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java.lang.Objectsbrt.shell.mng.AbstractProcessManager
sbrt.shell.mng.fba.FbaManager
sbrt.shell.mng.fba.SvCdHarFluxVectorManager
public final class SvCdHarFluxVectorManager
This class is used to manage flux space variation, coordinate direction hit-and-run random flux vector experiments.
Field Summary | |
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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 |
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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 |
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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 | |
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SvCdHarFluxVectorManager()
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Method Summary | |
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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.AbstractProcessManager |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface sbrt.shell.mng.ProcessManager |
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check, execute, setInput |
Field Detail |
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public static final java.lang.String OBSTRUCTED_MOVES_FILE_NAME
public static final UnmodifiableSet<java.lang.String> requiredKeywords
ManagerInput
objects supplied to instances of this class.
public static final UnmodifiableSet<java.lang.String> optionalKeywords
ManagerInput
objects supplied to instances of this class.
Constructor Detail |
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public SvCdHarFluxVectorManager()
Method Detail |
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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)
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.
public static OutputFile<java.lang.Integer> getObsructedMovesFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
input
- the input containing a value for
OBSTRUCTED_MOVES_FILE_NAME
.out
- the print writer to which a status message will be printed.
public static OutputFile<java.lang.Integer> getObstructedMovesFile(java.lang.String fileName)
fileName
- the name of the returned file.
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)
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.
public UnmodifiableSet<java.lang.String> getRequiredKeys()
ManagerInput
object must
contain.
ManagerInput
object must
contain.public UnmodifiableSet<java.lang.String> getOptionalKeys()
ManagerInput
object does
not necessarily have to contain.
ManagerInput
object does
not necessarily have to contain.public void setInput(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
input
- all of the information required to prepare this process
manager for execution.out
- the print writer to which all messages will be printed.public SvCdHarFluxVectorProcess getProcess()
java.lang.IllegalStateException
- if no input was provided to this process
manager via AbstractProcessManager.setInput(ManagerInput)
or
setInput(ManagerInput, PrintWriter)
public void execute(java.io.PrintWriter out)
out
- the print writer where status messages will be printed.
java.lang.IllegalStateException
- if no input was provided to this process
manager via AbstractProcessManager.setInput(ManagerInput)
or
setInput(ManagerInput, PrintWriter)
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