sbrt.shell.mng.fba
Class SvInitialPointManager

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

public final class SvInitialPointManager
extends FbaManager

This class is used to manage flux space variation-initial point experiments.

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

Field Summary
static java.lang.String AVG_P_FILE_NAME
          The keyword used to denote the name of the average P output file.
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
SvInitialPointManager()
           
 
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 OutputFile<java.lang.Double> getCentralityFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Parses and returns the value for AVG_P_FILE_NAME in the provided manager input.
static MapOutputFile<java.lang.String,java.lang.Double> getFluxVectorFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
          Returns an empty output file that is suitable for storing multiple flux vectors.
 UnmodifiableSet<java.lang.String> getOptionalKeys()
          Returns the set of keywords the provided ManagerInput object does not necessarily have to contain.
 SvInitialPointProcess 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

AVG_P_FILE_NAME

public static final java.lang.String AVG_P_FILE_NAME
The keyword used to denote the name of the average P output file.

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

SvInitialPointManager

public SvInitialPointManager()
Method Detail

getFluxVectorFile

public static MapOutputFile<java.lang.String,java.lang.Double> getFluxVectorFile(ManagerInput<java.lang.String,java.lang.String> input,
                                                                                 java.io.PrintWriter out,
                                                                                 Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple flux vectors.

Parameters:
input - the input containing values for the listed keywords.
out - the print writer to which status messages will be printed.
fluxome - the fluxome for which the data headers correspond.
Returns:
an empty output file that is suitable for storing multiple flux vectors.
See Also:
FbaManager.getMultiFluxVectorOutputFile(ManagerInput, PrintWriter, Fluxome)

getCentralityFile

public static OutputFile<java.lang.Double> getCentralityFile(ManagerInput<java.lang.String,java.lang.String> input,
                                                             java.io.PrintWriter out)
Parses and returns the value for AVG_P_FILE_NAME in the provided manager input.

Parameters:
input - the input containing a value for AVG_CENTRALITY_FILE_NAME.
out - the print writer to which a status message will be printed.
Returns:
the parsed value for AVG_P_FILE_NAME in 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.

getProcess

public SvInitialPointProcess 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)