.File file) Save the plot as a PBG image file.
void	setComparator(PhenotypicPhaseComparator comparator)
void	setShadowPriceGroups(java.util.Map<java.lang.Double,java.util.List<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 variables.

end

double end

Parameters of the varying variables.

deltaF

double deltaF

Parameters of the varying variables.

init2

double init2

Parameters of the varying variables.

end2

double end2

Parameters of the varying variables.

deltaF2

double deltaF2

Parameters of the varying variables.

COLORLIST

public static final java.awt.Color[] COLORLIST

reacName

private java.lang.String reacName

reacName2

private java.lang.String reacName2

objName

private java.lang.String objName

results

private java.util.List<double[]> results

Each double[] is a point x,y,z with x : reac1 flux value, y = reac2 flux value and z = objective value.

shadowPriceGroups

java.util.Map<java.lang.Double,java.util.List<double[]>> shadowPriceGroups

phenotype phases sorted by shadow-price value.

comparator

private PhenotypicPhaseComparator comparator

Comparator between phenotype phases.

pointIndex

java.util.Map<double[],java.lang.Integer> pointIndex

Map to get the group index of a point.

groupIndex

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

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

expValues

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

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

score

private double score

Constructor Detail

TwoReacsAnalysisResult

public TwoReacsAnalysisResult(java.lang.String objName,
                      java.lang.String reacName,
                      java.lang.String reacName2,
                      int minGrpsSize,
                      double init,
                      double end,
                      double deltaF,
                      double init2,
                      double end2,
                      double deltaF2)

Method Detail

addValue

public void addValue(double[] value)

Parameters:

value -

normalizeValues

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

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.

zLB - Lower bound of Z.

zUB - Upper bound of Z.

invertZ - True if Z is minimized in the objective.

setShadowPriceGroups

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

Orders the phenotype phases.

getShadowPriceGroups

public java.util.Map<java.lang.Double,java.util.List<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

savePng

public void savePng(org.math.plot.Plot3DPanel panel,
           java.io.File file)

Save the plot as a PBG image file.

Parameters:

panel - panel to save.

file - Path to the file to write.

drawGridPlot

public void drawGridPlot(org.math.plot.Plot3DPanel plot,
                java.lang.String name,
                double[] x,
                double[] y,
                double[] z)

Draws a 3D Grid plot

Parameters:

plot - plot to add the grid plot to.

name - Name of the plot.

x - X values.

y - Y values.

z - Z values.

getNewColor

protected java.awt.Color getNewColor(org.math.plot.canvas.PlotCanvas plotCanvas)

addExpValue

public void addExpValue(double val1,
               double val2,
               double val3)

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

Parameters:

val1 - The experimental value for X.

val2 - The experimental value for Y.

val3 - The experimental value for Z.

calculateScore

public void calculateScore()

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

getScore

public java.lang.Double getScore()

Adds up all the distance of the experimental values to the calculated line. Used for pareto analysis, not for phenotype phase.

Returns:

The score.