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java.lang.Objectsbrt.shell.mng.AbstractProcessManager
sbrt.shell.mng.fba.SbmlWriterManager
public final class SbmlWriterManager
This class is used to manage the translation of Systems Biology Markup Language (SBML) files into Systems Biology Research Tool (SBRT) Fluxome Files.
Field Summary | |
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static UnmodifiableSet<java.lang.String> |
optionalKeywords
The set of keywords understood, but not required, by this process manager. |
static UnmodifiableSet<java.lang.String> |
requiredKeywords
The set of keywords required by this process manager. |
static java.lang.String |
SBML_OUTPUT_FILE_NAME
The keyword used to denote the name of the SMBL output 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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SbmlWriterManager()
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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 informative messages to the provided print writer. |
UnmodifiableSet<java.lang.String> |
getOptionalKeys()
Returns the set of keywords understood, but not required, by this process manager. |
UnmodifiableSet<java.lang.String> |
getRequiredKeys()
Returns the set of keywords required by this process manager. |
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 SBML_OUTPUT_FILE_NAME
public static final UnmodifiableSet<java.lang.String> requiredKeywords
public static final UnmodifiableSet<java.lang.String> optionalKeywords
Constructor Detail |
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public SbmlWriterManager()
Method Detail |
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public UnmodifiableSet<java.lang.String> getRequiredKeys()
getRequiredKeys
in interface ProcessManager<java.lang.String,java.lang.String>
public UnmodifiableSet<java.lang.String> getOptionalKeys()
getOptionalKeys
in interface ProcessManager<java.lang.String,java.lang.String>
public void setInput(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
setInput
in interface ProcessManager<java.lang.String,java.lang.String>
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)
execute
in interface ProcessManager<java.lang.String,java.lang.String>
out
- the print writer where informative messagse will be written.
java.lang.IllegalStateException
- if no input was provided to this process manager.
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