org.helm.notation2.tools

Class ChangeObjects

java.lang.Object

org.helm.notation2.tools.ChangeObjects

public final class ChangeObjects
extends Object

ChangeObjects, class to provide simple methods to change the HELM2Notation objects

Author:

hecht

Constructor Summary

Constructors

Constructor and Description
ChangeObjects()

Method Summary

Methods

Modifier and Type	Method and Description
static void	addAnnotation(org.helm.notation2.parser.notation.annotation.AnnotationNotation notation, int position, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to add an annotation at a specific position of the HELM2Notation
static void	addAnnotationToConnection(int position, String annotation, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to add an annotation to a connection of the HELM2Notation
static void	addAnnotationToMonomerNotation(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer, int position, String annotation) method to add an annotation to a MonomerNotation
static org.helm.notation2.parser.notation.polymer.PolymerNotation	addAnnotationToPolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer, String annotation) method to add an annotation to a PolymerNotation
static void	addConnection(org.helm.notation2.parser.notation.connection.ConnectionNotation notation, int position, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to add a new connection at the position of the HELM2Notation
static void	addCountToMonomerNotation(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer, int position, String count) method to set the count of a MonomerNotation
static void	addGroup(org.helm.notation2.parser.notation.grouping.GroupingNotation notation, int position, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to add a group to the grouping section of the HELM2Notation
static org.helm.notation2.parser.notation.polymer.PolymerNotation	addMonomerNotation(int position, org.helm.notation2.parser.notation.polymer.PolymerNotation polymer, org.helm.notation2.parser.notation.polymer.MonomerNotation monomerNotation) method to add a new MonomerNotation to a PolymerNotation
static void	addPolymerNotation(int position, org.helm.notation2.parser.notation.polymer.PolymerNotation polymer, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to add a PolymerNotation at a specific position of the HELM2Notation
static void	changeAnnotation(org.helm.notation2.parser.notation.annotation.AnnotationNotation notation, int position, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to change an annotation at the position of the HELM2Notation
static void	changeConnection(int position, org.helm.notation2.parser.notation.connection.ConnectionNotation notation, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to change a connection at the position of the HELM2Notation
static void	changeGroup(org.helm.notation2.parser.notation.grouping.GroupingNotation notation, int position, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to change a group of the HELM2Notation
static void	changeMonomerNotation(int position, org.helm.notation2.parser.notation.polymer.PolymerNotation polymer, org.helm.notation2.parser.notation.polymer.MonomerNotation not) method to change the MonomerNotation on the specific position
static void	changePolymerNotation(int position, org.helm.notation2.parser.notation.polymer.PolymerNotation polymer, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to change the PolymerNotation at a specific position of the HELM2Notation
static void	deleteAllAnnotations(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to delete all annotations of the HELM2Notation
static void	deleteAllConnections(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to delete all connections of the HELM2Notation
static void	deleteAllGroups(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to delete all groups of the HELM2Notation
static void	deleteAnnotation(int position, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to delete the annotation at the specific position of the HELM2Notation
static void	deleteAnnotationFromMonomerNotation(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer, int position) method to delete the annotation of a MonomerNotation
static void	deleteConnection(int position, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to delete the connection at the specific position of the HELM2Notation
static void	deleteGroup(int position, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to delete a group at a specific position of the HELM2Notation
static void	deleteMonomerNotation(int position, org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to delete a MonomerNotation at a specific position of the PolymerNotation
static void	deletePolymerNotation(int position, org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to delete the PolymerNotation at a specific position of the HELM2Notation
static void	hybridize(org.helm.notation2.parser.notation.HELM2Notation helm2notation) this method will automatically add base pair info into notation only if it contains two RNA polymer notations and there is no base pairing info
static org.helm.notation2.parser.notation.polymer.MonomerNotationUnit	produceMonomerNotationUnitWithOtherID(org.helm.notation2.parser.notation.polymer.MonomerNotation monomerNotation, String newID) method to replace the MonomerNotationUnit having the MonomerID with the new MonomerID
static org.helm.notation2.parser.notation.polymer.PolymerNotation	removeAnnotationOfPolmyer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to remove a current annotation of a PolymerNotation
static void	replaceMonomer(org.helm.notation2.parser.notation.HELM2Notation helm2notation, String polymerType, String existingMonomerID, String newMonomerID) method to replace the MonomerID with the new MonomerID for a given polymer type
static org.helm.notation2.parser.notation.polymer.MonomerNotation	replaceMonomerNotation(org.helm.notation2.parser.notation.polymer.MonomerNotation monomerNotation, String existingMonomerID, String newMonomerID) method to replace the MonomerNotation having the MonomerID with the new MonomerID
static org.helm.notation2.parser.notation.polymer.MonomerNotationGroup	replaceMonomerNotationGroup(org.helm.notation2.parser.notation.polymer.MonomerNotationGroup monomerNotation, String existingMonomerID, String newMonomerID) method to replace the MonomerNotationGroup having the MonomerID with the new MonomerID
static org.helm.notation2.parser.notation.polymer.MonomerNotationList	replaceMonomerNotationList(org.helm.notation2.parser.notation.polymer.MonomerNotationList object, String existingMonomerID, String newMonomerID) method to replace the MonomerNotationList having the MonomerID with the new MonomerID
static void	replaceSMILESWithTemporaryIds(org.helm.notation2.parser.notation.HELM2Notation helm2notation) This function replaces smiles in complex notation with temporary ids
static void	setCountToDefault(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer, int position) method to set the count of a MonomerNotation to default (=1)

