gov.nih.nlm.mms.filters
Class SourcesToRemoveFilter

java.lang.Object
  gov.nih.nlm.mms.filters.AbstractFilter
      gov.nih.nlm.mms.filters.SourcesToRemoveFilter

All Implemented Interfaces:

Configurable, ConceptContentSelector, Filter, GUIConfigurable, SubsetListener, Comparable

public class SourcesToRemoveFilter
extends AbstractFilter
implements ConceptContentSelector

This Filter removes all CUIs that are from sources chosen to be excluded from the subset.

Author:

Deborah Shapiro

Field Summary

Fields inherited from class gov.nih.nlm.mms.filters.AbstractFilter

default_configuration, init_cui, subset_content, user_configuration, warnings

Constructor Summary

SourcesToRemoveFilter()
Instantiates an empty SourcesToRemoveFilter.

Method Summary

void	addSelectedSource(Source source) This method adds a Source to the data structure that holds the list of selected sources.
void	applySelections(Concept concept) Method which determines if a given Concept or its components will be removed from the release.
void	clearSelectedSources() This method clears the data structure that holds the list of selected sources.
void	clearSourceDependencies() Clears data structure that holds Dependency(s).
boolean	enforceDependentSourceSelection() This method indicates whether the Enforce Dependent Source Selection option has been chosen on the Advanced Source List Options dialog box.
boolean	enforceFamilySelection() This method indicates whether or not the Enforce Family Selection option has been chosen in the Advanced Source List Options dialog box.
boolean	getAutomaticSelection() This method returns whether or not the automatic_selection option has been chosen on the MetamorphoSys Options dialog box.
Color	getColor() Method indicates the Color that should be used to display the name.
ApplicationConfiguration	getConfiguration() Method returns the default ApplicationConfiguration.
String	getConfigurationDetails() Method returns a list of the sources to be excluded and sources to be kept for display in the configuration file.
List	getDefaultSourcesToRemove() This method returns a List of all Sources to be excluded.
Set	getDefaultSourcesToRemoveAsSet() This method returns a Set containing the default list of all Sources to be excluded.
List	getDependentSources(Source source) Method gets all dependent sources for a given Source.
Set	getDependentSourcesAsSet(Source source) Method gets all dependent sources for a given Source.
JPanel	getHelpPanel() Method provides a JPanel that will be added to the main GUI help menu to allow the user to consult a help window that is particular to this filter.
String	getName() Returns the name.
JPanel	getPanel() Method provides the GUI panel that will display the filter's screen as one of the tabs on the main GUI window.
Properties	getProperties() Method returns all properties specific to the filter.
List	getSelectedSources() This method returns the List containing all Sources selected.
Set	getSelectedSourcesAsSet() This method returns the Set containing all Sources selected.
List	getSelectedSourcesInverse() This method returns the List of Sources that are not selected.
Set	getSelectedSourcesInverseAsSet() This method returns the Set of Sources that are not selected.
List	getSourceDependencies() Method returns a List of Dependency(s).
Set	getSourceDependenciesAsSet() Method returns a Set of Dependency(s).
List	getSources() Returns the list of Sources from the default configuration.
List	getSourcesToRemove() This method is used by the SourcesToRemoveListener to determine which sources should be removed from the other Filter's displays.
String	getTabDescription() Method provides the description of the filter's screen and includes instructions on use.
boolean	hasAdvancedOptions() Indicates whether or not an options menu item should be supplied for advanced configuration options.
boolean	hasDependentSource(Source source) Returns if given Source has a dependent source.
void	initialize() Set initial values for filter specific variables from user config file.
boolean	isEfficientEnabled() Indicates if Filter can use the efficient mode during the "Initialize Cuis" phase of the subsetting process.
boolean	isSourceToRemove(Source s) This method returns a boolean depending on whether or not the Source is excluded from the subset.
void	removeSelectedSource(Source source) This method removes a Source from the data structure that holds the list of selected sources.
boolean	removeSelectedSources() This method indicates whether the selections represent sources to be excluded or sources to be kept.
void	resetToDefaults() Method allows the user to reset the filter's settings to defaults.
void	setConfiguration(ApplicationConfiguration c) Method provides the filter with values from the default properties file.
void	setConfiguration(UserConfiguration c) Method provides the filter with values from the user configuration file.
void	setEnforceDependentSourceSelection(boolean b) This method sets whether or not the Enforce Dependent Source Selection option will be executed on the gui.
void	setEnforceFamilySelection(boolean b) This method sets whether or not the Enforce Family Selection option will be executed on the gui.
void	setPanelSelections() Method makes selections on the filter's table
void	setProperties(Properties p) Method provides the filter with all properties specific to the filter.
void	setRemoveSelectedSources(boolean b) This method sets whether or not the selections represent sources to be excluded or sources to be kept.
void	setSelectedSources(List str) This method replaces the selected_sources list with the one provided.
void	setSelectedSources(Set str) This method replaces the selected_sources list with the one provided.
void	setSourceDependencies(List source_dependencies) Replaces the struction that holds Dependency(s) with the one given.
void	showOptions() Presents an advanced options GUI to the user.

