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java.lang.Objectsbrt.shell.mng.AbstractProcessManager
sbrt.shell.mng.fba.FbaManager
sbrt.shell.mng.fba.RandomConstraintsManager
public final class RandomConstraintsManager
This class is used to manage random constraints generators.
Field Summary | |
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static java.lang.String |
INACTIVE
The keyword used to denote the inactive constraint. |
static java.lang.String |
IRREV_CONSTRAINT
The keyword used to denote the constraint for irreversible reactions. |
static java.lang.String |
NUM_ACTIVE_FLUXES
The keyword used to denote the number of active fluxes. |
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 |
REV_CONSTRAINT
The keyword used to denote the constraint for reversible reactions. |
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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RandomConstraintsManager()
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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 Interval |
getInactive(ManagerInput<java.lang.String,java.lang.String> input)
Parses and returns the value for INACTIVE in the provided manager input. |
static Interval |
getIrrevConstraint(ManagerInput<java.lang.String,java.lang.String> input)
Parses and returns the value for IRREV_CONSTRAINT in the provided manager input. |
static int |
getNumActiveFluxes(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out)
Parses and returns the value for NUM_ACTIVE_FLUXES in the provided manager input. |
UnmodifiableSet<java.lang.String> |
getOptionalKeys()
Returns the set of keywords the provided ManagerInput object does not necessarily
have to contain. |
static MapTextOutputFile<java.lang.String,Interval> |
getOutputFile(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 sets of flux constraints. |
static MapTextOutputFile<java.lang.String,Interval> |
getOutputFile(java.lang.String fileName,
FileFormat format,
java.util.Set<java.lang.String> headers,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple sets of flux constraints. |
static MapTextOutputFile<java.lang.String,Interval> |
getOutputFile(java.lang.String fileName,
java.util.Set<java.lang.String> headers,
IrrevRxnFluxome fluxome)
Returns an empty output file that is suitable for storing multiple sets of flux constraints. |
RandConstGeneratorV1<MixedFluxome> |
getProcess()
Returns the process this process manager controls. |
UnmodifiableSet<java.lang.String> |
getRequiredKeys()
Returns the set of keywords the provided ManagerInput object must contain. |
static Interval |
getRevConstraint(ManagerInput<java.lang.String,java.lang.String> input)
Parses and returns the value for REV_CONSTRAINT in the provided manager input. |
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 REV_CONSTRAINT
public static final java.lang.String IRREV_CONSTRAINT
public static final java.lang.String INACTIVE
public static final java.lang.String NUM_ACTIVE_FLUXES
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 RandomConstraintsManager()
Method Detail |
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public static Interval getIrrevConstraint(ManagerInput<java.lang.String,java.lang.String> input)
input
- keyword-value pairs.
public static Interval getRevConstraint(ManagerInput<java.lang.String,java.lang.String> input)
input
- keyword-value pairs.
public static Interval getInactive(ManagerInput<java.lang.String,java.lang.String> input)
input
- keyword-value pairs.
public static int getNumActiveFluxes(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 MapTextOutputFile<java.lang.String,Interval> getOutputFile(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 to which the constraints correspond.
public static MapTextOutputFile<java.lang.String,Interval> getOutputFile(java.lang.String fileName, FileFormat format, java.util.Set<java.lang.String> headers, Fluxome fluxome)
fileName
- the name of the file to be created.format
- the format of the file to be created.
FileFormat.TEXT
and FileFormat.GZIP_TEXT
are currently
the only supported choices.headers
- the set of objects whose constraints will be written to
the file.fluxome
- the fluxome to which the constraints correspond.
public static MapTextOutputFile<java.lang.String,Interval> getOutputFile(java.lang.String fileName, java.util.Set<java.lang.String> headers, IrrevRxnFluxome fluxome)
fileName
- the name of the file to be created.headers
- the set of objects whose constraints will be written to
the file.fluxome
- the fluxome to which the constraints correspond.
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 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 RandConstGeneratorV1<MixedFluxome> 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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