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java.lang.Objectsbrt.shell.mng.AbstractProcessManager
sbrt.shell.mng.fba.FbaManager
sbrt.shell.mng.fba.InitialPointManager
public final class InitialPointManager
This class is used to manage initial point processes.
Field Summary | |
---|---|
static double |
DEFAULT_P
The default P intercept value. |
static java.lang.String |
FLUX_INTERVAL_FILE
The keyword used to denote the name of the file containing the set of flux intervals. |
static UnmodifiableSet<java.lang.String> |
optionalKeywords
The set of keywords understood, but not required, by instances of this class. |
static java.lang.String |
P_MAX
The keyword used to denote the P intercept (the value of positioning variables at the edge of the convex poytope). |
static java.lang.String |
P_VECTOR_FILE_NAME
The keyword used to denote the name of the C vector output file. |
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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InitialPointManager()
|
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 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 a single flux vector. |
static FluxConstraints |
getIntervals(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Opens the file denoted by FLUX_INTERVAL_FILE in the provided manager input and returns the set of flux intervals it contains. |
static FluxConstraints |
getIntervals(java.lang.String fileName,
Fluxome fluxome,
double tolerance)
Returns the set of flux intervals contained in the file with the provided name. |
static FbaOptimizer<MixedFluxome> |
getMixedComp(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Creates and returns an FBA optimization computer based on the provided input. |
static MixedFluxome |
getMixedFluxome(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
double tolerance)
Creates and returns a fluxome based on the provided input. |
UnmodifiableSet<java.lang.String> |
getOptionalKeys()
Returns the set of keywords the provided ManagerInput object does
not necessarily have to contain. |
static double |
getPIntercept(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Returns the parsed value for P_MAX in the provided input. |
InitialPointGenerator<MixedFluxome> |
getProcess()
Returns the process this process manager controls. |
static MapOutputFile<java.lang.String,java.lang.Double> |
getPVectorFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing a single C vector with the name denoted by P_VECTOR_FILE_NAME in the provided input. |
UnmodifiableSet<java.lang.String> |
getRequiredKeys()
Returns the set of keywords the provided ManagerInput object must
contain. |
static ApplicationException |
interpret(FbaOptException e,
FbaProcess<?,?> process)
Returns an ApplicationException whose message describes the error
that ocurred. |
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 P_MAX
public static final double DEFAULT_P
public static final java.lang.String P_VECTOR_FILE_NAME
public static final java.lang.String FLUX_INTERVAL_FILE
public static final UnmodifiableSet<java.lang.String> requiredKeywords
ManagerInput
objects supplied to instances of this class.
public static final UnmodifiableSet<java.lang.String> optionalKeywords
Constructor Detail |
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public InitialPointManager()
Method Detail |
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public static double getPIntercept(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
input
- the input whose P_INTERCEPT
value is to be parsed.out
- the print writer to which a status message will be printed.
P_INTERCEPT
exists.
ApplicationException
- if the parsed intercept is infinite, NaN, or <
10.public static MapOutputFile<java.lang.String,java.lang.Double> getFluxVectorFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
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.
FbaManager.getRxnNameHeaders(ManagerInput, Fluxome)
public static MapOutputFile<java.lang.String,java.lang.Double> getPVectorFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
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.
public static FbaOptimizer<MixedFluxome> getMixedComp(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
input
- the input containing values for the listed keywords.out
- the print writer to which status messages will be printed.
FbaManager.getMixedFluxome(ManagerInput, PrintWriter)
,
FbaOptManager.getSafetyLevel(ManagerInput, PrintWriter)
,
FbaManager.getConstraintTolerance(ManagerInput, PrintWriter)
,
ProgramSolverFactory.make(ManagerInput, PrintWriter)
public static MixedFluxome getMixedFluxome(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, double tolerance)
input
- the input containing values for the listed keywords.out
- the print writer to which status messages will be printed.tolerance
- the constraint tolerance.
FbaManager.getMixedFluxome(ManagerInput, PrintWriter)
,
getIntervals(ManagerInput, PrintWriter, Fluxome, double)
,
Fluxome.replaceConstraints(FluxConstraints, double)
public static FluxConstraints getIntervals(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 flux intervals correspond.tolerance
- the constraint tolerance.
#FLUX_INTERVAL_FILE
in the provided input.
ApplicationException
- if the file does not contain a flux interval
for each reaction in the provided fluxome, or if an interval in
unbounded.getIntervals(String, Fluxome, double)
public static FluxConstraints getIntervals(java.lang.String fileName, Fluxome fluxome, double tolerance)
fileName
- the name of the file to be read.fluxome
- the fluxome to which the flux intervals correspond.tolerance
- the contraint tolerance.
ApplicationException
- if the file does not contain a flux interval
for each reaction in the provided fluxome, or if an interval in
unbounded.
FormatException
- if any part of the file cannot be parsed.
java.lang.NullPointerException
- if any argument is null
.RomiFile
public static ApplicationException interpret(FbaOptException e, FbaProcess<?,?> process)
ApplicationException
whose message describes the error
that ocurred.
e
- an FBA optimization exception.process
- the FBA process from which the exception was thrown.
ApplicationException
wrapping the provided exception.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 InitialPointGenerator<MixedFluxome> getProcess()
java.lang.IllegalStateException
- if no input was provided to this process
manager via AbstractProcessManager.setInput(ManagerInput) or
setInput(ManagerInput, PrintWriter)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 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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