charite.christo.metannogen
Interface Species

All Superinterfaces:

Comparable, HasID

All Known Implementing Classes:

MSpecies

public interface Species
extends Comparable, HasID

Field Summary

static Species[]

NONE

Method Summary

String	getAttribute(String key) The network can contain additional implementation specific data.
double	getAttributeF(String key) Short for Double.parsDouble(getAttribute(key)).
int	getAttributeI(String key) Short for Integer.parsInt(getAttribute(key)).
ReactionCollection	getCollection() Returns the reference of the containing network object.
String	getID() The Identifier.
String	getName() The human readable name of the metabolite.
Reaction[]	getReactions() Get a list of Reactions with this metabolite.
boolean	isGeneral() General metabolites are for example "Sugar" or "Amino acid".

Methods inherited from interface java.lang.Comparable

compareTo

Field Detail

NONE

static final Species[] NONE

Method Detail

getAttribute

String getAttribute(String key)

The network can contain additional implementation specific data. In Metannogen this data is entered into the text pane or is provided by additional plain text files specified by command line parmeters. Syntax:

       $DEPENDSON="FAD"       
       

The method call getAttribute("DEPENDSON") would return "FAD"

getAttributeF

double getAttributeF(String key)

Short for Double.parsDouble(getAttribute(key)).

getAttributeI

int getAttributeI(String key)

Short for Integer.parsInt(getAttribute(key)).

getID

String getID()

The Identifier.

Specified by:

getID in interface HasID

getName

String getName()

The human readable name of the metabolite.

getCollection

ReactionCollection getCollection()

Returns the reference of the containing network object.

getReactions

Reaction[] getReactions()

Get a list of Reactions with this metabolite.

isGeneral

boolean isGeneral()

General metabolites are for example "Sugar" or "Amino acid".