chemaxon.checkers

Class AbstractStructureChecker

java.lang.Object

chemaxon.checkers.AbstractStructureChecker

All Implemented Interfaces:

StructureChecker, chemaxon.license.Licensable, java.beans.PropertyChangeListener, java.lang.Cloneable, java.util.EventListener

Direct Known Subclasses:

AbbreviatedGroupChecker, AbsentChiralFlagChecker, AbsoluteStereoConfigurationChecker, AromaticityErrorChecker, AtropisomerChecker, AttachedDataChecker, BondAngleChecker, BondLengthChecker, BracketsChecker, ChiralFlagChecker, ChiralFlagErrorChecker, CircularRGroupReferenceChecker, ComponentChecker, CoordinationSystemErrorChecker, CovalentCounterionChecker, EmptyStructureChecker, ExplicitHydrogenChecker, ExternalStructureChecker, EZDoubleBondChecker, IncorrectTetrahedralStereoChecker, MetalloceneErrorChecker, MissingRGroupChecker, MoleculeChargeChecker, MultiComponentChecker, MultipleStereocenterChecker, NonStandardWedgeSchemeChecker, NonStereoWedgeBondChecker, OCRErrorChecker, RatomChecker, ReactionChecker, RelativeStereoChecker, RgroupAttachmentErrorChecker, RgroupBridgeRatomChecker, RingStrainErrorChecker, SolventChecker, StereoCareBoxChecker, SubstructureChecker, UnbalancedReactionChecker, UnusedRGroupChecker, ValenceErrorChecker, WedgeErrorChecker, WigglyBondChecker, WigglyDoubleBondChecker

@PublicAPI
public abstract class AbstractStructureChecker
extends java.lang.Object
implements StructureChecker, chemaxon.license.Licensable, java.lang.Cloneable, java.beans.PropertyChangeListener

Abstract base class of all functions checking and repairing chemical structures.

Since:

Marvin 5.3

Version:

5.7

Author:

Attila Szabo, Istvan Rabel

Field Summary

Fields

Modifier and Type	Field and Description
protected StructureCheckerErrorType	errorType The error type of the current checker.
protected java.beans.PropertyChangeSupport	propertyChangeSupport property change support object bound to this

Fields inherited from interface chemaxon.checkers.StructureChecker

PROPERTY_KEY_VALID

Constructor Summary

Constructors

Constructor and Description
AbstractStructureChecker(StructureCheckerErrorType errorType) Constructor to create a Structure checker instance with the given errorType

