org.sbml.jsbml.validator

Class SyntaxChecker

java.lang.Object

org.sbml.jsbml.validator.SyntaxChecker

public class SyntaxChecker
extends java.lang.Object

A collection of methods for checking the validity of SBML identifiers.

This utility class provides static methods for checking the syntax of identifiers and other text used in an SBMLDocument. The methods allow callers to verify that Strings such as SBML identifiers and XHTML notes text conform to the SBML specifications.

In order to save memory, all patterns in this class are only initialized upon their first use.

Since:

1.0

Version:

$Rev$

Author:

Andreas Dräger

Field Summary

Fields

Modifier and Type	Field and Description
private static java.util.regex.Pattern	chemicalFormulaPattern
private java.util.regex.Pattern	emailPattern Definition of valid e-mail addresses.
private java.util.regex.Pattern	metaIdPattern Pattern to recognize valid meta-identifier strings for SBML elements.
private java.util.Set<java.lang.String>	reservedNamesL1V1 Collection of reserved names that must not be used as identifiers (names) in SBML documents in SBML Level 1 Version 1.
private java.util.Set<java.lang.String>	reservedNamesL1V2 Collection of reserved names that must not be used as identifiers (names) in SBML documents in SBML Level 1 Version 2.
private java.util.regex.Pattern	SIdL2Pattern Pattern to recognize valid SIds, i.e., identifier strings for SBML elements.
private java.util.regex.Pattern	simpleMetaIdPattern Simplified Pattern to recognize valid meta-identifier strings for SBML elements.
private java.util.regex.Pattern	SNameL1V1 Name Pattern for SBML Level 1 version 1.
private java.util.regex.Pattern	SNameL1V2 Name Pattern for SBML Level 1 version 2.
private static SyntaxChecker	syntaxChecker The only instance of this class.

Constructor Summary

Constructors

Modifier	Constructor and Description
private	SyntaxChecker() This is a singleton class and should only be used through static methods.

Method Summary

Modifier and Type	Method and Description
private java.util.Set<java.lang.String>	getReservedNamesL1V1()
private static java.util.regex.Pattern	initChemicalFormulaPattern()
private void	initL1V1SNamePattern() Initializes the pattern for the type SName (described in SBML L1V1 specification, p.
private void	initL1V2SNamePattern() Creates the pattern for SName as defined in SBML specification for L1V2 page 7.
private void	initMetaIdPatterns() Build the pattern for metaIds according to the definition in SBML L2V2R1 p.
private void	initReservedNamesL1V1() These reserved words can occur in case of UnitDefinitions: "substance", "time", "volume".
private void	initReservedNamesL1V2()
private void	initSIdL2Pattern()
static boolean	isValidChemicalFormula(java.lang.String chemicalFormula)
static boolean	isValidEmailAddress(java.lang.String email) Definition of valid e-mail address Strings.
static boolean	isValidId(java.lang.String idCandidate, int level, int version) Checks whether the given idCandidate is a valid identifier according to the SBML specifications.
static boolean	isValidMetaId(java.lang.String idCandidate) Checks if the given identifier candidate satisfies the requirements for a valid meta identifier (see SBML L2V4 p.

Methods inherited from class java.lang.Object

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

Field Detail

chemicalFormulaPattern

private static java.util.regex.Pattern chemicalFormulaPattern

syntaxChecker

private static final SyntaxChecker syntaxChecker

The only instance of this class.

emailPattern

private java.util.regex.Pattern emailPattern

Definition of valid e-mail addresses. Initialized upon first use.

metaIdPattern

private java.util.regex.Pattern metaIdPattern

Pattern to recognize valid meta-identifier strings for SBML elements.

reservedNamesL1V1

private java.util.Set<java.lang.String> reservedNamesL1V1

Collection of reserved names that must not be used as identifiers (names) in SBML documents in SBML Level 1 Version 1.

reservedNamesL1V2

private java.util.Set<java.lang.String> reservedNamesL1V2

Collection of reserved names that must not be used as identifiers (names) in SBML documents in SBML Level 1 Version 2.

SIdL2Pattern

private java.util.regex.Pattern SIdL2Pattern

Pattern to recognize valid SIds, i.e., identifier strings for SBML elements.

simpleMetaIdPattern

private java.util.regex.Pattern simpleMetaIdPattern

Simplified Pattern to recognize valid meta-identifier strings for SBML elements.

SNameL1V1

private java.util.regex.Pattern SNameL1V1

Name Pattern for SBML Level 1 version 1.

SNameL1V2

private java.util.regex.Pattern SNameL1V2

Name Pattern for SBML Level 1 version 2.

Constructor Detail

SyntaxChecker

private SyntaxChecker()

This is a singleton class and should only be used through static methods.

Method Detail

initChemicalFormulaPattern

private static java.util.regex.Pattern initChemicalFormulaPattern()

Returns:

isValidChemicalFormula

public static boolean isValidChemicalFormula(java.lang.String chemicalFormula)

Parameters:

chemicalFormula -

Returns:

isValidEmailAddress

public static boolean isValidEmailAddress(java.lang.String email)

Definition of valid e-mail address Strings.

Pattern	Explanation
^	start of the line
[_A-Za-z0-9-]+	must start with string in the bracket [ ], must contains one or more (+)
(	start of group #1
\\.[_A-Za-z0-9-]+	follow by a dot "." and string in the bracket [ ], must contains one or more (+)
)*	end of group #1, this group is optional (*)
@	must contains a "@" symbol
[A-Za-z0-9-]+	follow by string in the bracket [ ], must contains one or more (+)
(	start of group #2 - first level TLD checking
\\.[A-Za-z0-9-]+	follow by a dot "." and string in the bracket [ ], must contains one or more (+)
)*	end of group #2, this group is optional (*)
(	start of group #3 - second level TLD checking
\\.[A-Za-z]{2,}	follow by a dot "." and string in the bracket [ ], with minimum length of 2
)	end of group #3
$	end of the line

Parameters:

email -

Returns:

isValidId

public static final boolean isValidId(java.lang.String idCandidate,
                                      int level,
                                      int version)

Checks whether the given idCandidate is a valid identifier according to the SBML specifications.

Parameters:

idCandidate - The String to be tested.

level - Level of the SBML to be used.

version - Version of the SBML to be used.

Returns:

True if the argument satisfies the specification of identifiers in the SBML specifications or false otherwise.

isValidMetaId

public static final boolean isValidMetaId(java.lang.String idCandidate)

Checks if the given identifier candidate satisfies the requirements for a valid meta identifier (see SBML L2V4 p. 12 for details).

Parameters:

idCandidate -

Returns:

true if the given argument is a valid meta identifier String, false otherwise.

getReservedNamesL1V1

private java.util.Set<java.lang.String> getReservedNamesL1V1()

Returns:

initL1V1SNamePattern

private void initL1V1SNamePattern()

Initializes the pattern for the type SName (described in SBML L1V1 specification, p. 6).

initL1V2SNamePattern

private void initL1V2SNamePattern()

Creates the pattern for SName as defined in SBML specification for L1V2 page 7.

initMetaIdPatterns

private void initMetaIdPatterns()

Build the pattern for metaIds according to the definition in SBML L2V2R1 p. 12, Section 3.1.6 and the definition of the corresponding symbols at http://www.w3.org/TR/2000/REC-xml-20001006#NT-CombiningChar

initReservedNamesL1V1

private void initReservedNamesL1V1()

These reserved words can occur in case of UnitDefinitions: "substance", "time", "volume".

initReservedNamesL1V2

private void initReservedNamesL1V2()

initSIdL2Pattern

private void initSIdL2Pattern()