gov.nih.nlm.mms.filters
Class SuppressibleTermgroupsFilter

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

All Implemented Interfaces:

Configurable, ConceptContentSelector, ConceptManipulator, Filter, GUIConfigurable, SourcesToRemoveListener, SubsetListener, Comparable

public class SuppressibleTermgroupsFilter
extends AbstractFilter
implements SourcesToRemoveListener, ConceptContentSelector, ConceptManipulator

Computes which content is suppressible and (optionally) removes it.

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

SuppressibleTermgroupsFilter()
Instantiates an empty SuppressibleTermgroupsFilter.

Method Summary

protected void	addSuppressibleTermgroup(SourceTermType tg) Adds a SourceTermType to the list of suppressible termgroups.
void	applyChanges(Concept concept) Manipulates data in the Concept, but does not remove any data from the concept.
void	applySelections(Concept concept) Sets the suppressibility of atoms and removes suppressible content if advanced options indicate to do so.
void	clearConfirmDefaultSuppressibleTermgroups() Clears the list of SourceTermTypes that have been confirmed by the user to be suppressible.
protected void	clearSuppressibleTermgroups() Clears the list of suppressible SourceTermTypes.
Color	getColor() Returns the Color that should be used to display the name.
String	getConfigurationDetails() Returns configuration details for use in mmsys.log.
List	getConfirmDefaultSuppressibleTermgroups() Returns a list of SourceTermTypes that have been confirmed by the user via a dialog box to be suppressible.
List	getDefaultSuppressibleTermgroups() Returns an List containing all SourceTermTypes to be suppressed from the default termgroup list.
JPanel	getHelpPanel() Returns a help JPanel.
String	getName() Returns the filter name.
JPanel	getPanel() Returns the GUI panel that will display the filter's screen as one of the tabs on the main GUI window.
Properties	getProperties() Returns filter state.
int	getRowForTermgroup(SourceTermType tg) Maps a SourceTermType to a row number in the table.
List	getSuppressibleTermgroups() Returns the List containing all suppressible SourceTermTypes.
SortableJTable	getSuppressibleTermgroupsTable() Returns the table that includes SourceTermTypes with the suppressible termgroups highlighted.
String	getTabDescription() Returns the description.
SourceTermType	getTermgroupAtRow(int tg) Maps a row number to the SourceTermType.
boolean	hasAdvancedOptions() Indicates whether or not an options menu item should be supplied for advanced configuration options.
boolean	isEfficientEnabled() Indicates if Filter can use the efficient mode during the "Initialize Cuis" phase of the subsetting process.
boolean	removeEditorSuppressibleData() Indicates whether the Remove Editor Assigned Suppressible Data option has been chosen on the Advanced Suppressibility Options panel.
boolean	removeObsoleteData() Indicates whether the Remove Obsolete Data option has been chosen on the Advanced Suppressibility Options panel.
boolean	removeSourceTtySuppressibleData() Indicates whether the Remove Source Term Type Suppressible Data option has been chosen on the Advanced Suppressibility Options panel.
boolean	removeSuppressibleData() Indicates whether the Remove Suppressible Data option has been chosen on the Advanced Suppressibility Options panel.
protected void	removeSuppressibleTermgroup(SourceTermType tg) Removes a SourceTermType from the list of suppressible termgroups.
void	resetToDefaults() Resets state to defaults.
void	setConfiguration(ApplicationConfiguration c) Sets the ApplicationConfiguration.
void	setPanelSelections() Selects rows on the suppressiblity table for rows of termgroups that should be suppressed.
void	setProperties(Properties p) Sets filter state.
void	setRemoveEditorSuppressibleData(boolean b) Sets the flag indicating whether or not editor assigned suppressible data will be removed from the subset.
void	setRemoveObsoleteData(boolean b) Sets the flag indicating whether or not obsolete data will be removed from the subset.
void	setRemoveSourceTtySuppressibleData(boolean b) Sets the flag indicating whether or not source term type suppressible data will be removed from the subset.
void	setRemoveSuppressibleData(boolean b) Sets the flag indicating whether or not suppressible data will be removed from the subset.
void	setSuppressibleTermgroups(List stgs) Sets the suppressible termgroups list with the one provided.
void	showOptions() Shows an advanced options GUI to the user.
void	sourcesToRemoveChanged(SourcesToRemoveEvent e) Resets the suppressiblity table when the user tabs between filters.

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, setConfiguration, 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 gov.nih.nlm.mms.Configurable

setConfiguration

Methods inherited from interface java.lang.Comparable

compareTo

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

beginInitializeCuiList, beginSubsetContent, endInitializeCuiList, endSubsetContent, setCuiList

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 gov.nih.nlm.mms.Configurable

setConfiguration

Methods inherited from interface java.lang.Comparable

compareTo

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

beginInitializeCuiList, beginSubsetContent, endInitializeCuiList, endSubsetContent, setCuiList

Constructor Detail

SuppressibleTermgroupsFilter

public SuppressibleTermgroupsFilter()

Instantiates an empty SuppressibleTermgroupsFilter.

Method Detail

getPanel

public JPanel getPanel()

Returns 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 graphical interface for the filter

setPanelSelections

public void setPanelSelections()

Selects rows on the suppressiblity table for rows of termgroups that should be suppressed.

Specified by:

setPanelSelections in interface GUIConfigurable

getTabDescription

public String getTabDescription()

Returns the description.

Specified by:

getTabDescription in interface GUIConfigurable

Returns:

the description

resetToDefaults

public void resetToDefaults()

Resets state to defaults.

Specified by:

resetToDefaults in interface Configurable

showOptions

public void showOptions()

Shows 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()

Returns a help JPanel.

Specified by:

getHelpPanel in interface GUIConfigurable

Overrides:

getHelpPanel in class AbstractFilter

Returns:

a help JPanel

setConfiguration

public void setConfiguration(ApplicationConfiguration c)

Sets the ApplicationConfiguration. Used for "default" selections.

Specified by:

setConfiguration in interface Configurable

Overrides:

setConfiguration in class AbstractFilter

Parameters:

c - the ApplicationConfiguration

getProperties

public Properties getProperties()

Returns filter state.

Specified by:

getProperties in interface Configurable

Returns:

filter state as Properties

setProperties

public void setProperties(Properties p)

Sets filter state.

Specified by:

setProperties in interface Configurable

Parameters:

p - Properties representing filter state

applyChanges

public void applyChanges(Concept concept)

Manipulates data in the Concept, but does not remove any data from the concept.

Specified by:

applyChanges in interface ConceptManipulator

Parameters:

concept - Concept

applySelections

public void applySelections(Concept concept)

Sets the suppressibility of atoms and removes suppressible content if advanced options indicate to do so.

Specified by:

applySelections in interface ConceptContentSelector

Parameters:

concept - the current Concept

getName

public String getName()

Returns the filter name.

Specified by:

getName in interface GUIConfigurable

Returns:

the filter name

getConfigurationDetails

public String getConfigurationDetails()

Returns configuration details for use in mmsys.log.

Specified by:

getConfigurationDetails in interface Configurable

Returns:

configuration details for use in mmsys.log

clearSuppressibleTermgroups

protected void clearSuppressibleTermgroups()

Clears the list of suppressible SourceTermTypes.

addSuppressibleTermgroup

protected void addSuppressibleTermgroup(SourceTermType tg)

Adds a SourceTermType to the list of suppressible termgroups.

Parameters:

tg - the SourceTermType

removeSuppressibleTermgroup

protected void removeSuppressibleTermgroup(SourceTermType tg)

Removes a SourceTermType from the list of suppressible termgroups.

Parameters:

tg - SourceTermType

getDefaultSuppressibleTermgroups

public List getDefaultSuppressibleTermgroups()

Returns an List containing all SourceTermTypes to be suppressed from the default termgroup list.

Returns:

List of suppressed termgroups

getConfirmDefaultSuppressibleTermgroups

public List getConfirmDefaultSuppressibleTermgroups()

Returns a list of SourceTermTypes that have been confirmed by the user via a dialog box to be suppressible. Prevents user from being queried twice about a termgroup's suppressiblity.

Returns:

List of suppressed termgroups

clearConfirmDefaultSuppressibleTermgroups

public void clearConfirmDefaultSuppressibleTermgroups()

Clears the list of SourceTermTypes that have been confirmed by the user to be suppressible.

setSuppressibleTermgroups

public void setSuppressibleTermgroups(List stgs)

Sets the suppressible termgroups list with the one provided.

Parameters:

stgs - the List of SourceTermTypes

getSuppressibleTermgroups

public List getSuppressibleTermgroups()

Returns the List containing all suppressible SourceTermTypes.

Returns:

List of suppressible termgroups

removeSuppressibleData

public boolean removeSuppressibleData()

Indicates whether the Remove Suppressible Data option has been chosen on the Advanced Suppressibility Options panel.

Returns:

true if so, false otherwise

setRemoveSuppressibleData

public void setRemoveSuppressibleData(boolean b)

Sets the flag indicating whether or not suppressible data will be removed from the subset.

Parameters:

b - the flag indicating whether or not suppressible data will be removed from the subset

removeSourceTtySuppressibleData

public boolean removeSourceTtySuppressibleData()

Indicates whether the Remove Source Term Type Suppressible Data option has been chosen on the Advanced Suppressibility Options panel.

Returns:

true if so, false otherwise

setRemoveSourceTtySuppressibleData

public void setRemoveSourceTtySuppressibleData(boolean b)

Sets the flag indicating whether or not source term type suppressible data will be removed from the subset.

Parameters:

b - the flag indicating whether or not source term type suppressible data will be removed from the subset

removeEditorSuppressibleData

public boolean removeEditorSuppressibleData()

Indicates whether the Remove Editor Assigned Suppressible Data option has been chosen on the Advanced Suppressibility Options panel.

Returns:

true if so, false otherwise

setRemoveEditorSuppressibleData

public void setRemoveEditorSuppressibleData(boolean b)

Sets the flag indicating whether or not editor assigned suppressible data will be removed from the subset.

Parameters:

b - the flag indicating whether or not editor assigned suppressible data will be removed from the subset

getSuppressibleTermgroupsTable

public SortableJTable getSuppressibleTermgroupsTable()

Returns the table that includes SourceTermTypes with the suppressible termgroups highlighted.

Returns:

SortableJTable

removeObsoleteData

public boolean removeObsoleteData()

Indicates whether the Remove Obsolete Data option has been chosen on the Advanced Suppressibility Options panel.

Returns:

true if so, false otherwise

setRemoveObsoleteData

public void setRemoveObsoleteData(boolean b)

Sets the flag indicating whether or not obsolete data will be removed from the subset.

Parameters:

b - the flag indicating whether or not obsolete data will be removed from the subset

sourcesToRemoveChanged

public void sourcesToRemoveChanged(SourcesToRemoveEvent e)

Resets the suppressiblity table when the user tabs between filters. Removes entries visible in the table based on which sources are to be excluded.

Specified by:

sourcesToRemoveChanged in interface SourcesToRemoveListener

Parameters:

e - SourcesToRemoveEvent

getRowForTermgroup

public int getRowForTermgroup(SourceTermType tg)

Maps a SourceTermType to a row number in the table. This is necessary because only SourceTermTypes from sources that are not to be excluded will be visible in the table.

Parameters:

tg - the SourceTermType

Returns:

int row number of termgroup in table -1 if termgroup is to be excluded

getTermgroupAtRow

public SourceTermType getTermgroupAtRow(int tg)

Maps a row number to the SourceTermType. Adjusts for the SourceTermTypes that are not currently visible in the suppressibility table because their sources are to be excluded.

Parameters:

tg - int row in the suppressibility table

Returns:

SourceTermType located at that row in the table

getColor

public Color getColor()

Returns the Color that should be used to display the name.

Specified by:

getColor in interface GUIConfigurable

Overrides:

getColor in class AbstractFilter

Returns:

the 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