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java.lang.Objectsbrt.shell.mng.AbstractProcessManager
sbrt.shell.mng.fba.FbaManager
public abstract class FbaManager
This abstract class provides a foundation for Flux Balance Analysis process managers. It contains many of the keywords required by FBA managers, as well as a number of utility functions.
Field Summary | |
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static java.lang.String |
CONSTRAINT_TOLERANCE
The keyword used to denote a constraint tolerance. |
static double |
DEFAULT_CONSTRAINT_TOLERANCE
The default constraint tolerance. |
static java.lang.String |
FLUX_VECTOR_FILE
The keyword used to denote a flux vector input file. |
static java.lang.String |
FLUX_VECTOR_FILE_NAME
The keyword used to denote the name of a flux vector output file. |
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_CATALYST_FILE
The keyword used to denote the name of a file containing reaction-catalyst associations. |
static java.lang.String |
RXN_FILE
The keyword used to denote an FBA reaction file. |
static java.lang.String |
SYSTEM_SOLUTION_FILE
The keyword used to denote a file containing a solution to the system of linear equations formed by a fluxome. |
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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FbaManager()
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Method Summary | |
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static java.util.Map<java.lang.String,Or<And<java.lang.String>>> |
getCatalysts(Fluxome fluxome,
java.lang.String fileName)
Returns the reaction-catalyst associations contained in the file with the provided name. |
static java.util.Map<java.lang.String,Or<And<java.lang.String>>> |
getCatalysts(Fluxome fluxome,
java.lang.String fileName,
java.io.PrintWriter out)
Returns the reaction-catalyst associations contained in the file with the provided name. |
static double |
getConstraintTolerance(ManagerInput<java.lang.String,java.lang.String> input)
Parses and returns the value for CONSTRAINT_TOLERANCE in the provided manager input. |
static double |
getConstraintTolerance(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Parses and returns the value for CONSTRAINT_TOLERANCE in the provided manager input. |
static LinearSystemSolution<java.lang.String> |
getFluxomeSolution(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double coeffCutoff)
Opens the file denoted by SYSTEM_SOLUTION_FILE in the provided manager input and returns the linear system solution it contains. |
static IrrevRxnFluxome |
getIrrevRxnFluxome(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Opens the file denoted by RXN_FILE in the provided manager input and returns the fluxome it contains. |
static IrrevRxnFluxome |
getIrrevRxnFluxome(java.lang.String fileName)
Returns the fluxome contained in the file with the provided name. |
static IrrevRxnFluxome |
getIrrevRxnFluxome(java.lang.String fileName,
java.io.PrintWriter out)
Returns the fluxome contained in the file with the provided name. |
static IrrevRxnFluxome |
getIrrevRxnFluxome(java.lang.String rxnFileName,
java.lang.String catalystFileName)
Returns the fluxome contained in the files with the provided names. |
static IrrevRxnFluxome |
getIrrevRxnFluxome(java.lang.String rxnFileName,
java.lang.String catalystFileName,
java.io.PrintWriter out)
Returns the fluxome contained in the files with the provided names. |
static MixedFluxome |
getMixedFluxome(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Opens the file denoted by RXN_FILE in the provided manager input and returns the fluxome it contains. |
static MixedFluxome |
getMixedFluxome(java.lang.String fileName)
Returns the fluxome contained in the file with the provided name. |
static MixedFluxome |
getMixedFluxome(java.lang.String fileName,
java.io.PrintWriter out)
Returns the fluxome contained in the file with the provided name. |
static MixedFluxome |
getMixedFluxome(java.lang.String rxnFileName,
java.lang.String catalystFileName)
Returns the fluxome contained in the files with the provided names. |
static MixedFluxome |
getMixedFluxome(java.lang.String rxnFileName,
java.lang.String catalystFileName,
java.io.PrintWriter out)
Returns the fluxome contained in the files with the provided names. |
static MapOutputFile<java.lang.String,java.lang.Double> |
getMultiFluxVectorOutputFile(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. |
static MapOutputFile<java.lang.String,java.lang.Double> |
getMultiFluxVectorOutputFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<java.lang.String> rxnNameHeaders,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple flux vectors. |
static RxnNameExprFormat<LinearComb<java.lang.String>,java.lang.String> |
getRxnNameExprFormat(Fluxome f)
Returns the default reaction name expression format. |
static java.util.Set<java.lang.String> |