Methods inherited from class java.lang.Object

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

Constructor Detail

ChangeObjects

public ChangeObjects()

Method Detail

addAnnotation

public static final void addAnnotation(org.helm.notation2.parser.notation.annotation.AnnotationNotation notation,
                 int position,
                 org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to add an annotation at a specific position of the HELM2Notation

Parameters:

notation - new annotation

position - position of the new annotation

helm2notation - input HELM2Notation

changeAnnotation

public static final void changeAnnotation(org.helm.notation2.parser.notation.annotation.AnnotationNotation notation,
                    int position,
                    org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to change an annotation at the position of the HELM2Notation

Parameters:

notation - new changed annotation

position - position of the changed annotation

helm2notation - input HELM2Notation

deleteAnnotation

public static final void deleteAnnotation(int position,
                    org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to delete the annotation at the specific position of the HELM2Notation

Parameters:

position - position of the to be deleted annotation

helm2notation - input HELM2Notation

deleteAllAnnotations

public static final void deleteAllAnnotations(org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to delete all annotations of the HELM2Notation

Parameters:

helm2notation - input HELM2Notation

addConnection

public static final void addConnection(org.helm.notation2.parser.notation.connection.ConnectionNotation notation,
                 int position,
                 org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to add a new connection at the position of the HELM2Notation

Parameters:

notation - new ConnectionNotation

position - position of the new ConnectionNotation

helm2notation - input HELM2Notation

changeConnection

public static final void changeConnection(int position,
                    org.helm.notation2.parser.notation.connection.ConnectionNotation notation,
                    org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to change a connection at the position of the HELM2Notation

Parameters:

position - position of the changed Connection

notation - to be changed ConnectionNotation

helm2notation - input HELM2Notation

deleteConnection

public static final void deleteConnection(int position,
                    org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to delete the connection at the specific position of the HELM2Notation

Parameters:

position - of the to deleted connection

helm2notation - input HELM2Notation

addAnnotationToConnection

public static final void addAnnotationToConnection(int position,
                             String annotation,
                             org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to add an annotation to a connection of the HELM2Notation

Parameters:

position - position of the connection

annotation - new annotation

helm2notation - input HELM2Notation

deleteAllConnections

public static final void deleteAllConnections(org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to delete all connections of the HELM2Notation

Parameters:

helm2notation - input HELM2Notation

addGroup

public static final void addGroup(org.helm.notation2.parser.notation.grouping.GroupingNotation notation,
            int position,
            org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to add a group to the grouping section of the HELM2Notation

Parameters:

notation - new group

position - position of the new group

helm2notation - input HELM2Notation

changeGroup

public static final void changeGroup(org.helm.notation2.parser.notation.grouping.GroupingNotation notation,
               int position,
               org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to change a group of the HELM2Notation

Parameters:

notation - new group

position - position of the to be changed group

helm2notation - input HELM2Notation

deleteGroup

public static final void deleteGroup(int position,
               org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to delete a group at a specific position of the HELM2Notation

Parameters:

position - position of the to be deleted group

helm2notation - input HELM2Notation

deleteAllGroups

public static final void deleteAllGroups(org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to delete all groups of the HELM2Notation

Parameters:

helm2notation - input HELM2Notation

addAnnotationToPolymer

public static final org.helm.notation2.parser.notation.polymer.PolymerNotation addAnnotationToPolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
                                                                                String annotation)

method to add an annotation to a PolymerNotation

Parameters:

polymer - PolymerNotation

annotation - new annotation

Returns:

