sbrt.shell.mng.fba
Class MetatoolCycleIdManager

java.lang.Object
  extended by sbrt.shell.mng.AbstractProcessManager
      extended by sbrt.shell.mng.fba.FbaManager
          extended by sbrt.shell.mng.fba.MetatoolCycleIdManager
All Implemented Interfaces:
KernelProcessManager<java.lang.String,java.lang.String>, ProcessManager<java.lang.String,java.lang.String>

public final class MetatoolCycleIdManager
extends FbaManager

This class is used to manage steady state cycle identification.

Author:
This class was written and documented by Jeremiah Wright while in the Wagner lab.

Field Summary
static java.lang.String METATOOL_EXE
          The keyword used to denote the Metatool executable.
static UnmodifiableSet<java.lang.String> optionalKeywords
          The set of keywords understood, but not required, by 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.FbaManager
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
ALGORITHM, COMPLETED, DATA_HEADERS, DEV_NULL, ELAPSED_TIME, FILE_FORMAT, INPUT_FILE, INPUT_FILE_NAME_FILE, ITERATIONS, OUTPUT_FILE_NAME, OUTPUT_FILE_NAME_FILE, PERCENT, PERCENT_COMPLETED, SEED, ZERO_CUTOFF
 
Constructor Summary
MetatoolCycleIdManager()
           
 
Method Summary
 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 MetatoolCycleComputer getCycleComp(java.lang.String metatoolFileName)
          Returns a metatool cycle identifier.
static MetatoolExtCurrComputer getExtCurrComp(java.lang.String metatoolFileName)
          Returns a metatool cycle identifier.
 UnmodifiableSet<java.lang.String> getOptionalKeys()
          Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
static ComoFile<java.lang.String,java.lang.Double> getOutputFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, IrrevRxnFluxome fluxome)
          Returns an empty output file that is suitable for storing cycles.
 CycleIdProcess getProcess()
          Returns the process this process manager controls.
 UnmodifiableSet<java.lang.String> getRequiredKeys()
          Returns the set of keywords the provided ManagerInput object must contain.
 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.FbaManager
getCatalysts, getCatalysts, getConstraintTolerance, getConstraintTolerance, getFluxome, getFluxome, getFluxome, getFluxome, getFluxome, getFluxomeSolution, getMultiFluxVectorOutputFile, getMultiFluxVectorOutputFile, getRxnNameExprFormat, getRxnNameHeaders, getRxnNameHeaders, getSingleFluxVectorOutputFile, getSingleFluxVectorOutputFile, printFluxomeInfo, writeFluxome
 
Methods inherited from class sbrt.shell.mng.AbstractProcessManager
check, closeFile, closeRm, execute, getFileFormat, getFileFormat, getFileNameSource, getIterations, getSeed, getTextFileFormat, getZeroCutoff, getZeroCutoff, parseInt, parseLong, printProgress, printProgress, printProgress, runProcess, setInput
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface sbrt.shell.mng.ProcessManager
check, execute, setInput
 

Field Detail

METATOOL_EXE

public static final java.lang.String METATOOL_EXE
The keyword used to denote the Metatool executable.

See Also:
Constant Field Values

requiredKeywords

public static final UnmodifiableSet<java.lang.String> requiredKeywords
The set of keywords required to be present in the ManagerInput objects supplied to instances of this class.


optionalKeywords

public static final UnmodifiableSet<java.lang.String> optionalKeywords
The set of keywords understood, but not required, by instances of this class.

Constructor Detail

MetatoolCycleIdManager

public MetatoolCycleIdManager()
Method Detail

getOutputFile

public static ComoFile<java.lang.String,java.lang.Double> getOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
                                                                        java.io.PrintWriter out,
                                                                        IrrevRxnFluxome fluxome)
Returns an empty output file that is suitable for storing cycles. See ExtremeCurrentManager.getOutputFile(ManagerInput, PrintWriter, sbrt.kernel.fba.Fluxome) for further details.

Parameters:
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.
Returns:
an empty output file that is suitable for storing a single flux vector.
See Also:
AbstractProcessManager.getFileFormat(ManagerInput)

getCycleComp

public static MetatoolCycleComputer getCycleComp(java.lang.String metatoolFileName)
Returns a metatool cycle identifier.

Parameters:
metatoolFileName - the name of the metatool executable.
Returns:
a metatool cycle identifier.

getExtCurrComp

public static MetatoolExtCurrComputer getExtCurrComp(java.lang.String metatoolFileName)
Returns a metatool cycle identifier.

Parameters:
metatoolFileName - the name of the metatool executable.
Returns:
a metatool cycle identifier.

getRequiredKeys

public UnmodifiableSet<java.lang.String> getRequiredKeys()
Returns the set of keywords the provided ManagerInput object must contain.

Returns:
the set of keywords the provided ManagerInput object must contain.

getOptionalKeys

public UnmodifiableSet<java.lang.String> getOptionalKeys()
Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.

Returns:
the set of keywords the provided ManagerInput object does not necessarily have to contain.

getProcess

public CycleIdProcess getProcess()
Returns the process this process manager controls.

Returns:
the process this process manager controls.
Throws:
java.lang.IllegalStateException - if no input was provided to this process manager via AbstractProcessManager.setInput(ManagerInput) or setInput(ManagerInput, PrintWriter)

setInput

public 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. As the input is processed, informative messages are printed to the provided print writer.

Parameters:
input - all of the information required to prepare this process manager for execution.
out - the print writer to which all messages will be printed.

execute

public 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.

Parameters:
out - the print writer where status messages will be printed.
Throws:
java.lang.IllegalStateException - if no input was provided to this process manager via AbstractProcessManager.setInput(ManagerInput) or setInput(ManagerInput, PrintWriter)