sbrt.shell.mng.fba
Class FluxActivityManager

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

public final class FluxActivityManager
extends FbaManager

This class is used to manage flux activity processes.

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

Field Summary
static java.lang.String ACTIVITY_COUNT_FILE_NAME
          The keyword used to denote the name of the activity count output file.
static java.lang.String ACTIVITY_VECTOR_FILE_NAME
          The keyword used to denote the name of the activity vector output file.
static java.lang.String FLUX_VECTOR_FILE_FORMAT
          The keyword used to denote the format of the flux vector input file.
static UnmodifiableSet<java.lang.String> optionalKeywords
          The set of optional keywords 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.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
FluxActivityManager()
           
 
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,java.lang.Double> getFluxVectorFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
          Returns the flux vector input file specified by the provided input.
static MapInputFile<java.lang.String,java.lang.Double> getFluxVectorFile(java.lang.String fileName, FileFormat format, Fluxome fluxome)
          Returns the flux vector 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.
 FluxActivityProcess<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

ACTIVITY_COUNT_FILE_NAME

public static final java.lang.String ACTIVITY_COUNT_FILE_NAME
The keyword used to denote the name of the activity count output file.

See Also:
Constant Field Values

ACTIVITY_VECTOR_FILE_NAME

public static final java.lang.String ACTIVITY_VECTOR_FILE_NAME
The keyword used to denote the name of the activity vector output file.

See Also:
Constant Field Values

FLUX_VECTOR_FILE_FORMAT

public static final java.lang.String FLUX_VECTOR_FILE_FORMAT
The keyword used to denote the format of the flux vector 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 optional keywords in the ManagerInput objects supplied to instances of this class.

Constructor Detail

FluxActivityManager

public FluxActivityManager()
Method Detail

getFluxVectorFile

public static MapInputFile<java.lang.String,java.lang.Double> getFluxVectorFile(ManagerInput<java.lang.String,java.lang.String> input,
                                                                                java.io.PrintWriter out,
                                                                                Fluxome fluxome)
Returns the flux vector input file specified by the provided input. The values for FbaManager.FLUX_VECTOR_FILE and FLUX_VECTOR_FILE_FORMAT are parsed and used to call the method getFluxVectorFile(String, FileFormat, Fluxome).

Parameters:
input - keyword-value pairs.
out - the print writer to which status messages will be printed.
fluxome - the fluxome to which the flux vectors correspond.
Returns:
the flux vector input file specified by the provided input.

getFluxVectorFile

public static MapInputFile<java.lang.String,java.lang.Double> getFluxVectorFile(java.lang.String fileName,
                                                                                FileFormat format,
                                                                                Fluxome fluxome)
Returns the flux vector input file with the provided name. If this file is text-based, it must be a column-oriented map file that is parsable using FluxVectorFormatV1.

Parameters:
fileName - the name of the file to open.
format - the format of the file to open.
fluxome - the fluxome to which the flux vectors correspond.
Returns:
the flux vector 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 FluxActivityProcess<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)