sbrt.shell.text.fba
Class FluxCapFormatV1

java.lang.Object
  extended by sbrt.shell.text.AbstractMapFormat<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>
      extended by sbrt.shell.text.fba.FluxCapFormatV1
All Implemented Interfaces:
FluxCapFormat, Format, MapFormat<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>

public class FluxCapFormatV1
extends AbstractMapFormat<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>
implements FluxCapFormat

This class is a concrete implementation of FluxCapFormat.

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

Constructor Summary
FluxCapFormatV1(Fluxome fluxome)
          Constructs a new flux cap file line format using the provided fluxome.
 
Method Summary
 Fluxome getFluxome()
          Returns the fluxome used to verify reaction names.
 PipeListFormat<java.util.Set<LinearComb<java.lang.String>>> getListFormat()
          Returns the format used for lists of values.
 ColonMapEntryFormatV1<java.lang.String,java.lang.String> getMapEntryFormat()
          Returns the format used for variable-value pairs.
 PipeSetFormat<java.lang.String> getSetFormat()
          Returns the format used for sets of variables.
 
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
 
Methods inherited from interface sbrt.shell.text.MapFormat
formatKey, formatKeys, formatPair, formatPair, formatValue, formatValues, formatValues, parseAllKeys, parseAllPairs, parseAllValues, parseAllValues, parseKey, parsePair, parseValue
 

Constructor Detail

FluxCapFormatV1

public FluxCapFormatV1(Fluxome fluxome)
Constructs a new flux cap file line format using the provided fluxome.

Parameters:
fluxome - the fluxome with which to verify reaction names.
Throws:
java.lang.NullPointerException - if the provided argument is null.
Method Detail

getFluxome

public Fluxome getFluxome()
Returns the fluxome used to verify reaction names.

Specified by:
getFluxome in interface FluxCapFormat
Returns:
the fluxome used to verify reaction names.

getMapEntryFormat

public ColonMapEntryFormatV1<java.lang.String,java.lang.String> getMapEntryFormat()
Returns the format used for variable-value pairs.

Specified by:
getMapEntryFormat in class AbstractMapFormat<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>
Returns:
the format used for variable-value pairs.

getSetFormat

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

Specified by:
getSetFormat in class AbstractMapFormat<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>
Returns:
the format used for sets of variables.

getListFormat

public PipeListFormat<java.util.Set<LinearComb<java.lang.String>>> getListFormat()
Returns the format used for lists of values.

Specified by:
getListFormat in class AbstractMapFormat<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>
Returns:
the format used for lists of values.