Methods inherited from class gov.nih.nlm.mms.filters.AbstractFilter

addDataChangeListener, applyFilter, beginInitializeCuiList, beginSubsetContent, compareTo, endInitializeCuiList, endSubsetContent, fireDataChanged, fireNotUndoableDataChanged, getGUIConfigurableForValidationFailure, getValidateMessage, getValidationErrors, getValidationWarnings, getWarnings, hasDataChanged, removeDataChangeListener, resetDataChanged, setCuiList, setDataChanged, validate

Methods inherited from class java.lang.Object

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

Methods inherited from interface gov.nih.nlm.mms.filters.Filter

applyFilter, getWarnings

Methods inherited from interface gov.nih.nlm.mms.GUIConfigurable

addDataChangeListener, getGUIConfigurableForValidationFailure, getValidationErrors, getValidationWarnings, hasDataChanged, removeDataChangeListener, resetDataChanged, setDataChanged, validate

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface gov.nih.nlm.mms.SubsetListener

beginInitializeCuiList, beginSubsetContent, endInitializeCuiList, endSubsetContent, setCuiList

Constructor Detail

SourcesToRemoveFilter

public SourcesToRemoveFilter()

Instantiates an empty SourcesToRemoveFilter.

Method Detail

initialize

public void initialize()

Set initial values for filter specific variables from user config file.

getPanel

public JPanel getPanel()

Method provides the GUI panel that will display the filter's screen as one of the tabs on the main GUI window.

Specified by:

getPanel in interface GUIConfigurable

Returns:

JPanel that displays the graphical interface for the filter

setPanelSelections

public void setPanelSelections()

Method makes selections on the filter's table

Specified by:

setPanelSelections in interface GUIConfigurable

getTabDescription

public String getTabDescription()

Method provides the description of the filter's screen and includes instructions on use.

Specified by:

getTabDescription in interface GUIConfigurable

Returns:

String text of instructions for use of panel

resetToDefaults

public void resetToDefaults()

Method allows the user to reset the filter's settings to defaults.

Specified by:

resetToDefaults in interface Configurable

showOptions

public void showOptions()

Presents an advanced options GUI to the user.

Specified by:

showOptions in interface GUIConfigurable

Overrides:

showOptions in class AbstractFilter

hasAdvancedOptions

public boolean hasAdvancedOptions()

Indicates whether or not an options menu item should be supplied for advanced configuration options.

Specified by:

hasAdvancedOptions in interface GUIConfigurable

Overrides:

hasAdvancedOptions in class AbstractFilter

Returns:

true if so; false otherwise

getHelpPanel

public JPanel getHelpPanel()

Method provides a JPanel that will be added to the main GUI help menu to allow the user to consult a help window that is particular to this filter.

Specified by:

getHelpPanel in interface GUIConfigurable

Overrides:

getHelpPanel in class AbstractFilter

Returns:

JPanel to be added to the Help menu

setConfiguration

public void setConfiguration(ApplicationConfiguration c)

Method provides the filter with values from the default properties file.

Specified by:

setConfiguration in interface Configurable

Overrides:

setConfiguration in class AbstractFilter

Parameters:

c - ApplicationConfiguration

getConfiguration

public ApplicationConfiguration getConfiguration()

Method returns the default ApplicationConfiguration.

Returns:

ApplicationConfiguration

getProperties

public Properties getProperties()

Method returns all properties specific to the filter.

Specified by:

getProperties in interface Configurable

Returns:

Properties only those directly related to the filter. They will start with the filter's class name which will be concatenated to the name of the property. Filter.property_name

setProperties

public void setProperties(Properties p)

Method provides the filter with all properties specific to the filter.

Specified by:

setProperties in interface Configurable

Parameters:

p - Properties

applySelections

public void applySelections(Concept concept)

Method which determines if a given Concept or its components will be removed from the release.

Specified by:

applySelections in interface ConceptContentSelector

Parameters:

concept - Concept

getName

public String getName()

Returns the name.

Specified by:

getName in interface GUIConfigurable

Returns:

String

getConfigurationDetails

public String getConfigurationDetails()

Method returns a list of the sources to be excluded and sources to be kept for display in the configuration file.

Specified by:

getConfigurationDetails in interface Configurable

Returns:

String

clearSelectedSources

public void clearSelectedSources()

This method clears the data structure that holds the list of selected sources.

addSelectedSource

public void addSelectedSource(Source source)

This method adds a Source to the data structure that holds the list of selected sources.

Parameters:

source - Source

removeSelectedSource

public void removeSelectedSource(Source source)

This method removes a Source from the data structure that holds the list of selected sources.

Parameters:

source - Source

getSelectedSources

public List getSelectedSources()

This method returns the List containing all Sources selected.

Returns:

List selected_sources

getSelectedSourcesAsSet

public Set getSelectedSourcesAsSet()

This method returns the Set containing all Sources selected.

Returns:

Set selected_sources

getSourcesToRemove

public List getSourcesToRemove()

This method is used by the SourcesToRemoveListener to determine which sources should be removed from the other Filter's displays.

Returns:

List of Sources

getSelectedSourcesInverse

public List getSelectedSourcesInverse()

This method returns the List of Sources that are not selected.

Returns:

List of Sources not selected

getSelectedSourcesInverseAsSet

public Set getSelectedSourcesInverseAsSet()

This method returns the Set of Sources that are not selected.

Returns:

Set of Sources not selected

getDefaultSourcesToRemove

public List getDefaultSourcesToRemove()

This method returns a List of all Sources to be excluded.

Returns:

List

getDefaultSourcesToRemoveAsSet

public Set getDefaultSourcesToRemoveAsSet()

This method returns a Set containing the default list of all Sources to be excluded.

Returns:

Set

setSelectedSources

public void setSelectedSources(List str)

This method replaces the selected_sources list with the one provided.

Parameters:

str - List of Sources

setSelectedSources

public void setSelectedSources(Set str)

This method replaces the selected_sources list with the one provided.

Parameters:

str - Set of Sources

isSourceToRemove

public boolean isSourceToRemove(Source s)

This method returns a boolean depending on whether or not the Source is excluded from the subset.

Parameters:

s - Source

Returns:

boolean true if Source is to be removed false if Source is to be kept

enforceFamilySelection

public boolean enforceFamilySelection()

This method indicates whether or not the Enforce Family Selection option has been chosen in the Advanced Source List Options dialog box.

Returns:

boolean true all sources that share a source family will also be selected false otherwise

setEnforceFamilySelection

public void setEnforceFamilySelection(boolean b)

This method sets whether or not the Enforce Family Selection option will be executed on the gui.

Parameters:

b - boolean true all sources that share a source family will also be selected false otherwise

enforceDependentSourceSelection

public boolean enforceDependentSourceSelection()

This method indicates whether the Enforce Dependent Source Selection option has been chosen on the Advanced Source List Options dialog box.

Returns:

true all sources that are dependent on the chosen source will also be selected false otherwise

setEnforceDependentSourceSelection

public void setEnforceDependentSourceSelection(boolean b)

This method sets whether or not the Enforce Dependent Source Selection option will be executed on the gui.

Parameters:

b - boolean

removeSelectedSources

public boolean removeSelectedSources()

This method indicates whether the selections represent sources to be excluded or sources to be kept.

Returns:

true selected sources will be excluded false selected sources will be kept

setRemoveSelectedSources

public void setRemoveSelectedSources(boolean b)

This method sets whether or not the selections represent sources to be excluded or sources to be kept.

Parameters:

b - boolean

getAutomaticSelection

public boolean getAutomaticSelection()

This method returns whether or not the automatic_selection option has been chosen on the MetamorphoSys Options dialog box. Automatic selection allows the application to select dependent sources and sources sharing the source family without prompting the user. This occurs only if the enforce_dep_source_selection and enforce_family_selection flags are set to true on the Advanced Source List Options dialog box.

Returns:

true if automatic selection has been chosen false otherwise

setConfiguration

public void setConfiguration(UserConfiguration c)

Method provides the filter with values from the user configuration file.

Specified by:

setConfiguration in interface Configurable

Overrides:

setConfiguration in class AbstractFilter

Parameters:

c - UserConfiguration

getSourceDependencies

public List getSourceDependencies()

Method returns a List of Dependency(s).

Returns:

List

getSourceDependenciesAsSet

public Set getSourceDependenciesAsSet()

Method returns a Set of Dependency(s).

Returns:

Set

getDependentSources

public List getDependentSources(Source source)

Method gets all dependent sources for a given Source.

Parameters:

source - Source

Returns:

List of Sources

getDependentSourcesAsSet

public Set getDependentSourcesAsSet(Source source)

Method gets all dependent sources for a given Source.

Parameters:

source - Source

Returns:

Set of Sources

hasDependentSource

public boolean hasDependentSource(Source source)

Returns if given Source has a dependent source.

Parameters:

source - Source

Returns:

boolean true if source has a dependent source false otherwise

clearSourceDependencies

public void clearSourceDependencies()

Clears data structure that holds Dependency(s).

setSourceDependencies

public void setSourceDependencies(List source_dependencies)

Replaces the struction that holds Dependency(s) with the one given.

Parameters:

source_dependencies - List of Dependency(s)

getSources

public List getSources()

Returns the list of Sources from the default configuration.

Returns:

List of sources

getColor

public Color getColor()

Method indicates the Color that should be used to display the name.

Specified by:

getColor in interface GUIConfigurable

Overrides:

getColor in class AbstractFilter

Returns:

Color

isEfficientEnabled

public boolean isEfficientEnabled()

Indicates if Filter can use the efficient mode during the "Initialize Cuis" phase of the subsetting process. The efficient mode reads only MRCONSO and MRSTY during the "Initialize Cuis" phase.

Specified by:

isEfficientEnabled in interface Filter

Returns:

true if efficient mode is acceptable false if efficient mode is not acceptable