sbrt.shell.text.fba
Class FbaOptHeaderFormatterV1

java.lang.Object
  extended by sbrt.shell.text.fba.FbaOptHeaderFormatterV1
All Implemented Interfaces:
FbaOptHeaderFormatter, Formatter<java.lang.String>

public class FbaOptHeaderFormatterV1
extends java.lang.Object
implements FbaOptHeaderFormatter

This class is a concrete implemenation of FbaOptHeaderFormatter.

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
FbaOptHeaderFormatterV1(Fluxome fluxome)
          Constructs a new FBA optimization header formatter.
 
Method Summary
 java.lang.String format(java.lang.String header)
          Returns a formatted string representation of the provided header.
 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.
 
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

FbaOptHeaderFormatterV1

public FbaOptHeaderFormatterV1(Fluxome fluxome)
Constructs a new FBA optimization header formatter.

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 FbaOptHeaderFormatter
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 FbaOptHeaderFormatter
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 FbaOptHeaderFormatter
Parameters:
s - the string to compare.
Returns:
true if the provided string is equal to the string returned by getObjValueHeader(); false otherwise.

format

public java.lang.String format(java.lang.String header)
Returns a formatted string representation of the provided header.

Specified by:
format in interface Formatter<java.lang.String>
Parameters:
header - the header to be formatted.
Returns:
a formatted string representation of the provided header.