sbrt.shell.mng.fba
Class NetworkInfoManager

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

public final class NetworkInfoManager
extends FbaManager

This class is used to manage fluxome information processes.

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

Field Summary
static java.lang.String CATALYST_FILE_NAME
          The keyword used to denote teh name of the file to which all catalysts will be written.
static java.lang.String CHEM_SPECIES_FILE_NAME
          The keyword used to denote the name of the file to which the chemical species of a fluxome will be written.
static java.lang.String EQUATION_FILE_NAME
          The keyword used to denote the name of the file to which the system of linear equations formed by a fluxome will be written.
static java.lang.String EQUIV_RXN_FILE_NAME
          The keyword used to denote the name of the file to which stoichiometrically equivalent reactions will be written.
static UnmodifiableSet<java.lang.String> optionalKeywords
          The set of keywords understood, but not required, by 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_NAME_FILE_NAME
          The keyword used to denote the name of the file to which the names of reactions of a fluxome will be written.
static java.lang.String RXN_OUTPUT_FILE_NAME
          The keyword used to denote the name of the file to which a fluxome will be written.
static java.lang.String S_MATRIX_FILE_NAME
          The keyword used to denote the name of the file to which the stoichiometry matrix of a fluxome will be written.
 
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
NetworkInfoManager()
           
 
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.
 UnmodifiableSet<java.lang.String> getOptionalKeys()
          Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
 NetworkInfoProcess<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.
static void printBasicInfo(MixedFluxome fluxome, java.io.PrintWriter out)
          Prints basic information about the provided fluxome.
 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

EQUIV_RXN_FILE_NAME

public static final java.lang.String EQUIV_RXN_FILE_NAME
The keyword used to denote the name of the file to which stoichiometrically equivalent reactions will be written.

See Also:
Constant Field Values

EQUATION_FILE_NAME

public static final java.lang.String EQUATION_FILE_NAME
The keyword used to denote the name of the file to which the system of linear equations formed by a fluxome will be written.

See Also:
Constant Field Values

S_MATRIX_FILE_NAME

public static final java.lang.String S_MATRIX_FILE_NAME
The keyword used to denote the name of the file to which the stoichiometry matrix of a fluxome will be written.

See Also:
Constant Field Values

CHEM_SPECIES_FILE_NAME

public static final java.lang.String CHEM_SPECIES_FILE_NAME
The keyword used to denote the name of the file to which the chemical species of a fluxome will be written.

See Also:
Constant Field Values

RXN_NAME_FILE_NAME

public static final java.lang.String RXN_NAME_FILE_NAME
The keyword used to denote the name of the file to which the names of reactions of a fluxome will be written.

See Also:
Constant Field Values

RXN_OUTPUT_FILE_NAME

public static final java.lang.String RXN_OUTPUT_FILE_NAME
The keyword used to denote the name of the file to which a fluxome will be written.

See Also:
Constant Field Values

CATALYST_FILE_NAME

public static final java.lang.String CATALYST_FILE_NAME
The keyword used to denote teh name of the file to which all catalysts will be written.

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 understood, but not required, by instances of this class.

Constructor Detail

NetworkInfoManager

public NetworkInfoManager()
Method Detail

printBasicInfo

public static void printBasicInfo(MixedFluxome fluxome,
                                  java.io.PrintWriter out)
Prints basic information about the provided fluxome.

Parameters:
fluxome - the fluxome for which basic information will be printed.
out - the print writer to which basic information will be printed.

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.

getProcess

public NetworkInfoProcess<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)

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.

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)