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java.lang.Objectsbrt.shell.mng.AbstractProcessManager
sbrt.shell.mng.fba.FbaManager
sbrt.shell.mng.fba.ObjectiveFunctionManager
public final class ObjectiveFunctionManager
This class is used to manage objective function processes.
Field Summary | |
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static java.lang.String |
OBJ_FUNCT_FILE
The keyword used to denote the file containing objective functions. |
static java.lang.String |
OBJ_FUNCT_FILE_FORMAT
The keyword used to denote the format of the file containing objective functions. |
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. |
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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ObjectiveFunctionManager()
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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 TextInputFile<LinearComb<java.lang.String>> |
getInputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns the file denoted by OBJ_FUNCT_FILE in the provided manager input. |
static TextInputFile<LinearComb<java.lang.String>> |
getInputFile(java.lang.String fileName,
FileFormat format,
Fluxome fluxome)
Returns the input file with the provided name. |
static TextInputFile<LinearComb<java.lang.String>> |
getInputFile(java.lang.String fileName,
Fluxome fluxome)
Returns the input file with the provided name. |
UnmodifiableSet<java.lang.String> |
getOptionalKeys()
Returns the set of keywords the provided ManagerInput object does not necessarily
have to contain. |
ObjFunAnalysis<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. |
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 OBJ_FUNCT_FILE
public static final java.lang.String OBJ_FUNCT_FILE_FORMAT
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 ObjectiveFunctionManager()
Method Detail |
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public static TextInputFile<LinearComb<java.lang.String>> getInputFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
input
- the input containing a value for OBJ_FUNCT_FILE
,
and possibly even OBJ_FUNCT_FILE_FORMAT
.out
- the print writer to which a status message will be printed.fluxome
- the fluxome to which the objective functions correspond.
AbstractProcessManager.getFileFormat(String)
public static TextInputFile<LinearComb<java.lang.String>> getInputFile(java.lang.String fileName, FileFormat format, Fluxome fluxome)
fileName
- the name of the file to be opened.format
- the format of the file to be opened. FileFormat.TEXT
and FileFormat.GZIP_TEXT
are currently the only
supported choices.fluxome
- the fluxome to which the objective functions correspond.
FbaManager.getRxnNameExprFormat(Fluxome)
public static TextInputFile<LinearComb<java.lang.String>> getInputFile(java.lang.String fileName, Fluxome fluxome)
fileName
- the name of the file to be opened.fluxome
- the fluxome to which the objective functions correspond.
FbaManager.getRxnNameExprFormat(Fluxome)
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 ObjFunAnalysis<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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