sbrt.shell.text.fba
Class FbaOptHeaderParserV1

java.lang.Object
  extended by sbrt.shell.text.fba.FbaOptHeaderParserV1
All Implemented Interfaces:
FbaOptHeaderParser, Parser<java.util.LinkedHashSet<java.lang.String>>

public final class FbaOptHeaderParserV1
extends java.lang.Object
implements FbaOptHeaderParser

This class is a concrete implemenation of FbaOptHeaderParser.

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

Field Summary
static java.lang.String OBJ_VALUE
          The header used to indicate the value of the objective function.
 
Constructor Summary
FbaOptHeaderParserV1(Fluxome fluxome)
          Constructs a new FBA optimization header parser.
 
Method Summary
 Fluxome getFluxome()
          Returns the fluxome used to verify reaction names.
 java.lang.String getObjValueHeader()
          Returns the header used to indicate the value of the objective function.
 PipeSetFormat<java.lang.String> getPipeSetFormat()
          Returns the format used for sets of strings.
 RxnNameSetFormatV1 getRxnNameSetFormat()
          Returns the format used for reaction name sets.
 boolean isObjValueHeader(java.lang.String s)
          Indicates if the provided string is the header used to indicate the value of the objective function.
 java.util.LinkedHashSet<java.lang.String> parse(java.lang.String headerSet)
          Parses the provided string and returns its corresponding set of FBA optimization headers as a LinkedHashSet.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

OBJ_VALUE

public static final java.lang.String OBJ_VALUE
The header used to indicate the value of the objective function.

See Also:
Constant Field Values
Constructor Detail

FbaOptHeaderParserV1

public FbaOptHeaderParserV1(Fluxome fluxome)
Constructs a new FBA optimization header parser.

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 FbaOptHeaderParser
Returns:
the fluxome used to verify reaction names.

getRxnNameSetFormat

public RxnNameSetFormatV1 getRxnNameSetFormat()
Returns the format used for reaction name sets.

Returns:
the format used for reaction name sets.

getPipeSetFormat

public PipeSetFormat<java.lang.String> getPipeSetFormat()
Returns the format used for sets of strings.

Returns:
the format used for sets of strings.

getObjValueHeader

public java.lang.String getObjValueHeader()
Returns the header used to indicate the value of the objective function.

Specified by:
getObjValueHeader in interface FbaOptHeaderParser
Returns:
the header used to indicate the value of the objective function.

isObjValueHeader

public boolean isObjValueHeader(java.lang.String s)
Indicates if the provided string is the header used to indicate the value of the objective function.

Specified by:
isObjValueHeader in interface FbaOptHeaderParser
Parameters:
s - the string to compare.
Returns:
true if the provided string is equal to the string returned by getObjValueHeader(); false otherwise.

parse

public java.util.LinkedHashSet<java.lang.String> parse(java.lang.String headerSet)
Parses the provided string and returns its corresponding set of FBA optimization headers as a LinkedHashSet.

Specified by:
parse in interface Parser<java.util.LinkedHashSet<java.lang.String>>
Parameters:
headerSet - the string to be parsed.
Returns:
the set of FBA optimization headers corresponding to the provided string.