getRxnNameHeaders(ManagerInput<java.lang.String,java.lang.String> input,
Fluxome fluxome)
Parses and returns the value for AbstractProcessManager.DATA_HEADERS in the provided manager input. |
static java.util.LinkedHashSet<java.lang.String> |
getRxnNameHeaders(java.lang.String dataHeaders,
Fluxome fluxome)
Parses and returns the set of reaction names contained in the provided string. |
static MapOutputFile<java.lang.String,java.lang.Double> |
getSingleFluxVectorOutputFile(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 MapOutputFile<java.lang.String,java.lang.Double> |
getSingleFluxVectorOutputFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<java.lang.String> rxnNameHeaders,
Fluxome fluxome)
Returns an empty output file that is suitable for storing a single flux vector. |
static void |
printFluxomeInfo(Fluxome fluxome,
java.io.PrintWriter out)
Prints basic information about the provided fluxome. |
static void |
writeFluxome(IrrevRxnFluxome fluxome,
java.lang.String fileName)
Writes the provided fluxome to a file with the provided name. |
static void |
writeFluxome(IrrevRxnFluxome fluxome,
java.lang.String fileName,
java.io.PrintWriter out)
Writes the provided fluxome to a file with the provided name. |
static void |
writeFluxome(MixedFluxome fluxome,
java.lang.String fileName)
Writes the provided fluxome to a file with the provided name. |
static void |
writeFluxome(MixedFluxome fluxome,
java.lang.String fileName,
java.io.PrintWriter out)
Writes the provided fluxome to a file with the provided name. |
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 RXN_FILE
public static final java.lang.String RXN_CATALYST_FILE
public static final java.lang.String FLUX_VECTOR_FILE
public static final java.lang.String FLUX_VECTOR_FILE_NAME
public static final java.lang.String SYSTEM_SOLUTION_FILE
public static final java.lang.String CONSTRAINT_TOLERANCE
public static final double DEFAULT_CONSTRAINT_TOLERANCE
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 FbaManager()
Method Detail |
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public static void printFluxomeInfo(Fluxome fluxome, java.io.PrintWriter out)
fluxome
- the fluxome for which basic information will be printed.out
- the print writer to which basic information will be printed.public static RxnNameExprFormat<LinearComb<java.lang.String>,java.lang.String> getRxnNameExprFormat(Fluxome f)
f
- the fluxome for which the format will be created.
public static double getConstraintTolerance(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
input
- keyword-value pairs.out
- the print writer to which a status message will be printed.
ApplicationException
- if the parsed tolerance is infinite, NaN, or < 0.public static double getConstraintTolerance(ManagerInput<java.lang.String,java.lang.String> input)
input
- keyword-value pairs.
ApplicationException
- if the parsed tolerance is infinite, NaN, or < 0.public static java.util.Set<java.lang.String> getRxnNameHeaders(ManagerInput<java.lang.String,java.lang.String> input, Fluxome fluxome)
DATA_HEADERS
, the set of all reactions names from the
provided fluxome is returned.
input
- keyword-value pairs.fluxome
- the fluxome for which the data headers correspond.
public static java.util.LinkedHashSet<java.lang.String> getRxnNameHeaders(java.lang.String dataHeaders, Fluxome fluxome)
dataHeaders
- the data header string to be parsed.fluxome
- the fluxome for which the data headers correspond.
public static MapOutputFile<java.lang.String,java.lang.Double> getSingleFluxVectorOutputFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
input
- keyword-value pairs.out
- the print writer to which status messages will be printed.fluxome
- the fluxome for which the data headers correspond.
getRxnNameHeaders(ManagerInput, Fluxome)
,
AbstractProcessManager.getFileFormat(ManagerInput)
public static MapOutputFile<java.lang.String,java.lang.Double> getSingleFluxVectorOutputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<java.lang.String> rxnNameHeaders, Fluxome fluxome)
fileName
- the name of the file to be created.fileFormat
- the format of the file to be created.rxnNameHeaders
- the set of reaction names to be written to the
file.fluxome
- the fluxome to which the reaction names correspond.
public static MapOutputFile<java.lang.String,java.lang.Double> getMultiFluxVectorOutputFile(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.
getRxnNameHeaders(ManagerInput, Fluxome)
,
AbstractProcessManager.getFileFormat(ManagerInput)
public static MapOutputFile<java.lang.String,java.lang.Double> getMultiFluxVectorOutputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<java.lang.String> rxnNameHeaders, Fluxome fluxome)
fileName
- the name of the file to be created.fileFormat
- the format of the file to be created.rxnNameHeaders
- the set of reaction names to be written to the
file.fluxome
- the fluxome to which the reaction names correspond.