Method Summary

Modifier and Type	Method and Description
void	addPropertyChangeListener(java.beans.PropertyChangeListener listener) Add a PropertyChangeListener to the listener list.
void	addPropertyChangeListener(java.lang.String propertyName, java.beans.PropertyChangeListener listener) Add a PropertyChangeListener for a specific property.
StructureCheckerResult	check(Molecule molecule) Detects a specific error in the molecule.
protected abstract StructureCheckerResult	check1(Molecule molecule) This method contains the current checking mechanism.
AbstractStructureChecker	clone()
StructureChecker	cloneItem() Returns a clone of this StructureChecker instance
protected void	convertResult(Molecule originalMolecule, Molecule expandedMolecule, StructureCheckerResult result, java.util.Map<MolAtom,MolAtom> atomMap, java.util.Map<MolBond,MolBond> bondMap) Handles the mapping of a cloned and expanded molecule result to the original molecule.
boolean	equals(java.lang.Object obj)
protected Molecule	expandMolecule(Molecule molecule, java.util.Map<MolAtom,MolAtom> atomMap, java.util.Map<MolBond,MolBond> bondMap) Returns the original molecule if no groups to expand, or the clone of the original molecule with expanded groups.
java.lang.String	getDescription()
StructureCheckerDescriptor	getDescriptor() Returns a StructureCheckerDescriptor instance which represents the user interface related informations of the checker
java.lang.String	getEditorClassName()
java.lang.String	getErrorCode() Returns the String represented error code of the checker (this error code should be used for external implementation support instead of StructureChecker.getErrorType())
protected java.lang.String	getErrorDescription(int errorCount) Generate the error description depends on erroCount
StructureCheckerErrorType	getErrorType()
java.lang.String	getHelpText() Gets the help text of the checker
javax.swing.Icon	getIcon() Gets the Icon of the current checker
java.lang.String	getLocalMenuName() Gets the local menu name of the checker
java.lang.String	getName() Gets the name of the checker
int	hashCode()
boolean	isAvailable() Returns true if the checker is available, and can be used
boolean	isLicensed()
boolean	isValid() Returns true if the checker's configuration is valid, false otherwise
void	propertyChange(java.beans.PropertyChangeEvent evt)
void	removePropertyChangeListener(java.beans.PropertyChangeListener listener) Remove a PropertyChangeListener from the listener list.
void	removePropertyChangeListener(java.lang.String propertyName, java.beans.PropertyChangeListener listener) Remove a PropertyChangeListener for a specific property.
void	setDescription(java.lang.String description) Sets the description of the checker
void	setHelpText(java.lang.String helpText) Sets the detailed help of the checker which will shown in the tooltip on the GUI
void	setIcon(javax.swing.Icon icon) Sets the icon of the checker
void	setLicenseEnvironment(java.lang.String env)
void	setLocalMenuName(java.lang.String localMenuName) Set the local menu name of the checker
void	setMoreErrorMessage(java.lang.String moreErrorMessage) Sets the message which will given in the result if two or more error found
void	setName(java.lang.String name) Sets the name of the checker
void	setNoErrorMessage(java.lang.String noErrorMessage) Sets the message which will given in the result if no error found
void	setOneErrorMessage(java.lang.String oneErrorMessage) Sets the message which will given in the result if one error found
java.lang.String	toString()

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

errorType

protected final StructureCheckerErrorType errorType

The error type of the current checker. It is a value so can not assigned more than once

propertyChangeSupport

protected java.beans.PropertyChangeSupport propertyChangeSupport

property change support object bound to this

Constructor Detail

AbstractStructureChecker

public AbstractStructureChecker(StructureCheckerErrorType errorType)

Constructor to create a Structure checker instance with the given errorType

Parameters:

errorType - element of StructureCheckerErrorType

Method Detail

getName

public java.lang.String getName()

Description copied from interface: StructureChecker

Gets the name of the checker

Specified by:

getName in interface StructureChecker

Returns:

a human readable name

setName

public void setName(java.lang.String name)

Description copied from interface: StructureChecker

Sets the name of the checker

Specified by:

setName in interface StructureChecker

Parameters:

name - the human readable name of the checker

setNoErrorMessage

public void setNoErrorMessage(java.lang.String noErrorMessage)

Description copied from interface: StructureChecker

Sets the message which will given in the result if no error found

Specified by:

setNoErrorMessage in interface StructureChecker

Parameters:

noErrorMessage - the error message if no error found

setOneErrorMessage

public void setOneErrorMessage(java.lang.String oneErrorMessage)

Description copied from interface: StructureChecker

Sets the message which will given in the result if one error found

Specified by:

setOneErrorMessage in interface StructureChecker

Parameters:

oneErrorMessage - the error message if one error found

setMoreErrorMessage

public void setMoreErrorMessage(java.lang.String moreErrorMessage)

Description copied from interface: StructureChecker

Sets the message which will given in the result if two or more error found

Specified by:

setMoreErrorMessage in interface StructureChecker

Parameters:

moreErrorMessage - the error message if two or more error found

getErrorDescription

protected java.lang.String getErrorDescription(int errorCount)

Generate the error description depends on erroCount

Parameters:

errorCount - number of errors found

Returns:

a human readable description about how many and which kind of errors found

getLocalMenuName

public java.lang.String getLocalMenuName()

Description copied from interface: StructureChecker

Gets the local menu name of the checker

Specified by:

getLocalMenuName in interface StructureChecker

Returns:

the name for the local menu

setLocalMenuName

public void setLocalMenuName(java.lang.String localMenuName)

