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java.lang.Objectsbrt.kernel.fba.proc.FbaProcess<FbaOptComputer.Results>
sbrt.kernel.fba.proc.StoichVariationProcess
public final class StoichVariationProcess
This class is used to perform stoichiometry-variation FBA optimizations.
Constructor Summary | |
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StoichVariationProcess(FbaOptComputer computer)
Constructs a new constraint-variation FBA optimization process. |
Method Summary | |
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Fluxome |
getFluxome()
Returns the fluxome used in this process. |
MathExpr<java.lang.String> |
getObjectiveFunction()
Returns the current objective function. |
OptimizationSense |
getOptimizationSense()
Returns the current optimization sense. |
ProgressMonitor |
getProgress()
Returns a progress monitor for this process. |
void |
run(ResultsManager<FbaOptComputer.Results> resultsManager)
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method. |
void |
setMatrixSource(java.lang.Iterable<java.util.Map<IndexPair<java.lang.String,java.lang.String>,java.lang.Double>> matrixSource)
Sets the stoiciometry variation input source. |
void |
setObjectiveFunction(MathExpr<java.lang.String> objective)
Sets the objective function to the provided mathematical expression. |
void |
setOptimizationSense(OptimizationSense sense)
Sets the optimization sense to the provided value. |
Methods inherited from class sbrt.kernel.fba.proc.FbaProcess |
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toString |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public StoichVariationProcess(FbaOptComputer computer)
computer
- the computer with which all results will be computed.Method Detail |
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public Fluxome getFluxome()
getFluxome
in class FbaProcess<FbaOptComputer.Results>
public MathExpr<java.lang.String> getObjectiveFunction()
public OptimizationSense getOptimizationSense()
public void setObjectiveFunction(MathExpr<java.lang.String> objective)
objective
- a mathematical expression of reaction names.public void setOptimizationSense(OptimizationSense sense)
sense
- an optimization sense.public void setMatrixSource(java.lang.Iterable<java.util.Map<IndexPair<java.lang.String,java.lang.String>,java.lang.Double>> matrixSource)
matrixSource
- a source of stoichiometry variations whose effect
upon application is to be computed.public ProgressMonitor getProgress()
getProgress
in interface MonitoredProcess<FbaOptComputer.Results>
public void run(ResultsManager<FbaOptComputer.Results> resultsManager)
ResultsManager.addData(Object)
method.
A set of stoichiometry variations is retrieved from the matrix source, their effect is computed, and the results are added to the provided results manager. This is repeated until the end of the deletion source is reached.
run
in interface KernelProcess<FbaOptComputer.Results>
resultsManager
- the results manager to which the results will be
added.
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