sbrt.shell.mng.fba
Class ExtremeCurrentManager

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

public final class ExtremeCurrentManager
extends FbaManager

This class is used to manage FBA extreme current processes.

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

Nested Class Summary
protected static class ExtremeCurrentManager.Rm
           
 
Field Summary
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
ExtremeCurrentManager()
           
 
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 ExtremeCurrentComputer getComputer(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Returns an extreme current computer created from the provided input.
 UnmodifiableSet<java.lang.String> getOptionalKeys()
          Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
static ComoFile<java.lang.String,java.lang.Double> getOutputFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome, java.util.Set<java.lang.String> rxnNames)
          Returns an output file to which extreme currents can be written.
static ComoFile<java.lang.String,java.lang.Double> getOutputFile(java.lang.String fileName, java.io.PrintWriter out, Fluxome fluxome, java.util.Set<java.lang.String> rxnNames)
          Returns an output file to which extreme currents can be written.
 ExtremeCurrentProcess<IrrevRxnFluxome> 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

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

ExtremeCurrentManager

public ExtremeCurrentManager()
Method Detail

getOutputFile

public static ComoFile<java.lang.String,java.lang.Double> getOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
                                                                        java.io.PrintWriter out,
                                                                        Fluxome fluxome,
                                                                        java.util.Set<java.lang.String> rxnNames)
Returns an output file to which extreme currents can be written.

Parameters:
input - the manager input from which the value for AbstractProcessManager.OUTPUT_FILE_NAME is obtained.
out - the print writer to which status messages will be printed.
fluxome - the fluxome in which the reactions are contained.
rxnNames - the reactions names that will appear as column variables in the extreme current matrix.
Returns:
the output file with the name contained in input.

getOutputFile

public static ComoFile<java.lang.String,java.lang.Double> getOutputFile(java.lang.String fileName,
                                                                        java.io.PrintWriter out,
                                                                        Fluxome fluxome,
                                                                        java.util.Set<java.lang.String> rxnNames)
Returns an output file to which extreme currents can be written.

Parameters:
fileName - the name of the file to be created.
out - the print writer to which status messages will be printed.
fluxome - the fluxome in which the reactions are contained.
rxnNames - the reactions names that will appear as column variables in the extreme current matrix.
Returns:
the output file with the name contained in input.

getComputer

public static ExtremeCurrentComputer getComputer(ManagerInput<java.lang.String,java.lang.String> input,
                                                 java.io.PrintWriter out)
Returns an extreme current computer created from the provided input.

Parameters:
input - the manager input from which the necessary information is obtained.
out - the print writer to which status messages will be printed.
Returns:
an extreme current computer created from the provided input.

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 ExtremeCurrentProcess<IrrevRxnFluxome> 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)