sbrt.shell.text.fba
Class RxnNameOrExprFormatV1

java.lang.Object
  extended by sbrt.shell.text.fba.RxnNameOrExprFormatV1
All Implemented Interfaces:
RxnNameOrExprFormat, Format, Formatter<java.lang.Object>, Parser<java.lang.Object>, SimpleFormat<java.lang.Object>

public final class RxnNameOrExprFormatV1
extends java.lang.Object
implements RxnNameOrExprFormat

This class is a concrete implemenation of RxnNameOrExprFormat.

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

Constructor Summary
RxnNameOrExprFormatV1(Fluxome fluxome)
          Constructs a new reaction name and expression format.
 
Method Summary
 java.lang.String format(java.lang.Object rxnNameOrExpression)
          Returns the string representation of the provided object.
 Fluxome getFluxome()
          Returns the fluxome used to verify reaction names.
 RxnNameExprFormatV1 getLinearCombFormat()
          Returns the reaction name expression format.
 RxnNameVerifier getRxnNameChecker()
          Returns the reaction name verifier.
 java.lang.Object parse(java.lang.String rxnNameOrExpression)
          Parses the provided string and returns its corresponding object.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

RxnNameOrExprFormatV1

public RxnNameOrExprFormatV1(Fluxome fluxome)
Constructs a new reaction name and expression format.

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 RxnNameOrExprFormat
Returns:
the fluxome used to verify reaction names.

getRxnNameChecker

public RxnNameVerifier getRxnNameChecker()
Returns the reaction name verifier.

Returns:
the reaction name verifier.

getLinearCombFormat

public RxnNameExprFormatV1 getLinearCombFormat()
Returns the reaction name expression format.

Returns:
the reaction name expression format.

format

public java.lang.String format(java.lang.Object rxnNameOrExpression)
Returns the string representation of the provided object.

Specified by:
format in interface Formatter<java.lang.Object>
Parameters:
rxnNameOrExpression - a reaction name or LinearComb of reaction names.
Returns:
the string representation of the provided object.

parse

public java.lang.Object parse(java.lang.String rxnNameOrExpression)
Parses the provided string and returns its corresponding object.

Specified by:
parse in interface Parser<java.lang.Object>
Parameters:
rxnNameOrExpression - a string representation of a reaction name or expression.
Returns:
the reaction name or expression contained in the provided string.