sbrt.shell.mng.fba
Class RandomFluxVectorManager

java.lang.Object
  extended by sbrt.shell.mng.AbstractProcessManager
      extended by sbrt.shell.mng.fba.FbaManager
          extended by sbrt.shell.mng.fba.RandomFluxVectorManager
All Implemented Interfaces:
KernelProcessManager<java.lang.String,java.lang.String>, ProcessManager<java.lang.String,java.lang.String>
Direct Known Subclasses:
CdHarFluxVectorManager

public abstract class RandomFluxVectorManager
extends FbaManager

This abstract class provides a foundation for random flux vector managers. It contains a keyword as well as a set of utility functions.

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

Field Summary
static java.lang.String ALGORITHM
          The keyword used to denote a random flux vector algorithm.
 
Fields inherited from class sbrt.shell.mng.fba.FbaManager
CONSTRAINT_TOLERANCE, DEFAULT_CONSTRAINT_TOLERANCE, FLUX_VECTOR_FILE, FLUX_VECTOR_FILE_NAME, optionalKeywords, requiredKeywords, RXN_CATALYST_FILE, RXN_FILE, SYSTEM_SOLUTION_FILE
 
Fields inherited from class sbrt.shell.mng.AbstractProcessManager
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
RandomFluxVectorManager()
           
 
Method Summary
static FluxConstraints getConstraints(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome, double tolerance)
          Opens the file denoted by FbaOptManager.CONSTRAINTS_FILE in the provided manager input and returns the set of flux constraints it contains.
static FluxConstraints getConstraints(java.lang.String fileName, Fluxome fluxome, double tolerance)
          Returns the set of constraints contained in the file with the provided name.
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 FbaManager.FLUX_VECTOR_FILE in the provided manager input and returns the flux vector it contains.
static java.util.Map<java.lang.String,java.lang.Double> getFluxVector(java.lang.String fileName, Fluxome fluxome, double tolerance)
          Returns the flux vector contained in the file with the provided name.
static IrrevRxnFluxome getIrrevRxnFluxome(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Creates and returns a fluxome based on the provided input.
 
Methods inherited from class sbrt.shell.mng.fba.FbaManager
getCatalysts, getCatalysts, getConstraintTolerance, getConstraintTolerance, getFluxomeSolution, 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.KernelProcessManager
getProcess
 
Methods inherited from interface sbrt.shell.mng.ProcessManager
check, execute, execute, getOptionalKeys, getRequiredKeys, setInput, setInput
 

Field Detail

ALGORITHM

public static final java.lang.String ALGORITHM
The keyword used to denote a random flux vector algorithm.

See Also:
Constant Field Values
Constructor Detail

RandomFluxVectorManager

public RandomFluxVectorManager()
Method Detail

getFluxVector

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)
Opens the file denoted by FbaManager.FLUX_VECTOR_FILE in the provided manager input and returns the flux vector it contains.

Parameters:
input - the input containing a value for FLUX_VECTOR_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.
Returns:
the flux vector contained in the file indicated by #FLUX_VECTOR_FILE in the provided input.
See Also:
getFluxVector(String, Fluxome, double)

getFluxVector

public static java.util.Map<java.lang.String,java.lang.Double> getFluxVector(java.lang.String fileName,
                                                                             Fluxome fluxome,
                                                                             double tolerance)
Returns the flux vector contained in the file with the provided name. This file must have the format of a row-oriented map file, the lines must be parsable using FluxVectorFormatV1, and a flux must be present for every reaction in the provided fluxome. The flux vector must also lie within the flux space defined by the provided fluxome.

Parameters:
fileName - the name of the file to be read.
fluxome - the fluxome to which the fluxes correspond.
tolerance - the amount by which fluxes in the vector are allowed to violate their defined constraints.
Returns:
the flux vector contained in the file with the provided name.
Throws:
ApplicationException - if the flux vector in the file does not lie within the flux space defined by the provided fluxome.
See Also:
RomiFile, Fluxome.isFluxVector(Map, double)

getConstraints

public static FluxConstraints getConstraints(ManagerInput<java.lang.String,java.lang.String> input,
                                             java.io.PrintWriter out,
                                             Fluxome fluxome,
                                             double tolerance)
Opens the file denoted by FbaOptManager.CONSTRAINTS_FILE in the provided manager input and returns the set of flux constraints it contains.

Parameters:
input - keyword-value pairs.
out - the print writer to which a status message will be printed.
fluxome - the fluxome to which the constraints correspond.
tolerance - the constraint tolerance.
Returns:
the set of flux constraints contained in the file indicated by #CONSTRAINTS_FILE in the provided input.
See Also:
getConstraints(String, Fluxome, double)

getConstraints

public static FluxConstraints getConstraints(java.lang.String fileName,
                                             Fluxome fluxome,
                                             double tolerance)
Returns the set of constraints contained in the file with the provided name. This file must have the format of a row-oriented map file, the lines must be parsable using ConstraintsFileLineFormatV1, and a constraint must be present for every reaction in the provided fluxome.

Parameters:
fileName - the name of the file to be read.
fluxome - the fluxome to which the constraints correspond.
tolerance - the constraint tolerance.
Returns:
the set of constraints contained in the file with the provided name.
Throws:
java.lang.NullPointerException - if either argument is null.
See Also:
getConstraints(ManagerInput, PrintWriter, Fluxome, double), FbaOptManager.getConstraints(String, Fluxome, double), RomiFile

getIrrevRxnFluxome

public static IrrevRxnFluxome getIrrevRxnFluxome(ManagerInput<java.lang.String,java.lang.String> input,
                                                 java.io.PrintWriter out)
Creates and returns a fluxome based on the provided input. The values for FbaManager.RXN_FILE, FbaOptManager.CONSTRAINTS_FILE, and FbaManager.CONSTRAINT_TOLERANCE are parsed and combined to create the returned fluxome.

Parameters:
input - the input containing values for the listed keywords.
out - the print writer to which status messages will be printed.
Returns:
a fluxome based on the provided input.
See Also:
FbaManager.getIrrevRxnFluxome(ManagerInput, PrintWriter), FbaManager.getConstraintTolerance(ManagerInput, PrintWriter), getConstraints(ManagerInput, PrintWriter, Fluxome, double), Fluxome.replaceConstraints(FluxConstraints, double)