gov.nih.nlm.mms
Class OriginalMRMetamorphoSysInputStream

java.lang.Object
  gov.nih.nlm.umls.io.OriginalMRFilesConceptInputStream
      gov.nih.nlm.umls.io.OriginalMRMetathesaurusInputStream
          gov.nih.nlm.mms.OriginalMRMetamorphoSysInputStream

All Implemented Interfaces:

Configurable, GUIConfigurable, MetamorphoSysInputStream, SubsetListener, ConceptInputStream, MetathesaurusInputStream, LocalNullValueSupport, Comparable

public class OriginalMRMetamorphoSysInputStream
extends OriginalMRMetathesaurusInputStream
implements MetamorphoSysInputStream

Represents an MetamorphoSysInputStream containing Original Release Format MR files in a directory.

Author:

Deborah Shapiro

Field Summary

protected CuiList	cui_list
protected boolean	data_changed
protected ApplicationConfiguration	default_configuration
protected boolean	enable_efficient
protected boolean	ignore_events
protected boolean	init_cui
protected List<DataChangeListener>	listeners
protected boolean	subset_content
protected UserConfiguration	user_configuration

Fields inherited from class gov.nih.nlm.umls.io.OriginalMRMetathesaurusInputStream

current_index, index_counter, index_lines, mrcui_source, mrsab_source, mrx_sources

Fields inherited from class gov.nih.nlm.umls.io.OriginalMRFilesConceptInputStream

file_names, mr_dir, mratx_source, mrcoc_source, mrcon_counter, mrcon_lines, mrcon_source, mrcxt_source, mrdef_source, mrlo_source, mrrel_source, mrsat_source, mrso_source, mrsty_source, null_value, this_concept, tokens, warnings

Constructor Summary

OriginalMRMetamorphoSysInputStream()
Instantiates an empty OriginalMRMetamorphoSysInputStream.

Method Summary

void	addDataChangeListener(DataChangeListener dcl) Adds a DataChangeListener that will be notified every time a fireDataChanged() call is made.
void	addValidationError(String validation_error) Adds a validation error to the list of errors.
void	addValidationWarning(String validation_warning) Adds a validation warning to the list of warnings.
void	beginInitializeCuiList() Informs SubsetListener that the Initialize Cui List phase is starting.
void	beginSubsetContent() Informs SubsetListener that the Subset Content phase is starting.
void	clearValidationErrors() Clears the list of validation errors.
void	clearValidationWarnings() Clears the list of validation warnings.
int	compareTo(Object o) Compares this object with the specified object for order.
void	endInitializeCuiList() Informs SubsetListener that the Initialize Cui List phase is ending.
void	endSubsetContent() Informs SubsetListener that the Subset Content phase is ending.
protected void	fireDataChanged() Enables filters to inform listeners of data changed event.
protected void	fireNotUndoableDataChanged() Enables filters to indicate that data has changed without notifying the listeners or making this change undoable.
int	getChooserType() Indicates the type of file accepted by the JFileChooser.
Color	getColor() Returns the Color that should be used to display the name.
String	getConfigurationDetails() Returns a message for the log.
GUIConfigurable	getGUIConfigurableForValidationFailure() Returns the GUIConfigurable whose tab should next be displayed to allow the user to correct an error or warning.
JPanel	getHelpPanel() Returns a JPanel that will be displayed when the user selects the corresponding menu item from the Help menu and will provide the user with detailed instructions on the tab's use.
String	getName() Returns the short name for display purposes.
JPanel	getPanel() Returns GUI panel that will be displayed on one of the tabs on the main GUI window.
Properties	getProperties() Returns the current state of the input stream as a Properties object.
String	getTabDescription() Returns the description of the screen and includes instructions on use.
String[]	getValidationErrors() Returns the messages indicating why validation failed.
String[]	getValidationWarnings() Returns warnings that were indicated during validation.
boolean	hasAdvancedOptions() Indicates whether or not an options menu item should be supplied for advanced configuration options.
boolean	hasDataChanged() Returns a boolean indicating whether or not the values on this gui have changed.
boolean	hasFullContextData() Indicates whether this input source has full context data, such as that included in a MRCXT file.
boolean	isEfficientMode() Returns the mode in which subsetting will be run.
void	open(String[] install_paths) Opens all target files in the specified directory.
Concept	readConcept() Returns a Concept containing data from the MR Files.
void	removeDataChangeListener(DataChangeListener dcl) Removes a DataChangeListener so that it will no longer be notified every time a fireDataChanged() call is made from this gui.
void	resetDataChanged() Resets the "has data changed" flag to indicate that no changes have taken place since the last save.
void	resetToDefaults() Resets the variables on a tab back to their default values.
void	setConfiguration(ApplicationConfiguration c) Sets the ApplicationConfiguration used for the default settings.
void	setConfiguration(UserConfiguration user_configuration) Sets the UserConfiguration.
void	setCuiList(CuiList cui_list) Provides input stream access to the cui list.
void	setDataChanged(boolean b) Sets the "has data changed" flag.
void	setEfficientMode(boolean efficient) Sets the subsetting mode to efficient.
void	setPanelSelections() Applies the input stream state to the GUI panel.
void	setProperties(Properties p) Sets the current state of the input stream from a Properties object.
void	showOptions() Presents an advanced options GUI to the user.
boolean	validate() Indicates whether or not the GUIConfigurable is valid.
boolean	validateSourcePath(String source_path) Validates the source path.
boolean	validateSourcePaths(String[] source_paths) Validates the source paths.
boolean	validateVersion(String source_path) Attempts to determine the version of the release being used and validate it against the version from the properties file.
boolean	validateVersions(String[] paths) For each source path it attempts to determine the version of the release being used and validate it against the version from the properties file.

