sbrt.shell.mng.fba
Class SvCdHarFluxVectorManager

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

public final class SvCdHarFluxVectorManager
extends FbaManager

This class is used to manage flux space variation, coordinate direction hit-and-run random flux vector experiments.

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

Field Summary
static java.lang.String OBSTRUCTED_MOVES_FILE_NAME
          The keyword used to denote the name of a file to which the number of obstructed moves will be written for each set of constraint variations.
static UnmodifiableSet<java.lang.String> optionalKeywords
          The set of keywords required to be present 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
SvCdHarFluxVectorManager()
           
 
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 InputFile<java.util.Map<java.lang.String,java.lang.Double>> getInitialFluxVectorFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
          Returns the input file containing a collection of initial flux vectors.
static MultiOutputFiles<ComoFile<java.lang.String,java.lang.Double>,java.util.Map<? extends java.lang.String,? extends java.lang.Double>> getMulitComoFiles(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, java.util.Iterator<java.lang.String> fileNameSource, Fluxome fluxome)
          Returns a source of output files.
static OutputFile<java.lang.Integer> getObsructedMovesFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Returns an output file used to store the number of obstructed moves per flux space.
static OutputFile<java.lang.Integer> getObstructedMovesFile(java.lang.String fileName)
          Returns an output file used to store the number of obstructed moves per flux space.
 UnmodifiableSet<java.lang.String> getOptionalKeys()
          Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
 SvCdHarFluxVectorProcess 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, getFluxome, getFluxome, getFluxome, getFluxome, getFluxome, getFluxomeSolution, getMultiFluxVectorOutputFile, getMultiFluxVectorOutputFile, getRxnNameExprFormat, getRxnNameHeaders, getRxnNameHeaders, getSingleFluxVectorOutputFile, getSingleFluxVectorOutputFile, printFluxomeInfo, 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

OBSTRUCTED_MOVES_FILE_NAME

public static final java.lang.String OBSTRUCTED_MOVES_FILE_NAME
The keyword used to denote the name of a file to which the number of obstructed moves will be written for each set of constraint variations.

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 required to be present in the ManagerInput objects supplied to instances of this class.

Constructor Detail

SvCdHarFluxVectorManager

public SvCdHarFluxVectorManager()
Method Detail

getMulitComoFiles

public static MultiOutputFiles<ComoFile<java.lang.String,java.lang.Double>,java.util.Map<? extends java.lang.String,? extends java.lang.Double>> getMulitComoFiles(ManagerInput<java.lang.String,java.lang.String> input,
                                                                                                                                                                   java.io.PrintWriter out,
                                                                                                                                                                   java.util.Iterator<java.lang.String> fileNameSource,
                                                                                                                                                                   Fluxome fluxome)
Returns a source of output files.

Parameters:
input - the input containing all necessary keyword-value pairs.
out - the print writer to which a status message will be printed.
fileNameSource - the source for output file names.
fluxome - the fluxome for which the flux vectors will correspond.
Returns:
a source of output files.

getObsructedMovesFile

public static OutputFile<java.lang.Integer> getObsructedMovesFile(ManagerInput<java.lang.String,java.lang.String> input,
                                                                  java.io.PrintWriter out)
Returns an output file used to store the number of obstructed moves per flux space.

Parameters:
input - the input containing a value for OBSTRUCTED_MOVES_FILE_NAME.
out - the print writer to which a status message will be printed.
Returns:
an output file used to store the number of obstructed moves per flux space.

getObstructedMovesFile

public static OutputFile<java.lang.Integer> getObstructedMovesFile(java.lang.String fileName)
Returns an output file used to store the number of obstructed moves per flux space.

Parameters:
fileName - the name of the returned file.
Returns:
an output file used to store the number of obstructed moves per flux space.

getInitialFluxVectorFile

public static InputFile<java.util.Map<java.lang.String,java.lang.Double>> getInitialFluxVectorFile(ManagerInput<java.lang.String,java.lang.String> input,
                                                                                                   java.io.PrintWriter out,
                                                                                                   Fluxome fluxome)
Returns the input file containing a collection of initial flux vectors.

Parameters:
input - the input containing a value for CdHarManager.INITIAL_POINT_FILE.
out - the print writer to which a status message will be printed.
fluxome - the fluxome for which the flux vectors correspond.
Returns:
the input file containing a collection of initial flux vectors.

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.

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.

getProcess

public SvCdHarFluxVectorProcess 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)

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)