sbrt.shell.text.fba
Class RxnNameExprFormatV1

java.lang.Object
  extended by sbrt.shell.text.fba.RxnNameExprFormatV1
All Implemented Interfaces:
RxnNameExprFormat<LinearComb<java.lang.String>,java.lang.String>, Format, Formatter<LinearComb<java.lang.String>>, Parser<LinearComb<java.lang.String>>, SimpleFormat<LinearComb<java.lang.String>>

public final class RxnNameExprFormatV1
extends java.lang.Object
implements RxnNameExprFormat<LinearComb<java.lang.String>,java.lang.String>

This class is used to format linear combinations of reaction names.

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

Constructor Summary
RxnNameExprFormatV1(Fluxome fluxome)
          Constructs a new reaction name expression format using the provided fluxome.
RxnNameExprFormatV1(Fluxome fluxome, double coeffCutoff)
          Constructs a new reaction name expression format using the provided fluxome.
 
Method Summary
 java.lang.String format(LinearComb<java.lang.String> rxnNameExpr)
          Returns a formatted string representation of the provided linear combination of reaction names.
 Fluxome getFluxome()
          Returns the fluxome used to verify reaction names.
 LinearCombFormatV1<java.lang.String> getLinerCombFormat()
          Returns the format used for linear combination.
 RxnNameVerifier getRxnNameChecker()
          Returns the reaction name verifier.
 LinearComb<java.lang.String> parse(java.lang.String rxnNameExpr)
          Parses the provided string and returns its corresponding linear combination of reaction names.
 
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

RxnNameExprFormatV1

public RxnNameExprFormatV1(Fluxome fluxome)
Constructs a new reaction name expression format using the provided fluxome.

Parameters:
fluxome -

RxnNameExprFormatV1

public RxnNameExprFormatV1(Fluxome fluxome,
                           double coeffCutoff)
Constructs a new reaction name expression format using the provided fluxome.

Parameters:
fluxome -
coeffCutoff - the smallest value that the absolute value of a coefficient can attain.
See Also:
LinearComb.getZeroCutoff()
Method Detail

getFluxome

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

Specified by:
getFluxome in interface RxnNameExprFormat<LinearComb<java.lang.String>,java.lang.String>
Returns:
the fluxome used to verify reaction names.

getRxnNameChecker

public RxnNameVerifier getRxnNameChecker()
Returns the reaction name verifier.

Returns:
the reaction name verifier.

getLinerCombFormat

public LinearCombFormatV1<java.lang.String> getLinerCombFormat()
Returns the format used for linear combination.

Returns:
the format used for linear combination.

format

public java.lang.String format(LinearComb<java.lang.String> rxnNameExpr)
Returns a formatted string representation of the provided linear combination of reaction names.

Parameters:
rxnNameExpr - the linear combination to be formatted.
Returns:
a formatted string representation of the provided linear combination of reaction names.

parse

public LinearComb<java.lang.String> parse(java.lang.String rxnNameExpr)
Parses the provided string and returns its corresponding linear combination of reaction names.

Specified by:
parse in interface Parser<LinearComb<java.lang.String>>
Parameters:
rxnNameExpr - the string to be parsed.
Returns:
the linear combination of reaction names corresponding to the provided string.