Methods inherited from class gov.nih.nlm.umls.io.OriginalMRMetathesaurusInputStream

close, getAmbiguousStringIdentifiers, getAmbiguousStringIdentifiersAsList, getAmbiguousTermIdentifiers, getAmbiguousTermIdentifiersAsList, getIndexProgress, getLineCounts, readIndexEntry, readReleaseMetadata

Methods inherited from class gov.nih.nlm.umls.io.OriginalMRFilesConceptInputStream

getAtoms, getAttributes, getConceptProgress, getContexts, getCoocurrences, getDefinitions, getLocators, getMappings, getNullValue, getRelationships, getSemanticTypes, getWarnings, isEmptyValue, openSourceFile, setNullValue

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.MetamorphoSysInputStream

getConceptProgress, getIndexProgress

Methods inherited from interface gov.nih.nlm.umls.io.MetathesaurusInputStream

getAmbiguousStringIdentifiers, getAmbiguousStringIdentifiersAsList, getAmbiguousTermIdentifiers, getAmbiguousTermIdentifiersAsList, readIndexEntry, readReleaseMetadata

Methods inherited from interface gov.nih.nlm.umls.io.ConceptInputStream

close, getWarnings

Methods inherited from interface gov.nih.nlm.util.LocalNullValueSupport

getNullValue, isEmptyValue, setNullValue

Field Detail

user_configuration

protected UserConfiguration user_configuration

default_configuration

protected ApplicationConfiguration default_configuration

cui_list

protected CuiList cui_list

init_cui

protected boolean init_cui

subset_content

protected boolean subset_content

data_changed

protected boolean data_changed

enable_efficient

protected boolean enable_efficient

ignore_events

protected boolean ignore_events

listeners

protected List<DataChangeListener> listeners

Constructor Detail

OriginalMRMetamorphoSysInputStream

public OriginalMRMetamorphoSysInputStream()

Instantiates an empty OriginalMRMetamorphoSysInputStream.

Method Detail

setConfiguration

public void setConfiguration(UserConfiguration user_configuration)

Sets the UserConfiguration.

Specified by:

setConfiguration in interface Configurable

Parameters:

user_configuration - the UserConfiguration.

setConfiguration

public void setConfiguration(ApplicationConfiguration c)

Sets the ApplicationConfiguration used for the default settings.

Specified by:

setConfiguration in interface Configurable

Parameters:

c - ApplicationConfiguration

getName

public String getName()

Returns the short name for display purposes.

Specified by:

getName in interface GUIConfigurable

Returns:

the short name for display purposes.

getConfigurationDetails

public String getConfigurationDetails()

Returns a message for the log.

Specified by:

getConfigurationDetails in interface Configurable

Returns:

a message for the log

setCuiList

public void setCuiList(CuiList cui_list)

Provides input stream access to the cui list.

Specified by:

setCuiList in interface SubsetListener

Parameters:

cui_list - CuiList

readConcept

public Concept readConcept()
                    throws IOException

Returns a Concept containing data from the MR Files.

