sbrt.shell.mng.fba
Class FluxPlasticityManager

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

public final class FluxPlasticityManager
extends FbaManager

This class is used to manage flux plasticity processes.

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

Field Summary
static java.lang.String ALWAYS_ACTIVE_FILE_NAME
          The keyword used to denote the name of the output file for the names of always-active reactions.
static java.lang.String FLUX_INTERVAL_FILE
          The keyword used to denote the name of the file containing the sets of flux intervals.
static java.lang.String NEVER_ACTIVE_FILE_NAME
          The keyword used to denote the name of the output file for the names of never-active reactions.
static UnmodifiableSet<java.lang.String> optionalKeywords
          The set of keywords understood, but not required, by instances of this class.
static java.lang.String POT_ACTIVE_FILE_NAME
          The keyword used to denote the name of the output file for the names of potentially-active reactions.
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
FluxPlasticityManager()
           
 
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 MapInputFile<java.lang.String,Interval> getFluxIntervalFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
          Returns the flux interval input with the name denoted by FLUX_INTERVAL_FILE in the provided manager input.
static MapInputFile<java.lang.String,Interval> getFluxIntervalFile(java.lang.String fileName, Fluxome fluxome)
          Returns the flux interval input file with the provided name.
 UnmodifiableSet<java.lang.String> getOptionalKeys()
          Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
 FluxPlasticityProcess<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.
 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_INTERVAL_FILE

public static final java.lang.String FLUX_INTERVAL_FILE
The keyword used to denote the name of the file containing the sets of flux intervals.

See Also:
Constant Field Values

ALWAYS_ACTIVE_FILE_NAME

public static final java.lang.String ALWAYS_ACTIVE_FILE_NAME
The keyword used to denote the name of the output file for the names of always-active reactions.

See Also:
Constant Field Values

POT_ACTIVE_FILE_NAME

public static final java.lang.String POT_ACTIVE_FILE_NAME
The keyword used to denote the name of the output file for the names of potentially-active reactions.

See Also:
Constant Field Values

NEVER_ACTIVE_FILE_NAME

public static final java.lang.String NEVER_ACTIVE_FILE_NAME
The keyword used to denote the name of the output file for the names of never-active reactions.

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

FluxPlasticityManager

public FluxPlasticityManager()
Method Detail

getFluxIntervalFile

public static MapInputFile<java.lang.String,Interval> getFluxIntervalFile(ManagerInput<java.lang.String,java.lang.String> input,
                                                                          java.io.PrintWriter out,
                                                                          Fluxome fluxome)
Returns the flux interval input with the name denoted by FLUX_INTERVAL_FILE in the provided manager input.

Parameters:
input - keyword-value pairs.
out - the print writer to which a status message will be printed.
fluxome - the fluxome to which the reaction names correspond.
Returns:
the flux interval input with the name denoted by FLUX_INTERVAL_FILE in the provided manager input.

getFluxIntervalFile

public static MapInputFile<java.lang.String,Interval> getFluxIntervalFile(java.lang.String fileName,
                                                                          Fluxome fluxome)
Returns the flux interval input file with the provided name.

Parameters:
fileName - the name of the flux interval file to open.
fluxome - the fluxome to which the reaction names correspond.
Returns:
the flux interval input file with the provided name.

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 FluxPlasticityProcess<MixedFluxome> 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)