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java.lang.Objectsbrt.shell.mng.AbstractProcessManager
sbrt.shell.mng.fba.FbaManager
sbrt.shell.mng.fba.RandomFluxVectorManager
sbrt.shell.mng.fba.CdHarFluxVectorManager
public final class CdHarFluxVectorManager
This class is used to manage FBA coordinate direction hit-and-run random flux vector processes.
Field Summary | |
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static UnmodifiableSet<java.lang.String> |
optionalKeywords
The set of keywords required to be present in the ManagerInput
objects supplied to instances of this class. |
static UnmodifiableSet<java.lang.String> |
requiredKeywords
The set of keywords required to be present in the ManagerInput
objects supplied to instances of this class. |
Fields inherited from class sbrt.shell.mng.fba.RandomFluxVectorManager |
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ALGORITHM |
Fields inherited from class sbrt.shell.mng.fba.FbaManager |
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CONSTRAINT_TOLERANCE, DEFAULT_CONSTRAINT_TOLERANCE, FLUX_VECTOR_FILE, FLUX_VECTOR_FILE_NAME, RXN_CATALYST_FILE, RXN_FILE, SYSTEM_SOLUTION_FILE |
Fields inherited from class sbrt.shell.mng.AbstractProcessManager |
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COMPLETED, DATA_HEADERS, DEV_NULL, ELAPSED_TIME, FILE_FORMAT, INPUT_FILE, INPUT_FILE_FORMAT, INPUT_FILE_NAME_FILE, ITERATIONS, OUTPUT_FILE_FORMAT, OUTPUT_FILE_NAME, OUTPUT_FILE_NAME_FILE, PERCENT, PERCENT_COMPLETED, SEED, ZERO_CUTOFF |
Constructor Summary | |
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CdHarFluxVectorManager()
|
Method Summary | |
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void |
execute(java.io.PrintWriter out)
Executes the process this process manager controls, and writes the status or results of this process to the provided print writer. |
static java.util.Map<java.lang.String,java.lang.Double> |
getFluxVector(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Opens the file denoted by CdHarManager.INITIAL_POINT_FILE in the provided manager input and returns the flux vector it contains. |
static CdHarFluxComp<MixedFluxome> |
getMixedComp(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Creates and returns a coordinate-direction hit-and-run flux vector computer using the provided input. |
static CdHarFluxComp<MixedFluxome> |
getMixedComp(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
MixedFluxome fluxome,
double tolerance)
Creates and returns a coordinate-direction hit-and-run flux vector computer using the provided input. |
static MapOutputFile<java.lang.String,java.lang.Double> |
getMultiFluxVectorOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple flux vectors. |
UnmodifiableSet<java.lang.String> |
getOptionalKeys()
Returns the set of keywords the provided ManagerInput object does
not necessarily have to contain. |
CdHarFluxVectorProcess<MixedFluxome> |
getProcess()
Returns the process this process manager controls. |
UnmodifiableSet<java.lang.String> |
getRequiredKeys()
Returns the set of keywords the provided ManagerInput object must
contain. |
static ApplicationException |
interpret(DimensionException e)
Returns an ApplicationException whose message describes the error
that ocurred. |
static ApplicationException |
interpret(ExceededLimitException e)
Returns an ApplicationException whose message describes the error
that ocurred. |
static ApplicationException |
interpret(InfeasibleSolutionException e)
Returns an ApplicationException whose message describes the error
that ocurred. |
static ApplicationException |
interpret(InvalidFluxVectorException e)
Returns an ApplicationException whose message describes the error
that ocurred. |
static ApplicationException |
interpret(java.lang.RuntimeException e)
Attempts to interpret the provided RuntimeException. |
static ApplicationException |
interpret(UnboundedVariableException e)
Returns an ApplicationException whose message describes the error
that ocurred. |
void |
setInput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Uses the provided input to prepare this process manager for execution. |
Methods inherited from class sbrt.shell.mng.fba.RandomFluxVectorManager |
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getConstraints, getConstraints, getFluxVector, getIrrevRxnFluxome |
Methods inherited from class sbrt.shell.mng.AbstractProcessManager |
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check, closeFile, closeRm, execute, getFileFormat, getFileFormat, getFileNameSource, getIterations, getSeed, getTextFileFormat, getTextFileFormat, getZeroCutoff, getZeroCutoff, parseInt, parseLong, printProgress, printProgress, printProgress, runProcess, setInput |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface sbrt.shell.mng.ProcessManager |
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check, execute, setInput |
Field Detail |
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public static final UnmodifiableSet<java.lang.String> requiredKeywords
ManagerInput
objects supplied to instances of this class.
public static final UnmodifiableSet<java.lang.String> optionalKeywords
ManagerInput
objects supplied to instances of this class.