Specified by:

readConcept in interface ConceptInputStream

Overrides:

readConcept in class OriginalMRFilesConceptInputStream

Returns:

a Concept containing data from the MR Files.

Throws:

IOException - if files could not be read

getPanel

public JPanel getPanel()

Returns GUI panel that will be displayed on one of the tabs on the main GUI window.

Specified by:

getPanel in interface GUIConfigurable

Returns:

JPanel that displays graphical interface for a tab

hasDataChanged

public boolean hasDataChanged()

Returns a boolean indicating whether or not the values on this gui have changed.

Specified by:

hasDataChanged in interface GUIConfigurable

Returns:

boolean true if data has changed false otherwise

setDataChanged

public void setDataChanged(boolean b)

Sets the "has data changed" flag.

Specified by:

setDataChanged in interface GUIConfigurable

Parameters:

b - boolean indicating whether or not the GUI configuration has changed

fireDataChanged

protected void fireDataChanged()

Enables filters to inform listeners of data changed event.

fireNotUndoableDataChanged

protected void fireNotUndoableDataChanged()

Enables filters to indicate that data has changed without notifying the listeners or making this change undoable.

getProperties

public Properties getProperties()

Returns the current state of the input stream as a Properties object.

Specified by:

getProperties in interface Configurable

Returns:

Properties only those directly related to the gui

setProperties

public void setProperties(Properties p)

Sets the current state of the input stream from a Properties object.

Specified by:

setProperties in interface Configurable

Parameters:

p - Properties pertaining to the gui

resetDataChanged

public void resetDataChanged()

Resets the "has data changed" flag to indicate that no changes have taken place since the last save.

Specified by:

resetDataChanged in interface GUIConfigurable

addDataChangeListener

public void addDataChangeListener(DataChangeListener dcl)

Adds a DataChangeListener that will be notified every time a fireDataChanged() call is made. Allows main GUI to record all changes to this gui in the undo/redo mechanism.

Specified by:

addDataChangeListener in interface GUIConfigurable

Parameters:

dcl - DataChangeListener

removeDataChangeListener

public void removeDataChangeListener(DataChangeListener dcl)

Removes a DataChangeListener so that it will no longer be notified every time a fireDataChanged() call is made from this gui.

Specified by:

removeDataChangeListener in interface GUIConfigurable

Parameters:

dcl - DataChangeListener

getColor

public Color getColor()

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

Specified by:

getColor in interface GUIConfigurable

Returns:

Color

getTabDescription

public String getTabDescription()

Returns the description of the screen and includes instructions on use.

Specified by:

getTabDescription in interface GUIConfigurable

Returns:

String text of filter instructions

resetToDefaults

public void resetToDefaults()

Resets the variables on a tab back to their default values. This is not used to actually change the gui. setPanelSelections() is always called after this method and will update the gui based on the variable values.

Specified by:

resetToDefaults in interface Configurable

showOptions

public void showOptions()

Presents an advanced options GUI to the user.

Specified by:

showOptions in interface GUIConfigurable

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

Returns:

true if so; false otherwise

getHelpPanel

public JPanel getHelpPanel()

Returns a JPanel that will be displayed when the user selects the corresponding menu item from the Help menu and will provide the user with detailed instructions on the tab's use.

Specified by:

getHelpPanel in interface GUIConfigurable

Returns:

JPanel to be added to the Help menu

setPanelSelections

public void setPanelSelections()

Applies the input stream state to the GUI panel.

Specified by:

setPanelSelections in interface GUIConfigurable

validate

public boolean validate()

Indicates whether or not the GUIConfigurable is valid.

Specified by:

validate in interface GUIConfigurable

Returns:

booleantrue if GUIConfigurable is valid false if GUIConfigurable is invalid

addValidationError

public void addValidationError(String validation_error)

Adds a validation error to the list of errors.

Parameters:

validation_error - String

clearValidationErrors

public void clearValidationErrors()

Clears the list of validation errors.

getValidationErrors

public String[] getValidationErrors()

Returns the messages indicating why validation failed. Should only be called if validate() returns false.

Specified by:

getValidationErrors in interface GUIConfigurable

Returns:

the failure messages

getValidationWarnings

public String[] getValidationWarnings()

Returns warnings that were indicated during validation.

Specified by:

getValidationWarnings in interface GUIConfigurable

Returns:

the warning messages

addValidationWarning

public void addValidationWarning(String validation_warning)

Adds a validation warning to the list of warnings.

