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java.lang.Objectsbrt.shell.mng.AbstractProcessManager
sbrt.shell.mng.fba.FbaManager
sbrt.shell.mng.fba.IntervalVariationManager
public abstract class IntervalVariationManager
This abstract class provides utitlity functions for managing flux interval variation processes.
Field Summary | |
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static java.lang.String |
CV_FILE
The keyword used to denote a constraint variation input file. |
static java.lang.String |
FLUX_INTERVAL_FILE
The keyword used to denote a flux interval input file. |
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, optionalKeywords, requiredKeywords, 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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IntervalVariationManager()
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Method Summary | |
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static FluxIntervalInputFile |
getCvInputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Returns the constraint variation input with the name denoted by CV_FILE in the provided manager input. |
static FluxIntervalInputFile |
getCvInputFile(java.lang.String fileName,
Fluxome fluxome,
double tolerance)
Returns the constraint variation input file with the provided name. |
static FluxIntervalInputFile |
getIntervalInputFile(java.lang.String fileName,
Fluxome fluxome,
double tolerance)
Returns the flux interval input file with the provided name. |
static FluxIntervalInputFile |
getIntervalInputFile(java.lang.String fileName,
Fluxome fluxome,
MapFormat<LinearComb<java.lang.String>,Interval> mapFormat,
double tolerance)
Returns the flux interval input file with the provided name. |
static FluxIntervalInputFile |
getSvInputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Returns the space variation input with the name denoted by FLUX_INTERVAL_FILE in the provided manager input. |
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.KernelProcessManager |
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getProcess |
Methods inherited from interface sbrt.shell.mng.ProcessManager |
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check, execute, execute, getOptionalKeys, getRequiredKeys, setInput, setInput |
Field Detail |
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public static final java.lang.String CV_FILE
public static final java.lang.String FLUX_INTERVAL_FILE
Constructor Detail |
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public IntervalVariationManager()
Method Detail |
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public static FluxIntervalInputFile getCvInputFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome, double tolerance)
input
- the input containing a value for CV_FILE
.out
- the print writer to which a status message will be printed.fluxome
- the fluxome to which the constraints correspond.tolerance
- the constraint tolerance.
public static FluxIntervalInputFile getCvInputFile(java.lang.String fileName, Fluxome fluxome, double tolerance)
fileName
- the name of the constraint variation file to open.fluxome
- the fluxome to which the constraints correspond.tolerance
- the constraint tolerance.
public static FluxIntervalInputFile getSvInputFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome, double tolerance)
input
- the input containing a value for FLUX_INTERVAL_FILE
.out
- the print writer to which a status message will be printed.fluxome
- the fluxome to which the constraints correspond.tolerance
- the constraint tolerance.
public static FluxIntervalInputFile getIntervalInputFile(java.lang.String fileName, Fluxome fluxome, MapFormat<LinearComb<java.lang.String>,Interval> mapFormat, double tolerance)
fileName
- the name of the flux interval file to open.fluxome
- the fluxome to which the constraints correspond.mapFormat
- the parser.tolerance
- the constraint tolerance.
public static FluxIntervalInputFile getIntervalInputFile(java.lang.String fileName, Fluxome fluxome, double tolerance)
fileName
- the name of the flux interval file to open.fluxome
- the fluxome to which the constraints correspond.tolerance
- the constraint tolerance.
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