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java.lang.Objectsbrt.shell.mng.AbstractProcessManager
sbrt.shell.proc.fba.BiggSbmlReaderManager
public final class BiggSbmlReaderManager
This class is used to manage the reading of SBML files obtained from the BiGG Database.
Field Summary | |
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static java.lang.String |
GENE_FILE_NAME
Used to denote the name of the file to which gene-reaction relationships should be written. |
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 |
RXN_FILE_NAME
Used to denote the name of the file to which chemical reactions should be written. |
static java.lang.String |
SBML_INPUT_FILE
The keyword used to denote the name of the SBML input 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_NAME_FILE, ITERATIONS, OUTPUT_FILE_NAME, OUTPUT_FILE_NAME_FILE, PERCENT, PERCENT_COMPLETED, SEED, ZERO_CUTOFF |
Constructor Summary | |
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BiggSbmlReaderManager()
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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, 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 GENE_FILE_NAME
public static final java.lang.String RXN_FILE_NAME
public static final java.lang.String SBML_INPUT_FILE
public static final UnmodifiableSet<java.lang.String> requiredKeywords
public static final UnmodifiableSet<java.lang.String> optionalKeywords
Constructor Detail |
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public BiggSbmlReaderManager()
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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