PolymerNotation with the annotation

removeAnnotationOfPolmyer

public static final org.helm.notation2.parser.notation.polymer.PolymerNotation removeAnnotationOfPolmyer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)

method to remove a current annotation of a PolymerNotation

Parameters:

polymer - PolymerNotation

Returns:

PolymerNotation with no annotation

addMonomerNotation

public static final org.helm.notation2.parser.notation.polymer.PolymerNotation addMonomerNotation(int position,
                                                                            org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
                                                                            org.helm.notation2.parser.notation.polymer.MonomerNotation monomerNotation)

method to add a new MonomerNotation to a PolymerNotation

Parameters:

position - position of the new MonomerNotation

polymer - PolymerNotation

monomerNotation - new MonomerNotation

Returns:

PolymerNotation with the new MonomerNotation

changeMonomerNotation

public static final void changeMonomerNotation(int position,
                         org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
                         org.helm.notation2.parser.notation.polymer.MonomerNotation not)

method to change the MonomerNotation on the specific position

Parameters:

position - position of the changed MonomerNotation

polymer - PolymerNotation

not - changed MonomerNotation

deleteMonomerNotation

public static final void deleteMonomerNotation(int position,
                         org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                        throws org.helm.notation2.parser.exceptionparser.NotationException

method to delete a MonomerNotation at a specific position of the PolymerNotation

Parameters:

position - position of the to be deleted MonomerNotation

polymer - PolymerNotation

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if the generated PolymerNotation has no elements after deleting the MonomerNotation

addAnnotationToMonomerNotation

public static final void addAnnotationToMonomerNotation(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
                                  int position,
                                  String annotation)

method to add an annotation to a MonomerNotation

Parameters:

polymer - PolymerNotation

position - position of the monomerNotation

annotation - new annotation

addCountToMonomerNotation

public static final void addCountToMonomerNotation(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
                             int position,
                             String count)

method to set the count of a MonomerNotation

Parameters:

polymer - PolymerNotation

position - position of the MonomerNotation

count - new count of the MonomerNotation

deleteAnnotationFromMonomerNotation

public static final void deleteAnnotationFromMonomerNotation(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
                                       int position)

method to delete the annotation of a MonomerNotation

Parameters:

polymer - PolymerNotation

position - position of the MonomerNotation

setCountToDefault

public static final void setCountToDefault(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
                     int position)

method to set the count of a MonomerNotation to default (=1)

Parameters:

polymer - PolymerNotation

position - position of the MonomerNotation

changePolymerNotation

public static final void changePolymerNotation(int position,
                         org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
                         org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to change the PolymerNotation at a specific position of the HELM2Notation

Parameters:

position - position of the PolymerNotation

polymer - new PolymerNotation

helm2notation - input HELM2Notation

deletePolymerNotation

public static final void deletePolymerNotation(int position,
                         org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to delete the PolymerNotation at a specific position of the HELM2Notation

Parameters:

position - position of the PolymerNotation

helm2notation - input HELM2Notation

addPolymerNotation

public static final void addPolymerNotation(int position,
                      org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
                      org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to add a PolymerNotation at a specific position of the HELM2Notation

Parameters:

position - position of the PolymerNotation

polymer - new PolymerNotation

helm2notation - input HELM2Notation

replaceMonomer

public static final void replaceMonomer(org.helm.notation2.parser.notation.HELM2Notation helm2notation,
                  String polymerType,
                  String existingMonomerID,
                  String newMonomerID)
                                 throws org.helm.notation2.parser.exceptionparser.NotationException,
                                        MonomerException,
                                        ChemistryException,
                                        org.helm.chemtoolkit.CTKException,
                                        IOException,
                                        org.jdom2.JDOMException

method to replace the MonomerID with the new MonomerID for a given polymer type

Parameters:

helm2notation - HELM2Notation

polymerType - String of the polymer type

existingMonomerID - old MonomerID

newMonomerID - new MonomerID

Throws:

