sbrt.shell.text.fba
Class CatalystSetFormatV1

java.lang.Object
  extended by sbrt.shell.text.fba.CatalystSetFormatV1
All Implemented Interfaces:
CatalystSetFormat, 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 CatalystSetFormatV1
extends java.lang.Object
implements CatalystSetFormat

This class is a concrete implemenation of CatalystSetFormat.

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

Constructor Summary
CatalystSetFormatV1(CatalyzedFluxome fluxome)
          Constructs a new catalyst name collection format using the provided fluxome.
 
Method Summary
 java.lang.String format(java.util.Set<java.lang.String> catalystNames)
          Returns a formatted string representation of the provided set of catalyst names.
 CatalystVerifier getEnzymeChecker()
          Returns the catalyst name verifier.
 CatalyzedFluxome getFluxome()
          Returns the fluxome used to verify catalyst names.
 PipeSetFormat<java.lang.String> getSetFormat()
          Returns the format used for sets of catalyst names.
 java.util.LinkedHashSet<java.lang.String> parse(java.lang.String catalystNames)
          Parses the provided string and returns the set of catalyst 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

CatalystSetFormatV1

public CatalystSetFormatV1(CatalyzedFluxome fluxome)
Constructs a new catalyst name collection format using the provided fluxome.

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

getFluxome

public CatalyzedFluxome getFluxome()
Returns the fluxome used to verify catalyst names.

Specified by:
getFluxome in interface CatalystSetFormat
Returns:
the fluxome used to verify catalyst names.

getSetFormat

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

Returns:
the format used for sets of catalyst names.

getEnzymeChecker

public CatalystVerifier getEnzymeChecker()
Returns the catalyst name verifier.

Returns:
the catalyst name verifier.

format

public java.lang.String format(java.util.Set<java.lang.String> catalystNames)
Returns a formatted string representation of the provided set of catalyst names.

Specified by:
format in interface CatalystSetFormat
Parameters:
catalystNames - the set of catalyst names to be formatted.
Returns:
a formatted string representation of the provided set of catalyst names.

parse

public java.util.LinkedHashSet<java.lang.String> parse(java.lang.String catalystNames)
Parses the provided string and returns the set of catalyst names it contains.

Specified by:
parse in interface CatalystSetFormat
Specified by:
parse in interface Parser<java.util.Set<java.lang.String>>
Parameters:
catalystNames - the string to be parsed.
Returns:
the set of catalyst names contained in the provided string.