chemaxon.standardizer

Class StandardizerUtil

java.lang.Object

chemaxon.standardizer.StandardizerUtil

@PublicAPI
public class StandardizerUtil
extends java.lang.Object

Utility class for standardizer
Functionalities of old standardizer can be simulated using this class.

Since:

5.11

Author:

Imre Barna

Constructor Summary

Constructors

Constructor and Description
StandardizerUtil()

Method Summary

Modifier and Type	Method and Description
static boolean	addInactiveTasks(Standardizer standardizer, java.lang.String configuration) Adds the Standardizer tasks specified in the configuration parameter to the inactive tasks list.
static void	clearInactiveTasks(Standardizer standardizer) Clears the inactive tasks list.
static StandardizerConfigurationReader	initializeReader(java.lang.String configuration) Initializes a configuration reader based on a configuration string
static boolean	isLastTaskClean(Standardizer standardizer) Returns true if last task is clean or there are no tasks (final clean not needed before output to file).
static boolean	removeInactiveTasks(Standardizer standardizer, java.lang.String configuration) Removes the Standardizer tasks specified in the configuration parameter from the inactive tasks list.
static void	setCleanTemplates(Standardizer standardizer, Molecule[] templates) Sets the default clean templates.
static void	setInactiveTasks(Standardizer standardizer, java.lang.String configuration) Sets the tasks with the provided ID inactive.

Methods inherited from class java.lang.Object

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

Constructor Detail

StandardizerUtil

public StandardizerUtil()

Method Detail

addInactiveTasks

public static boolean addInactiveTasks(Standardizer standardizer,
                                       java.lang.String configuration)
                                throws java.lang.IllegalArgumentException

Adds the Standardizer tasks specified in the configuration parameter to the inactive tasks list. Only the task type is checked. E.g. if "RemoveExplicitH" tasks are added, then these tasks are always inactivated regardless to the parameters (e.g.: Mapped="true") they use. Inactive tasks are not performed during standardization. To remove a task from the inactive task list use removeInactiveTasks(Standardizer, String), to clear the inactive tasks list use clearInactiveTasks(Standardizer) method. For internal use only.

Parameters:

standardizer - the target standardizer

configuration - is the XML configuration string or else the simple config string, items separated by ".."

Returns:

true if the inactive task list has changed

Throws:

java.lang.IllegalArgumentException - if the configuration string is invalid

See Also:

clearInactiveTasks(Standardizer), removeInactiveTasks(Standardizer, String)

removeInactiveTasks

public static boolean removeInactiveTasks(Standardizer standardizer,
                                          java.lang.String configuration)
                                   throws java.lang.IllegalArgumentException

Removes the Standardizer tasks specified in the configuration parameter from the inactive tasks list. Only the task type is checked. For internal use only.

Parameters:

standardizer - the target standardizer

configuration - is the XML configuration string or else the simple config string, items separated by ".."

Returns:

true if the inactive task list has changed

Throws:

java.lang.IllegalArgumentException - if the configuration string is invalid

See Also:

setInactiveTasks(Standardizer, String), clearInactiveTasks(Standardizer)

setInactiveTasks

public static void setInactiveTasks(Standardizer standardizer,
                                    java.lang.String configuration)

Sets the tasks with the provided ID inactive.

Parameters:

standardizer - the target standardizer

configuration - the provided ID

clearInactiveTasks

public static void clearInactiveTasks(Standardizer standardizer)

Clears the inactive tasks list. For internal use only.

Parameters:

standardizer - the target standardizer

See Also:

setInactiveTasks(Standardizer, String), removeInactiveTasks(Standardizer, String)

initializeReader

public static StandardizerConfigurationReader initializeReader(java.lang.String configuration)

Initializes a configuration reader based on a configuration string

Parameters:

configuration - the string representation of the configuration

Returns:

the configuration reader for the provided configuration

isLastTaskClean

public static boolean isLastTaskClean(Standardizer standardizer)

Returns true if last task is clean or there are no tasks (final clean not needed before output to file).

Parameters:

standardizer - the target standardizer

Returns:

true if last task is clean or there are no tasks

setCleanTemplates

public static void setCleanTemplates(Standardizer standardizer,
                                     Molecule[] templates)

Sets the default clean templates. Used in template based clean tasks that do not specify the template file:

• <Clean Type="TemplateBased"/>
• "clean:tb"

Parameters:

standardizer - the target standardizer instance

templates - is the template molecule array