sbrt.shell.text.fba
Class MixedFluxomeFormatV1

java.lang.Object
  extended by sbrt.shell.text.AbstractMapFormat<java.lang.String,ChemRxn>
      extended by sbrt.shell.text.fba.MixedFluxomeFormatV1
All Implemented Interfaces:
Format, MapFormat<java.lang.String,ChemRxn>

public final class MixedFluxomeFormatV1
extends AbstractMapFormat<java.lang.String,ChemRxn>

This class is used to format irreversible reaction fluxome files.

Author:
This class was written and documented by Jeremiah Wright while in the Wagner lab.

Constructor Summary
MixedFluxomeFormatV1()
          Constructs a new irreversible reaction fluxome format.
 
Method Summary
 PipeListFormat<ChemRxn> getListFormat()
          Returns the format used for lists of reactions.
 EqualsMapEntryFormatV1<java.lang.String,java.lang.String> getMapEntryFormat()
          Returns the format used for reaction name-reaction pairs.
 RxnFormatV1 getRxnFormat()
          Returns the format used for reactions.
 RxnNameFormatV1 getRxnNameFormat()
          Returns the format used for reaction names.
 PipeSetFormat<java.lang.String> getSetFormat()
          Returns the format used for sets of reaction names.
 
Methods inherited from class sbrt.shell.text.AbstractMapFormat
formatKey, formatKeys, formatPair, formatPair, formatValue, formatValues, formatValues, getKeyFormatter, getKeyParser, getValueFormatter, getValueParser, parseAllKeys, parseAllPairs, parseAllValues, parseAllValues, parseKey, parsePair, parseValue
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MixedFluxomeFormatV1

public MixedFluxomeFormatV1()
Constructs a new irreversible reaction fluxome format.

Method Detail

getRxnNameFormat

public RxnNameFormatV1 getRxnNameFormat()
Returns the format used for reaction names.

Returns:
the format used for reaction names.

getRxnFormat

public RxnFormatV1 getRxnFormat()
Returns the format used for reactions.

Returns:
the format used for reactions.

getMapEntryFormat

public EqualsMapEntryFormatV1<java.lang.String,java.lang.String> getMapEntryFormat()
Returns the format used for reaction name-reaction pairs.

Specified by:
getMapEntryFormat in class AbstractMapFormat<java.lang.String,ChemRxn>
Returns:
the format used for reaction name-reaction pairs.

getSetFormat

public PipeSetFormat<java.lang.String> getSetFormat()
Returns the format used for sets of reaction names.

Specified by:
getSetFormat in class AbstractMapFormat<java.lang.String,ChemRxn>
Returns:
the format used for sets of reaction names.

getListFormat

public PipeListFormat<ChemRxn> getListFormat()
Returns the format used for lists of reactions.

Specified by:
getListFormat in class AbstractMapFormat<java.lang.String,ChemRxn>
Returns:
the format used for lists of reactions.