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java.lang.Objectsbrt.shell.mng.AbstractProcessManager
sbrt.shell.proc.fba.PalssonSbmlTranslaterManager
public final class PalssonSbmlTranslaterManager
This class is used to manage the translation of SBML files from Palsson's website into the Systems Biology Research Tool's FBA Reaction Files and FBA Catalyst Files.
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 java.lang.String |
PROTEIN_FILE_NAME
Used to denote the name of the file to which protein-reaction relationships should be written. |
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 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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PalssonSbmlTranslaterManager()
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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 PROTEIN_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 PalssonSbmlTranslaterManager()
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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