Package org.helm.notation2.tools

Class Validation

java.lang.Object

org.helm.notation2.tools.Validation

public final class Validation
extends Object

Validation class to validate the whole HELM string

Author:

hecht

Method Summary

Modifier and Type	Method	Description
static List<Monomer>	getAllMonomers(org.helm.notation2.parser.notation.polymer.MonomerNotation not, int position)	method to get for one MonomerNotation all valid contained monomers
static List<Monomer>	getAllMonomersOnlyBase(org.helm.notation2.parser.notation.polymer.MonomerNotation not)	method to get for one MonomerNotation all valid contained monomers.
static boolean	validateConnections(org.helm.notation2.parser.notation.HELM2Notation helm2notation)	method to valid all existent connections in the Notation objects
static boolean	validateGrouping(org.helm.notation2.parser.notation.HELM2Notation helm2notation)	method to validate every GroupNotation of the Notation objects
protected static boolean	validateMonomers(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> mon)	method to validate a list of MonomerNotation objects
static void	validateNotationObjects(org.helm.notation2.parser.notation.HELM2Notation helm2notation)	method to check if the generated notation objects by the parser are correct the polymer ids have to be unique; all monomers have to be valid; all used polymer ids in the grouping section have to be there; all connections have to be valid
static boolean	validateUniquePolymerIDs(org.helm.notation2.parser.notation.HELM2Notation helm2notation)	method to check if all existent polymer ids are unique

Methods inherited from class java.lang.Object

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

Method Details

validateNotationObjects

public static void validateNotationObjects(org.helm.notation2.parser.notation.HELM2Notation helm2notation) throws PolymerIDsException, MonomerException, GroupingNotationException, ConnectionNotationException, NotationException, ChemistryException, MonomerLoadingException, org.helm.notation2.parser.exceptionparser.NotationException

method to check if the generated notation objects by the parser are correct the polymer ids have to be unique; all monomers have to be valid; all used polymer ids in the grouping section have to be there; all connections have to be valid

Parameters:

helm2notation - HELM2Notation object

Throws:

PolymerIDsException - if the polymer section is not valid

MonomerException - if a monomer is not valid

GroupingNotationException - if the grouping section is not valid

ConnectionNotationException - if the connection section is not valid

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

MonomerLoadingException - monomers can not be loaded

org.helm.notation2.parser.exceptionparser.NotationException - if notation is not valid

validateMonomers

protected static boolean validateMonomers(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> mon) throws ChemistryException, MonomerLoadingException, org.helm.notation2.parser.exceptionparser.NotationException

method to validate a list of MonomerNotation objects

Parameters:

mon - List of MonomerNotation objects

Returns:

true if all monomers are valid, false otherwise

Throws:

ChemistryException - if the Chemistry Engine can not be initialized

MonomerLoadingException - if monomer loading was not successfull

org.helm.notation2.parser.exceptionparser.NotationException - if notation is not valid

validateConnections

public static boolean validateConnections(org.helm.notation2.parser.notation.HELM2Notation helm2notation) throws NotationException, ChemistryException

method to valid all existent connections in the Notation objects

Parameters:

helm2notation - HELM2Notation object

Returns:

true if all connections are valid, false otherwise

Throws:

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

validateGrouping

public static boolean validateGrouping(org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to validate every GroupNotation of the Notation objects

Parameters:

helm2notation - HELM2Notation object

Returns:

true if the grouping is valid, false otherwise

validateUniquePolymerIDs

public static boolean validateUniquePolymerIDs(org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to check if all existent polymer ids are unique

Parameters:

helm2notation - HELM2Notation object

Returns:

true if all polymers are unique, false otherwise

getAllMonomers

public static List<Monomer> getAllMonomers(org.helm.notation2.parser.notation.polymer.MonomerNotation not, int position) throws HELM2HandledException, MonomerException, NotationException, ChemistryException, org.helm.chemtoolkit.CTKException, MonomerLoadingException

method to get for one MonomerNotation all valid contained monomers

Parameters:

not - MonomerNotation

position - position of monomer notation

Returns:

List of Monomer

Throws:

HELM2HandledException - if HELM2 features were there

MonomerException - if monomer is not valid

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

MonomerLoadingException - if monomer store can not be loaded

getAllMonomersOnlyBase

public static List<Monomer> getAllMonomersOnlyBase(org.helm.notation2.parser.notation.polymer.MonomerNotation not) throws HELM2HandledException, MonomerException, NotationException, ChemistryException, org.helm.chemtoolkit.CTKException, MonomerLoadingException

method to get for one MonomerNotation all valid contained monomers. But only the Base

Parameters:

not - MonomerNotation

Returns:

List of all base monomers

Throws:

HELM2HandledException - if HELM2 features were there

MonomerException - if monomer is not valid

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

MonomerLoadingException - if monomers can not be loaded