sbrt.shell.text.fba
Class RxnNameSetFormatV1

java.lang.Object
  extended by sbrt.shell.text.fba.RxnNameSetFormatV1
All Implemented Interfaces:
RxnNameSetFormat, Format, Formatter<java.util.Set<java.lang.String>>, Parser<java.util.Set<java.lang.String>>, SimpleFormat<java.util.Set<java.lang.String>>

public final class RxnNameSetFormatV1
extends java.lang.Object
implements RxnNameSetFormat

This class is a concrete implemenation of RxnNameSetFormat.

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

Field Summary
static java.lang.String ALL_RXNS
          The string used to indicate every reaction in a fluxome.
 
Constructor Summary
RxnNameSetFormatV1(Fluxome fluxome)
          Constructs a new reaction name collection format using the provided fluxome.
 
Method Summary
 java.lang.String format(java.util.Set<java.lang.String> reactionNames)
          Returns a formatted string representation of the provided set of reaction names.
 Fluxome getFluxome()
          Returns the fluxome used to verify reaction names.
 RxnNameVerifier getRxnNameChecker()
          Returns the reaction name verifier.
 PipeSetFormat<java.lang.String> getSetFormat()
          Returns the format used for sets of reaction names.
 java.util.LinkedHashSet<java.lang.String> parse(java.lang.String set)
          Parses the provided string and returns its corresponding collection of reaction names as a LinkedHashSet.
 
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
 

Field Detail

ALL_RXNS

public static final java.lang.String ALL_RXNS
The string used to indicate every reaction in a fluxome.

See Also:
Constant Field Values
Constructor Detail

RxnNameSetFormatV1

public RxnNameSetFormatV1(Fluxome fluxome)
Constructs a new reaction name collection 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 RxnNameSetFormat
Returns:
the fluxome used to verify reaction names.

getSetFormat

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

Returns:
the format used for sets 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.Set<java.lang.String> reactionNames)
Returns a formatted string representation of the provided set of reaction names.

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

parse

public java.util.LinkedHashSet<java.lang.String> parse(java.lang.String set)
Parses the provided string and returns its corresponding collection of reaction names as a LinkedHashSet. If the string ALL_RXNS is present the set will contain the name of every reaction in this format's fluxome.

Specified by:
parse in interface RxnNameSetFormat
Specified by:
parse in interface Parser<java.util.Set<java.lang.String>>
Parameters:
set - the string to be parsed.
Returns:
the set of reaction names corresponding to the provided string.