org.sbml.jsbml.util

Class SBMLtools

java.lang.Object

org.sbml.jsbml.util.SBMLtools

public class SBMLtools
extends java.lang.Object

Since:

1.0

Author:

Andreas Dräger

Constructor Summary

Constructors

Constructor and Description
SBMLtools()

Method Summary

Modifier and Type	Method and Description
static void	addPredefinedUnitDefinitions(Model model)
static java.lang.String	getIdOrName(SBase nsb)
static java.lang.String	getNameOrId(SBase nsb)
static boolean	isLetter(char c)
static java.lang.String	nameToSId(java.lang.String name, SBMLDocument doc) Generates a valid SId from a given name.
static java.lang.String	nextId(Model model) Generate a valid SBML identifier using UUID.
static <T extends SBase> T	setLevelAndVersion(T sbase, int level, int version)
static void	setSBOTerm(SBase sbase, int term)
static java.lang.String	toSId(java.lang.String name)
static java.lang.String	toXML(XMLNode xml)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SBMLtools

public SBMLtools()

Method Detail

addPredefinedUnitDefinitions

public static final void addPredefinedUnitDefinitions(Model model)

Parameters:

model -

getIdOrName

public static final java.lang.String getIdOrName(SBase nsb)

Parameters:

nsb -

Returns:

preferably the id if it is set, otherwise the name or an empty String if both is undefined.

getNameOrId

public static final java.lang.String getNameOrId(SBase nsb)

Parameters:

nsb -

Returns:

preferably the name if is set otherwise the id or an empty String if both is undefined.

setLevelAndVersion

public static final <T extends SBase> T setLevelAndVersion(T sbase,
                                                           int level,
                                                           int version)

Parameters:

sbase -

level -

version -

Returns:

toXML

public static final java.lang.String toXML(XMLNode xml)

Parameters:

xml -

Returns:

nextId

public static java.lang.String nextId(Model model)

Generate a valid SBML identifier using UUID.

Parameters:

model -

Returns:

setSBOTerm

public static final void setSBOTerm(SBase sbase,
                                    int term)

Parameters:

sbase -

term -

nameToSId

public static java.lang.String nameToSId(java.lang.String name,
                                         SBMLDocument doc)

Generates a valid SId from a given name. If the name already is a valid SId, the name is returned. If the SId already exists in this document, "_<number>" will be appended and the next free number is being assigned. => See SBML L2V4 document for the Definition of SId. (Page 12/13)

Parameters:

name -

Returns:

SId

toSId

public static java.lang.String toSId(java.lang.String name)

Parameters:

name -

Returns:

isLetter

public static boolean isLetter(char c)

Parameters:

c -

Returns:

true if c is out of A-Z or a-z