sbrt.shell.mng.fba
Class IntervalVariationManager

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

public abstract class IntervalVariationManager
extends FbaManager

This abstract class provides utitlity functions for managing flux interval variation processes.

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

Field Summary
static java.lang.String CV_FILE
          The keyword used to denote a constraint variation input file.
static java.lang.String FLUX_INTERVAL_FILE
          The keyword used to denote a flux interval input file.
 
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
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
IntervalVariationManager()
           
 
Method Summary
static FluxIntervalInputFile getCvInputFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome, double tolerance)
          Returns the constraint variation input with the name denoted by CV_FILE in the provided manager input.
static FluxIntervalInputFile getCvInputFile(java.lang.String fileName, Fluxome fluxome, double tolerance)
          Returns the constraint variation input file with the provided name.
static FluxIntervalInputFile getIntervalInputFile(java.lang.String fileName, Fluxome fluxome, double tolerance)
          Returns the flux interval input file with the provided name.
static FluxIntervalInputFile getIntervalInputFile(java.lang.String fileName, Fluxome fluxome, MapFormat<LinearComb<java.lang.String>,Interval> mapFormat, double tolerance)
          Returns the flux interval input file with the provided name.
static FluxIntervalInputFile getSvInputFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome, double tolerance)
          Returns the space variation input with the name denoted by FLUX_INTERVAL_FILE in the provided manager input.
 
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.KernelProcessManager
getProcess
 
Methods inherited from interface sbrt.shell.mng.ProcessManager
check, execute, execute, getOptionalKeys, getRequiredKeys, setInput, setInput
 

Field Detail

CV_FILE

public static final java.lang.String CV_FILE
The keyword used to denote a constraint variation input file.

See Also:
Constant Field Values

FLUX_INTERVAL_FILE

public static final java.lang.String FLUX_INTERVAL_FILE
The keyword used to denote a flux interval input file.

See Also:
Constant Field Values
Constructor Detail

IntervalVariationManager

public IntervalVariationManager()
Method Detail

getCvInputFile

public static FluxIntervalInputFile getCvInputFile(ManagerInput<java.lang.String,java.lang.String> input,
                                                   java.io.PrintWriter out,
                                                   Fluxome fluxome,
                                                   double tolerance)
Returns the constraint variation input with the name denoted by CV_FILE in the provided manager input.

Parameters:
input - the input containing a value for CV_FILE.
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 constraint variation input with the name denoted by CV_FILE in the provided manager input.

getCvInputFile

public static FluxIntervalInputFile getCvInputFile(java.lang.String fileName,
                                                   Fluxome fluxome,
                                                   double tolerance)
Returns the constraint variation input file with the provided name.

Parameters:
fileName - the name of the constraint variation file to open.
fluxome - the fluxome to which the constraints correspond.
tolerance - the constraint tolerance.
Returns:
the constraint variation input file with the provided name.

getSvInputFile

public static FluxIntervalInputFile getSvInputFile(ManagerInput<java.lang.String,java.lang.String> input,
                                                   java.io.PrintWriter out,
                                                   Fluxome fluxome,
                                                   double tolerance)
Returns the space variation input with the name denoted by FLUX_INTERVAL_FILE in the provided manager input.

Parameters:
input - the input containing a value for FLUX_INTERVAL_FILE.
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 space variation input with the name denoted by FLUX_INTERVAL_FILE in the provided manager input.

getIntervalInputFile

public static FluxIntervalInputFile getIntervalInputFile(java.lang.String fileName,
                                                         Fluxome fluxome,
                                                         MapFormat<LinearComb<java.lang.String>,Interval> mapFormat,
                                                         double tolerance)
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 constraints correspond.
mapFormat - the parser.
tolerance - the constraint tolerance.
Returns:
the flux interval input file with the provided name.

getIntervalInputFile

public static FluxIntervalInputFile getIntervalInputFile(java.lang.String fileName,
                                                         Fluxome fluxome,
                                                         double tolerance)
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 constraints correspond.
tolerance - the constraint tolerance.
Returns:
the flux interval input file with the provided name.