sbrt.shell.mng.fba
Class RxnDeletionManager

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

public final class RxnDeletionManager
extends FbaManager

This class is used to manage FBA reaction deletion processes.

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

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.
static java.lang.String RXN_DELETION_FILE
          The keyword used to denote the name of a file containing sets of names of reactions whose effect upon deletion will be computed.
 
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
RxnDeletionManager()
           
 
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.Set<java.lang.String>> getInputFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
          Parses and returns the value for RXN_DELETION_FILE in the provided manager input.
static InputFile<java.util.Set<java.lang.String>> getInputFile(java.lang.String fileName, Fluxome fluxome)
          Returns the reaction name input file with the provided name.
static RxnDeletionComputer<MixedFluxome> getMixedDelComp(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Returns a reaction deletion 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.
 RxnDeletionProcess<MixedFluxome> 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

RXN_DELETION_FILE

public static final java.lang.String RXN_DELETION_FILE
The keyword used to denote the name of a file containing sets of names of reactions whose effect upon deletion will be computed.

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 optional keywords in the ManagerInput objects supplied to instances of this class.

Constructor Detail

RxnDeletionManager

public RxnDeletionManager()
Method Detail

getInputFile

public static InputFile<java.util.Set<java.lang.String>> getInputFile(ManagerInput<java.lang.String,java.lang.String> input,
                                                                      java.io.PrintWriter out,
                                                                      Fluxome fluxome)
Parses and returns the value for RXN_DELETION_FILE in the provided manager input. The non-commented lines of this file must be parsable with RxnNameSetFormatV1.

Parameters:
input - keyword-value pairs.
out - the print writer to which status messages will be printed.
fluxome - the fluxome in which the reactions are contained.
Returns:
the reaction name input file with the name contained in input.

getInputFile

public static InputFile<java.util.Set<java.lang.String>> getInputFile(java.lang.String fileName,
                                                                      Fluxome fluxome)
Returns the reaction name input file with the provided name. The non-commented lines of this file must be parsable with RxnNameSetFormatV1.

Parameters:
fileName - the name of the file containing sets of reaction names.
fluxome - the fluxome in which the reactions are contained.
Returns:
the reaction name input file with the provided name.

getMixedDelComp

public static RxnDeletionComputer<MixedFluxome> getMixedDelComp(ManagerInput<java.lang.String,java.lang.String> input,
                                                                java.io.PrintWriter out)
Returns a reaction deletion 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:
a reaction deletion computer created from the provided input.
See Also:
getMixedDelComp(ManagerInput, PrintWriter), AbstractProcessManager.getZeroCutoff(ManagerInput, PrintWriter)

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 RxnDeletionProcess<MixedFluxome> 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)