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java.lang.Objectsbrt.shell.proc.fba.SimpleRxnFileReader
public class SimpleRxnFileReader
This class is used to translate simple reaction files from, say, spreadsheets into FBA Reaction Files.
Constructor Summary | |
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SimpleRxnFileReader()
Constructs a new simple reaction file reader. |
Method Summary | |
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IrrevRxnFormatV2 |
getInputIrrevRxnFormat()
Returns the parser used for irreversible reactions in the provided input file. |
RevRxnFormatV2 |
getInputRevRxnFormat()
Returns the parser used for reversible reactions in the provided input file. |
EqualsMapEntryFormatV1<java.lang.String,java.lang.String> |
getLineFormat()
Returns the format used for individual lines in the input and output files. |
RxnFormatV1 |
getOutputRxnFormat()
Returns the formatter used for writing reactions to the output file. |
void |
translate(java.lang.String simpleRxnFileName,
java.lang.String outputFileName)
Translates a simple reaction file into an FBA Reaction File. |
void |
translate(java.lang.String simpleRxnFileName,
java.lang.String outputFileName,
java.io.PrintWriter out)
Translates a simple reaction file into an FBA Reaction File. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SimpleRxnFileReader()
Method Detail |
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public RevRxnFormatV2 getInputRevRxnFormat()
public IrrevRxnFormatV2 getInputIrrevRxnFormat()
public RxnFormatV1 getOutputRxnFormat()
public EqualsMapEntryFormatV1<java.lang.String,java.lang.String> getLineFormat()
public void translate(java.lang.String simpleRxnFileName, java.lang.String outputFileName)
simpleRxnFileName
- the name of the simple reaction file.outputFileName
- the desired name of the FBA Reaction File.public void translate(java.lang.String simpleRxnFileName, java.lang.String outputFileName, java.io.PrintWriter out)
simpleRxnFileName
- the name of the simple reaction file.outputFileName
- the desired name of the FBA Reaction File.out
- the print writer to which descriptive messages will be written.
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