analyses

Class TwoReacsAnalysis

java.lang.Object

analyses.Analysis

analyses.TwoReacsAnalysis

public class TwoReacsAnalysis
extends Analysis

Class to run an analysis with two varying fluxes.

Author:

lmarmiesse 18 avr. 2013

Field Summary

Fields

Modifier and Type	Field and Description
(package private) double	deltaF Differences between each step.
(package private) double	deltaF2 Differences between each step.
(package private) double	end Final values
(package private) double	end2 Final values
private java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double>	entities1 First varying entity with it's coefficient (1) to make a constraint.
private java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double>	entities2 Second varying entity with it's coefficient (1) to make a constraint.
private boolean	fva Determines if FVA's must be performed on each phenotype phase.
(package private) double	init Initial values.
(package private) double	init2 Initial values.
(package private) int	minGrpsSize Minimal group size to consider it is a phenotype phase.
(package private) java.lang.String	reacName Names of the varying variables.
(package private) java.lang.String	reacName2 Names of the varying variables.
private java.util.Map<java.lang.Double,java.util.List<double[]>>	shadowPriceGroups phenotype phases sorted by shadow-price value.
protected java.util.List<ThreadTwoReacs>	threads

Fields inherited from class analyses.Analysis

b

Constructor Summary

Constructors

Constructor and Description
TwoReacsAnalysis(Bind bind, java.lang.String reac, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities1, java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities2, double init, double end, double deltaF, java.lang.String reac2, double init2, double end2, double deltaF2, boolean fva)

Method Summary

Methods

Modifier and Type	Method and Description
TwoReacsAnalysisResult	runAnalysis() Runs the analysis.

Methods inherited from class java.lang.Object

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

Field Detail

reacName

java.lang.String reacName

Names of the varying variables.

reacName2

java.lang.String reacName2

Names of the varying variables.

init

double init

Initial values.

init2

double init2

Initial values.

end

double end

Final values

end2

double end2

Final values

deltaF

double deltaF

Differences between each step.

deltaF2

double deltaF2

Differences between each step.

threads

protected java.util.List<ThreadTwoReacs> threads

shadowPriceGroups

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

phenotype phases sorted by shadow-price value.

minGrpsSize

int minGrpsSize

Minimal group size to consider it is a phenotype phase.

fva

private boolean fva

Determines if FVA's must be performed on each phenotype phase.

entities1

private java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities1

First varying entity with it's coefficient (1) to make a constraint.

entities2

private java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities2

Second varying entity with it's coefficient (1) to make a constraint.

Constructor Detail

TwoReacsAnalysis

public TwoReacsAnalysis(Bind bind,
                java.lang.String reac,
                java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities1,
                java.util.Map<parsebionet.biodata.BioEntity,java.lang.Double> entities2,
                double init,
                double end,
                double deltaF,
                java.lang.String reac2,
                double init2,
                double end2,
                double deltaF2,
                boolean fva)

Method Detail

runAnalysis

public TwoReacsAnalysisResult runAnalysis()

Description copied from class: Analysis

Runs the analysis.

Specified by:

runAnalysis in class Analysis

Returns:

An object containing the result of the analysis.