sbrt.shell.mng.fba
Class MsFluxIntervalManager

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

public final class MsFluxIntervalManager
extends FbaManager

This class is used to manage Mahadevan-Schilling flux interval processes.

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

Field Summary
static java.lang.String FLUX_CAP_FILE
          The keyword used to denote the flux cap input file.
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_FORMAT, INPUT_FILE_NAME_FILE, ITERATIONS, OUTPUT_FILE_FORMAT, OUTPUT_FILE_NAME, OUTPUT_FILE_NAME_FILE, PERCENT, PERCENT_COMPLETED, SEED, ZERO_CUTOFF
 
Constructor Summary
MsFluxIntervalManager()
           
 
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 UnmodifiableMap<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> getFluxCaps(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
          Returns the flux caps contained in the file with the name specified by FLUX_CAP_FILE in the provided input.
static MsFluxIntervalComputer<IrrevRxnFluxome> getIrrevComp(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Returns the flux interval computer specified by the provided input.
 UnmodifiableSet<java.lang.String> getOptionalKeys()
          Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
 FluxIntervalProcess<IrrevRxnFluxome> 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(FluxRangeException e, FbaProcess<?,?> process)
          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.FbaManager
getCatalysts, getCatalysts, getConstraintTolerance, getConstraintTolerance, getFluxomeSolution, getIrrevRxnFluxome, getIrrevRxnFluxome, getIrrevRxnFluxome, getIrrevRxnFluxome, getIrrevRxnFluxome, getMixedFluxome, getMixedFluxome, getMixedFluxome, getMixedFluxome, getMixedFluxome, getMultiFluxVectorOutputFile, getMultiFluxVectorOutputFile, getRxnNameExprFormat, getRxnNameHeaders, getRxnNameHeaders, getSingleFluxVectorOutputFile, getSingleFluxVectorOutputFile, printFluxomeInfo, writeFluxome, writeFluxome, writeFluxome, writeFluxome
 
Methods inherited from class sbrt.shell.mng.AbstractProcessManager
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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface sbrt.shell.mng.ProcessManager
check, execute, setInput
 

Field Detail

FLUX_CAP_FILE

public static final java.lang.String FLUX_CAP_FILE
The keyword used to denote the flux cap input file.

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

MsFluxIntervalManager

public MsFluxIntervalManager()
Method Detail

getFluxCaps

public static UnmodifiableMap<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> getFluxCaps(ManagerInput<java.lang.String,java.lang.String> input,
                                                                                                        java.io.PrintWriter out,
                                                                                                        Fluxome fluxome)
Returns the flux caps contained in the file with the name specified by FLUX_CAP_FILE in the provided input.

Parameters:
input - the input containing a value for FLUX_CAP_FILE.
out - the print writer to which status messages will be printed.
fluxome - the fluxome to which the flux caps correspond.
Returns:
the flux caps contained in the file with the name specified by FLUX_CAP_FILE in the provided input.

getIrrevComp

public static MsFluxIntervalComputer<IrrevRxnFluxome> getIrrevComp(ManagerInput<java.lang.String,java.lang.String> input,
                                                                   java.io.PrintWriter out)
Returns the flux interval computer specified by the provided input. This method calls FbaOptManager.getMixedComp(ManagerInput, PrintWriter).

Parameters:
input - the input containing all required keywords to construct the flux interval computer.
out - the print writer to which status messages will be printed.
Returns:
the flux interval computer specified by the provided input.

interpret

public static ApplicationException interpret(FluxRangeException e,
                                             FbaProcess<?,?> process)
Returns an ApplicationException whose message describes the error that ocurred.

Parameters:
e - a program solver exception.
process - the FBA process from which the exception was thrown.
Returns:
an ApplicationException wrapping the provided exception.

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.

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.

getProcess

public FluxIntervalProcess<IrrevRxnFluxome> 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)

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)