Constructor Detail |
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public CdHarFluxVectorManager()
Method Detail |
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public static CdHarFluxComp<MixedFluxome> getMixedComp(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
input
- the input containing all necessary values.out
- the print writer to which status messages will be printed.
FbaManager.getMixedFluxome(ManagerInput, PrintWriter)
,
FbaManager.getConstraintTolerance(ManagerInput)
,
getMixedComp(ManagerInput, PrintWriter, MixedFluxome, double)
public static CdHarFluxComp<MixedFluxome> getMixedComp(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, MixedFluxome fluxome, double tolerance)
input
- the input containing all necessary values.out
- the print writer to which status messages will be printed.fluxome
- the fluxome with which the computer is created.tolerance
- the constraint tolerance.
FbaManager.getFluxomeSolution(ManagerInput, PrintWriter, Fluxome, double)
,
AbstractProcessManager.getSeed(ManagerInput, PrintWriter)
,
CdHarManager.getMinChordLength(ManagerInput, PrintWriter)
public static java.util.Map<java.lang.String,java.lang.Double> getFluxVector(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome, double tolerance)
input
- the input containing a value for INITIAL_POINT_FILE
.out
- the print writer to which a status message will be printed.fluxome
- the fluxome to which the flux vector corresponds.tolerance
- the amount by which fluxes in the vector are allowed to
violate their defined constraints.
CdHarManager#INITIAL_POINT_FILE
in the provided input.RandomFluxVectorManager.getFluxVector(String, Fluxome, double)
public static MapOutputFile<java.lang.String,java.lang.Double> getMultiFluxVectorOutputFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
input
- the input containing values for the listed keywords.out
- the print writer to which status messages will be printed.fluxome
- the fluxome for which the data headers correspond.
FbaManager.getRxnNameHeaders(ManagerInput, Fluxome)
,
AbstractProcessManager.getFileFormat(ManagerInput)
public static ApplicationException interpret(java.lang.RuntimeException e)
e
- the exception to interpret.
java.lang.RuntimeException
- the orignal exception if it could not be
interpretted.public static ApplicationException interpret(DimensionException e)
ApplicationException
whose message describes the error
that ocurred.
e
- a dimension exception.
ApplicationException
wrapping the provided exception.public static ApplicationException interpret(InfeasibleSolutionException e)
ApplicationException
whose message describes the error
that ocurred.
e
- an infeasible solution exception.
ApplicationException
wrapping the provided exception.public static ApplicationException interpret(UnboundedVariableException e)
ApplicationException
whose message describes the error
that ocurred.
e
- an unbounded variable exception.
ApplicationException
wrapping the provided exception.public static ApplicationException interpret(InvalidFluxVectorException e)
ApplicationException
whose message describes the error
that ocurred.
e
- an invalid flux vector exception.
ApplicationException
wrapping the provided exception.public static ApplicationException interpret(ExceededLimitException e)
ApplicationException
whose message describes the error
that ocurred.
e
- an exceeded limit exception.
ApplicationException
wrapping the provided exception.public UnmodifiableSet<java.lang.String> getRequiredKeys()
ManagerInput
object must
contain.
ManagerInput
object must
contain.public UnmodifiableSet<java.lang.String> getOptionalKeys()
ManagerInput
object does
not necessarily have to contain.
ManagerInput
object does
not necessarily have to contain.public void setInput(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
input
- all of the information required to prepare this process
manager for execution.out
- the print writer to which all messages will be printed.public CdHarFluxVectorProcess<MixedFluxome> getProcess()
java.lang.IllegalStateException
- if no input was provided to this process
manager via AbstractProcessManager.setInput(ManagerInput) or
setInput(ManagerInput, PrintWriter)public void execute(java.io.PrintWriter out)
out
- the print writer where status messages will be printed.
java.lang.IllegalStateException
- if no input was provided to this process
manager via AbstractProcessManager.setInput(ManagerInput) or
setInput(ManagerInput, PrintWriter)
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