Description copied from interface: StructureChecker

Set the local menu name of the checker

Specified by:

setLocalMenuName in interface StructureChecker

Parameters:

localMenuName - a String to be shown in the local menu

getHelpText

public java.lang.String getHelpText()

Description copied from interface: StructureChecker

Gets the help text of the checker

Specified by:

getHelpText in interface StructureChecker

Returns:

the help text of the checker

setHelpText

public void setHelpText(java.lang.String helpText)

Description copied from interface: StructureChecker

Sets the detailed help of the checker which will shown in the tooltip on the GUI

Specified by:

setHelpText in interface StructureChecker

Parameters:

helpText - a String to be shown in the tooltip

getIcon

public javax.swing.Icon getIcon()

Description copied from interface: StructureChecker

Gets the Icon of the current checker

Specified by:

getIcon in interface StructureChecker

Returns:

the Icon of the current checker

setIcon

public void setIcon(javax.swing.Icon icon)

Description copied from interface: StructureChecker

Sets the icon of the checker

Specified by:

setIcon in interface StructureChecker

Parameters:

icon - is an instance of Icon

check

public final StructureCheckerResult check(Molecule molecule)
                                   throws java.lang.NullPointerException,
                                          chemaxon.license.LicenseException

Description copied from interface: StructureChecker

Detects a specific error in the molecule.

Specified by:

check in interface StructureChecker

Parameters:

molecule - a Molecule instance have to be checked

Returns:

an instance of StructureCheckerResult (which contains all data needed to fix the problem) if the molecule contains the examined error, null otherwise

Throws:

java.lang.NullPointerException - if molecule is null

chemaxon.license.LicenseException

check1

protected abstract StructureCheckerResult check1(Molecule molecule)

This method contains the current checking mechanism.

Parameters:

molecule - the Molecule instance to be checked for problems

Returns:

a StructureCheckerResult which represents the problem or null if no problem found

expandMolecule

protected Molecule expandMolecule(Molecule molecule,
                                  java.util.Map<MolAtom,MolAtom> atomMap,
                                  java.util.Map<MolBond,MolBond> bondMap)

Returns the original molecule if no groups to expand, or the clone of the original molecule with expanded groups.

Parameters:

molecule - the molecule to check

Returns:

the original molecule, or a clone with expanded sgroups

Since:

5.9

convertResult

protected void convertResult(Molecule originalMolecule,
                             Molecule expandedMolecule,
                             StructureCheckerResult result,
                             java.util.Map<MolAtom,MolAtom> atomMap,
                             java.util.Map<MolBond,MolBond> bondMap)

Handles the mapping of a cloned and expanded molecule result to the original molecule.

Parameters:

originalMolecule - the original molecule

expandedMolecule - the cloned then expanded molecule

result - the structure checker result on cloned molecule

atomMap - the mapping of cloned molecule and original molecule atoms

bondMap - the mapping of cloned molecule and original molecule bonds

Since:

5.9

isLicensed

public boolean isLicensed()

Specified by:

isLicensed in interface chemaxon.license.Licensable

setLicenseEnvironment

public void setLicenseEnvironment(java.lang.String env)

Specified by:

setLicenseEnvironment in interface chemaxon.license.Licensable

getErrorType

public StructureCheckerErrorType getErrorType()

Specified by:

getErrorType in interface StructureChecker

Returns:

the error type of this checker

getErrorCode

public java.lang.String getErrorCode()

Description copied from interface: StructureChecker

Returns the String represented error code of the checker (this error code should be used for external implementation support instead of StructureChecker.getErrorType())

Specified by:

getErrorCode in interface StructureChecker

Returns:

the String represented error code of the checker (this error code should be used for external implementation support instead of StructureChecker.getErrorType())

getEditorClassName

public java.lang.String getEditorClassName()

Specified by:

getEditorClassName in interface StructureChecker

Returns:

the name of the editor class of the checker

getDescription

public java.lang.String getDescription()

Specified by:

getDescription in interface StructureChecker

Returns:

the description

isValid

public boolean isValid()

