|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectsbrt.kernel.fba.proc.FbaProcess<F,FbaOptimizer.Results>
sbrt.kernel.fba.proc.CvRxnDeletionProcess<F>
F
- the fluxome type.public final class CvRxnDeletionProcess<F extends Fluxome>
This class is used to perform constraint-variation reaction deletion processes.
Constructor Summary | |
---|---|
CvRxnDeletionProcess(RxnDeletionComputer<F> computer)
Constructs a new constraint-variation reaction deletion process. |
Method Summary | |
---|---|
static void |
checkForConflict(FluxConstraints fc,
java.util.Set<java.lang.String> deletionNames)
Ensures that the provided flux constraints and set of reaction names do not conflict. |
F |
getFluxome()
Returns the fluxome used by the reaction deletion computer. |
MathExpr<java.lang.String> |
getObjectiveFunction()
Returns the current objective function. |
OptSense |
getOptimizationSense()
Returns the current optimization sense. |
ProgressMonitor |
getProgress()
Returns a progress monitor for this process. |
double |
getZeroCutoff()
Returns the current zero cutoff used by the reaction deletion computer. |
void |
run(ResultsManager<FbaOptimizer.Results> resultsManager)
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method. |
void |
setConstraintSource(java.lang.Iterable<FluxConstraints> constraintSource)
Sets the constraint variation input source. |
void |
setObjectiveFunction(MathExpr<java.lang.String> objective)
Sets the objective function to the provided mathematical expression. |
void |
setOptimizationSense(OptSense sense)
Sets the optimization sense to the provided value. |
void |
setRxnDeletionSource(java.lang.Iterable<java.util.Set<java.lang.String>> deletionSource)
Sets the reaction deletion input source. |
void |
setZeroCutoff(double zeroCutoff)
Sets the zero cutoff to the provided value. |
Methods inherited from class sbrt.kernel.fba.proc.FbaProcess |
---|
toString |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
---|
public CvRxnDeletionProcess(RxnDeletionComputer<F> computer)
computer
- the computer with which all results will be computed.Method Detail |
---|
public F getFluxome()
getFluxome
in class FbaProcess<F extends Fluxome,FbaOptimizer.Results>
public double getZeroCutoff()
public MathExpr<java.lang.String> getObjectiveFunction()
public OptSense getOptimizationSense()
public void setObjectiveFunction(MathExpr<java.lang.String> objective)
objective
- a mathematical expression of reaction names.public void setOptimizationSense(OptSense sense)
sense
- an optimization sense.public void setRxnDeletionSource(java.lang.Iterable<java.util.Set<java.lang.String>> deletionSource)
deletionSource
- a source of reaction names sets whose effect upon
deletion is to be computed.public void setConstraintSource(java.lang.Iterable<FluxConstraints> constraintSource)
constraintSource
- a source of constraint sets whose effect upon application is
to be computed.public void setZeroCutoff(double zeroCutoff)
zeroCutoff
- the zero cutoff.public ProgressMonitor getProgress()
getProgress
in interface MonitoredProcess<FbaOptimizer.Results>
public void run(ResultsManager<FbaOptimizer.Results> resultsManager)
First, a set of flux constraints is retrieved from the constraint source
and applied. Then a set of reaction names in the deletion source is
retrieved. The results are computed and added to the results manager.
Each set of reaction names is iterated through in the same fashion. When
the end of the deletion source is reached, the flux constraints are
restored to their original value and resultsManager.breakPoint()
is called. At this point, the next set of flux constraints is retrieved
from the constraint source. The entire process is repeated until the end
of the constraint source is reached.
run
in interface KernelProcess<FbaOptimizer.Results>
resultsManager
- the results manager to which the results will be added.public static void checkForConflict(FluxConstraints fc, java.util.Set<java.lang.String> deletionNames)
fc
- a set of flux constraints.deletionNames
- a set of reaction names.
ConflictingInputException
- if reaction names occur in both
the provided flux constraints and set of reaction names. A list
of common reaction names can be retrieved with
ConflictingInputException#getConflicts()
.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |