sbrt.shell.mng.fba
Class RandomFluxVectorManager
java.lang.Object
sbrt.shell.mng.AbstractProcessManager
sbrt.shell.mng.fba.FbaManager
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.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 |
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 |
ALGORITHM
public static final java.lang.String ALGORITHM
- The keyword used to denote a random flux vector algorithm.
- See Also:
- Constant Field Values
RandomFluxVectorManager
public RandomFluxVectorManager()
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)