sbrt.shell.text.fba
Class RxnNameListFormatV1

java.lang.Object
  extended by sbrt.shell.text.fba.RxnNameListFormatV1
All Implemented Interfaces:
RxnNameListFormat, Format, Formatter<java.util.List<java.lang.String>>, Parser<java.util.List<java.lang.String>>, SimpleFormat<java.util.List<java.lang.String>>

public final class RxnNameListFormatV1
extends java.lang.Object
implements RxnNameListFormat

This class is a concrete implemenation of RxnNameListFormat.

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

Constructor Summary
RxnNameListFormatV1(Fluxome fluxome)
          Constructs a new reaction name list format using the provided fluxome.
 
Method Summary
 java.lang.String format(java.util.List<java.lang.String> reactionNames)
          Returns a formatted string representation of the provided list of reaction names.
 Fluxome getFluxome()
          Returns the fluxome used to verify reaction names.
 WhitespaceListFormat<java.lang.String> getListFormat()
          Returns the format used for lists of reaction names.
 RxnNameVerifier getRxnNameChecker()
          Returns the reaction name verifier.
 java.util.List<java.lang.String> parse(java.lang.String reactionNames)
          Parses the provided string and returns the list of reaction names it contains.
 
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.Formatter
format
 

Constructor Detail

RxnNameListFormatV1

public RxnNameListFormatV1(Fluxome fluxome)
Constructs a new reaction name list format using the provided fluxome.

Parameters:
fluxome - the fluxome used to verify reaction names.
Method Detail

getFluxome

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

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

getListFormat

public WhitespaceListFormat<java.lang.String> getListFormat()
Returns the format used for lists of reaction names.

Returns:
the format used for lists of reaction names.

getRxnNameChecker

public RxnNameVerifier getRxnNameChecker()
Returns the reaction name verifier.

Returns:
the reaction name verifier.

format

public java.lang.String format(java.util.List<java.lang.String> reactionNames)
Returns a formatted string representation of the provided list of reaction names.

Specified by:
format in interface RxnNameListFormat
Parameters:
reactionNames - the list of reaction names to be formatted.
Returns:
a formatted string representation of the provided list of reaction names.

parse

public java.util.List<java.lang.String> parse(java.lang.String reactionNames)
Parses the provided string and returns the list of reaction names it contains.

Specified by:
parse in interface RxnNameListFormat
Specified by:
parse in interface Parser<java.util.List<java.lang.String>>
Parameters:
reactionNames - the string to be parsed.
Returns:
the list of reaction names contained in the provided string.