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

MonomerException - if monomer is not valid

ChemistryException - if chemistry engine could not be initialized

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

IOException - IO error

org.jdom2.JDOMException - jdome error

replaceMonomerNotation

public static final org.helm.notation2.parser.notation.polymer.MonomerNotation replaceMonomerNotation(org.helm.notation2.parser.notation.polymer.MonomerNotation monomerNotation,
                                                                                String existingMonomerID,
                                                                                String newMonomerID)
                                                                                               throws org.helm.notation2.parser.exceptionparser.NotationException,
                                                                                                      ChemistryException,
                                                                                                      org.helm.chemtoolkit.CTKException,
                                                                                                      MonomerLoadingException

method to replace the MonomerNotation having the MonomerID with the new MonomerID

Parameters:

monomerNotation - given monomer notation

existingMonomerID - existing monomer id

newMonomerID - new monomer id

Returns:

MonomerNotation, if it had the old MonomerID, null otherwise

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if new monomer id is not valid

ChemistryException - if chemistry engine can not be initialized

org.helm.chemtoolkit.CTKException - if it contains an invalid smiles

MonomerLoadingException - if monomers can not be loaded

replaceMonomerNotationGroup

public static final org.helm.notation2.parser.notation.polymer.MonomerNotationGroup replaceMonomerNotationGroup(org.helm.notation2.parser.notation.polymer.MonomerNotationGroup monomerNotation,
                                                                                          String existingMonomerID,
                                                                                          String newMonomerID)
                                                                                                         throws org.helm.notation2.parser.exceptionparser.NotationException

method to replace the MonomerNotationGroup having the MonomerID with the new MonomerID

Parameters:

monomerNotation - the to replace monomernotationgroup

existingMonomerID - the to replace existing monomer id of the monomernotationgroup

newMonomerID - the new monomerid

Returns:

MonomerNotationGroup, if it had the old MonomerID, null otherwise

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if the new monomer id is not valid

produceMonomerNotationUnitWithOtherID

public static final org.helm.notation2.parser.notation.polymer.MonomerNotationUnit produceMonomerNotationUnitWithOtherID(org.helm.notation2.parser.notation.polymer.MonomerNotation monomerNotation,
                                                                                                   String newID)
                                                                                                                  throws org.helm.notation2.parser.exceptionparser.NotationException

method to replace the MonomerNotationUnit having the MonomerID with the new MonomerID

Parameters:

monomerNotation - given monomer notation

newID - new monomer id

Returns:

MonomerNotationUnit

Throws:

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

replaceMonomerNotationList

public static final org.helm.notation2.parser.notation.polymer.MonomerNotationList replaceMonomerNotationList(org.helm.notation2.parser.notation.polymer.MonomerNotationList object,
                                                                                        String existingMonomerID,
                                                                                        String newMonomerID)
                                                                                                       throws org.helm.notation2.parser.exceptionparser.NotationException,
                                                                                                              ChemistryException,
                                                                                                              org.helm.chemtoolkit.CTKException,
                                                                                                              MonomerLoadingException

method to replace the MonomerNotationList having the MonomerID with the new MonomerID

Parameters:

object - MonomerNotationList to change

existingMonomerID - monomer to change

newMonomerID - new monomer

Returns:

MonomerNotationList, if it had the old MonomerID, null otherwise

Throws:

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

ChemistryException - if chemistry could not be initialized

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

MonomerLoadingException - could not load monomers from source

replaceSMILESWithTemporaryIds

public static final void replaceSMILESWithTemporaryIds(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
                                                throws org.helm.notation2.parser.exceptionparser.NotationException,
                                                       HELM2HandledException,
                                                       ChemistryException,
                                                       org.helm.chemtoolkit.CTKException,
                                                       MonomerLoadingException,
                                                       org.jdom2.JDOMException

This function replaces smiles in complex notation with temporary ids

Parameters:

helm2notation - given helm2 notation

Throws:

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

ChemistryException - if chemistry engine can not be initialized

HELM2HandledException - if it contains HELM2 specific features, so that it can not be casted to HELM1 Format

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

MonomerLoadingException - if monomers can not be loaded

org.jdom2.JDOMException - if smiles can not be replace with the temporary ids

hybridize

public static void hybridize(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
                      throws org.helm.notation2.parser.exceptionparser.NotationException,
                             RNAUtilsException,
                             HELM2HandledException,
                             NotationException,
                             ChemistryException

this method will automatically add base pair info into notation only if it contains two RNA polymer notations and there is no base pairing info

Parameters:

helm2notation - HELM2Notation object

Throws:

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

RNAUtilsException - if the polymer is not a RNA/DNA

HELM2HandledException - if it contains HELM2 specific features, so that it can not be casted to HELM1 Format

NotationException - if notation is not valid

ChemistryException - if chemistry engine can not be initialized