Description copied from interface: StructureChecker

Returns true if the checker's configuration is valid, false otherwise

Specified by:

isValid in interface StructureChecker

Returns:

true if the checker's configuration is valid, false otherwise

isAvailable

public boolean isAvailable()

Description copied from interface: StructureChecker

Returns true if the checker is available, and can be used

Specified by:

isAvailable in interface StructureChecker

Returns:

true if the checker is available, and can be used

cloneItem

public StructureChecker cloneItem()

Description copied from interface: StructureChecker

Returns a clone of this StructureChecker instance

Specified by:

cloneItem in interface StructureChecker

Returns:

a clone of this StructureChecker instance

clone

public AbstractStructureChecker clone()
                               throws java.lang.CloneNotSupportedException

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

setDescription

public void setDescription(java.lang.String description)

Description copied from interface: StructureChecker

Sets the description of the checker

Specified by:

setDescription in interface StructureChecker

Parameters:

description - the description to set

addPropertyChangeListener

public void addPropertyChangeListener(java.beans.PropertyChangeListener listener)

Description copied from interface: StructureChecker

Add a PropertyChangeListener to the listener list. The listener is registered for all properties. The same listener object may be added more than once, and will be called as many times as it is added. If listener is null, no exception is thrown and no action is taken.

Specified by:

addPropertyChangeListener in interface StructureChecker

Parameters:

listener - The PropertyChangeListener to be added

See Also:

PropertyChangeSupport.addPropertyChangeListener(PropertyChangeListener)

removePropertyChangeListener

public void removePropertyChangeListener(java.beans.PropertyChangeListener listener)

Description copied from interface: StructureChecker

Remove a PropertyChangeListener from the listener list. This removes a PropertyChangeListener that was registered for all properties. If listener was added more than once to the same event source, it will be notified one less time after being removed. If listener is null, or was never added, no exception is thrown and no action is taken.

Specified by:

removePropertyChangeListener in interface StructureChecker

Parameters:

listener - The PropertyChangeListener to be removed

See Also:

PropertyChangeSupport.removePropertyChangeListener(PropertyChangeListener)

addPropertyChangeListener

public void addPropertyChangeListener(java.lang.String propertyName,
                                      java.beans.PropertyChangeListener listener)

Description copied from interface: StructureChecker

Add a PropertyChangeListener for a specific property. The listener will be invoked only when a call on firePropertyChange names that specific property. The same listener object may be added more than once. For each property, the listener will be invoked the number of times it was added for that property. If propertyName or listener is null, no exception is thrown and no action is taken.

Specified by:

addPropertyChangeListener in interface StructureChecker

Parameters:

propertyName - The name of the property to listen on.

listener - The PropertyChangeListener to be added

See Also:

PropertyChangeSupport.addPropertyChangeListener(String, PropertyChangeListener)

removePropertyChangeListener

public void removePropertyChangeListener(java.lang.String propertyName,
                                         java.beans.PropertyChangeListener listener)

Description copied from interface: StructureChecker

Remove a PropertyChangeListener for a specific property. If listener was added more than once to the same event source for the specified property, it will be notified one less time after being removed. If propertyName is null, no exception is thrown and no action is taken. If listener is null, or was never added for the specified property, no exception is thrown and no action is taken.

Specified by:

removePropertyChangeListener in interface StructureChecker

Parameters:

propertyName - The name of the property that was listened on.

listener - The PropertyChangeListener to be removed

See Also:

PropertyChangeSupport.removePropertyChangeListener(String, PropertyChangeListener)

getDescriptor

public StructureCheckerDescriptor getDescriptor()

Description copied from interface: StructureChecker

Returns a StructureCheckerDescriptor instance which represents the user interface related informations of the checker

Specified by:

getDescriptor in interface StructureChecker

Returns:

a StructureCheckerDescriptor instance which represents the user interface related informations of the checker

propertyChange

public void propertyChange(java.beans.PropertyChangeEvent evt)

Specified by:

propertyChange in interface java.beans.PropertyChangeListener

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object