Parameters:

validation_warning - String

clearValidationWarnings

public void clearValidationWarnings()

Clears the list of validation warnings.

getGUIConfigurableForValidationFailure

public GUIConfigurable getGUIConfigurableForValidationFailure()

Returns the GUIConfigurable whose tab should next be displayed to allow the user to correct an error or warning.

Specified by:

getGUIConfigurableForValidationFailure in interface GUIConfigurable

Returns:

GUIConfigurable to be displayed

validateSourcePaths

public boolean validateSourcePaths(String[] source_paths)

Validates the source paths. This involves checking that they both exist, are readable and that they have access to MR data.

Specified by:

validateSourcePaths in interface MetamorphoSysInputStream

Parameters:

source_paths - String[] to be validated

Returns:

true if validation passes false otherwise

validateSourcePath

public boolean validateSourcePath(String source_path)

Validates the source path. This involves checking that it both exists, is readable and that it has access to MR data.

Specified by:

validateSourcePath in interface MetamorphoSysInputStream

Parameters:

source_path - path to be validated

Returns:

true if validation passes false otherwise

validateVersions

public boolean validateVersions(String[] paths)

For each source path it attempts to determine the version of the release being used and validate it against the version from the properties file. If the version is determined to be a mismatch of if it cannot be determined, false is returned.

Specified by:

validateVersions in interface MetamorphoSysInputStream

Parameters:

paths - to be validated

Returns:

true if validation passes false otherwise

validateVersion

public boolean validateVersion(String source_path)

Attempts to determine the version of the release being used and validate it against the version from the properties file. If the version is determined to be a mismatch of if it cannot be determined, false is returned.

Specified by:

validateVersion in interface MetamorphoSysInputStream

Parameters:

source_path - to be validated

Returns:

true if validation passes false otherwise

beginInitializeCuiList

public void beginInitializeCuiList()

Informs SubsetListener that the Initialize Cui List phase is starting.

Specified by:

beginInitializeCuiList in interface SubsetListener

endInitializeCuiList

public void endInitializeCuiList()

Informs SubsetListener that the Initialize Cui List phase is ending.

Specified by:

endInitializeCuiList in interface SubsetListener

beginSubsetContent

public void beginSubsetContent()

Informs SubsetListener that the Subset Content phase is starting.

Specified by:

beginSubsetContent in interface SubsetListener

endSubsetContent

public void endSubsetContent()

Informs SubsetListener that the Subset Content phase is ending.

Specified by:

endSubsetContent in interface SubsetListener

getChooserType

public int getChooserType()

Indicates the type of file accepted by the JFileChooser.

Specified by:

getChooserType in interface MetamorphoSysInputStream

Returns:

int

setEfficientMode

public void setEfficientMode(boolean efficient)

Sets the subsetting mode to efficient. In the efficient mode, the "Initialize Cuis" phase of the subsetting only references MRCONSO and MRSTY.

Specified by:

setEfficientMode in interface MetamorphoSysInputStream

Parameters:

efficient - true if subsetting should be run in efficient mode false if not

isEfficientMode

public boolean isEfficientMode()

Returns the mode in which subsetting will be run. In the efficient mode, the "Initialize Cuis" phase of the subsetting only references MRCONSO and MRSTY.

Specified by:

isEfficientMode in interface MetamorphoSysInputStream

Returns:

true if subsetting will be run in efficent mode false otherwise

hasFullContextData

public boolean hasFullContextData()

Indicates whether this input source has full context data, such as that included in a MRCXT file.

Specified by:

hasFullContextData in interface MetamorphoSysInputStream

Returns:

true if this input source has full context data; false otherwise.

open

public void open(String[] install_paths)
          throws IOException

Opens all target files in the specified directory. The set of target files is the standard MR files.

Specified by:

open in interface ConceptInputStream

Overrides:

open in class OriginalMRMetathesaurusInputStream

Parameters:

install_paths - the subset directory

Throws:

IOException - if the files cannot be opened

compareTo

public int compareTo(Object o)

Compares this object with the specified object for order. Returns a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

Required method for implementing Comparable interface. Indicates the means for comparison between two MetamorphoSysInputStreams.

Specified by:

compareTo in interface Comparable

Parameters:

o - the Object to be compared.

Returns:

a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.

Throws:

ClassCastException - if the specified object's type is not GUIConfigurable.