public static MixedFluxome getMixedFluxome(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
input
- keyword-value pairs.out
- the print writer to which a status message will be printed.
public static IrrevRxnFluxome getIrrevRxnFluxome(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
input
- keyword-value pairs.out
- the print writer to which a status message will be printed.
public static IrrevRxnFluxome getIrrevRxnFluxome(java.lang.String fileName, java.io.PrintWriter out)
fileName
- the name of a file containing a fluxome parsable with
IrfFormatV1.out
- the print writer to which a status message will be printed.
public static MixedFluxome getMixedFluxome(java.lang.String fileName, java.io.PrintWriter out)
fileName
- the name of a file containing a fluxome parsable with
MixedFluxomeFormatV1.out
- the print writer to which a status message will be printed.
public static IrrevRxnFluxome getIrrevRxnFluxome(java.lang.String fileName)
fileName
- the name of a file containing a fluxome parsable with
IrfFormatV1.
public static MixedFluxome getMixedFluxome(java.lang.String fileName)
fileName
- the name of a file containing a fluxome parsable with
MixedFluxomeFormatV1.
public static IrrevRxnFluxome getIrrevRxnFluxome(java.lang.String rxnFileName, java.lang.String catalystFileName)
rxnFileName
- the name of a file containing a fluxome parsable with
IrfFormatV1.catalystFileName
- the name of a file containing reaction-catalyst associations
parsable with BoolRelFormatV1
public static MixedFluxome getMixedFluxome(java.lang.String rxnFileName, java.lang.String catalystFileName)
rxnFileName
- the name of a file containing a fluxome parsable with
MixedFluxomeFormatV1.catalystFileName
- the name of a file containing reaction-catalyst associations
parsable with BoolRelFormatV1
public static IrrevRxnFluxome getIrrevRxnFluxome(java.lang.String rxnFileName, java.lang.String catalystFileName, java.io.PrintWriter out)
rxnFileName
- the name of a file containing a fluxome parsable with
IrfFormatV1.catalystFileName
- the name of a file containing reaction-catalyst associations
parsable with BoolRelFormatV1out
- the print writer to which descriptive message will be written.
public static MixedFluxome getMixedFluxome(java.lang.String rxnFileName, java.lang.String catalystFileName, java.io.PrintWriter out)
rxnFileName
- the name of a file containing a fluxome parsable with
MixedFluxomeFormatV1.catalystFileName
- the name of a file containing reaction-catalyst associations
parsable with BoolRelFormatV1out
- the print writer to which descriptive message will be written.
public static java.util.Map<java.lang.String,Or<And<java.lang.String>>> getCatalysts(Fluxome fluxome, java.lang.String fileName)
fluxome
- the fluxome with which reaction names are verified.fileName
- the name of the catalyst file.
public static java.util.Map<java.lang.String,Or<And<java.lang.String>>> getCatalysts(Fluxome fluxome, java.lang.String fileName, java.io.PrintWriter out)
fluxome
- the fluxome with which reaction names are verified.fileName
- the name of the catalyst file.out
- the print writer to which descriptive messages will be
written.
public static void writeFluxome(IrrevRxnFluxome fluxome, java.lang.String fileName)
fluxome
- the fluxome to be written to file.fileName
- the name of the file to which the fluxome will be written.public static void writeFluxome(IrrevRxnFluxome fluxome, java.lang.String fileName, java.io.PrintWriter out)
fluxome
- the fluxome to be written to file.fileName
- the name of the file to which the fluxome will be written.out
- the print writer to which descriptive messages will be written.public static void writeFluxome(MixedFluxome fluxome, java.lang.String fileName)
fluxome
- the fluxome to be written to file.fileName
- the name of the file to which the fluxome will be written.public static void writeFluxome(MixedFluxome fluxome, java.lang.String fileName, java.io.PrintWriter out)
fluxome
- the fluxome to be written to file.fileName
- the name of the file to which the fluxome will be written.out
- the print writer to which descriptive messages will be written.public static LinearSystemSolution<java.lang.String> getFluxomeSolution(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome, double coeffCutoff)
input
- keyword-value pairs.out
- the print writer to which a status message will be printed.fluxome
- the fluxome to which the solution corresponds.coeffCutoff
- the smallest value that the absolute value of a coefficient
can attain.
LinearComb.getZeroCutoff()
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