gov.nih.nlm.mms
Class RichMRMetamorphoSysOutputStream

java.lang.Object
  gov.nih.nlm.umls.io.RichMRFilesConceptOutputStream
      gov.nih.nlm.umls.io.RichMRMetathesaurusOutputStream
          gov.nih.nlm.mms.RichMRMetamorphoSysOutputStream

All Implemented Interfaces:

Configurable, GUIConfigurable, MetamorphoSysOutputStream, SubsetListener, ConceptOutputStream, MetathesaurusOutputStream, LocalNullValueSupport, ProgressReporter, Comparable

public class RichMRMetamorphoSysOutputStream
extends RichMRMetathesaurusOutputStream
implements MetamorphoSysOutputStream

This MetamorphoSysOutputStream obtains data from the MetamorphoSys subset routine and generates a subset of Rich Release MR files.

Author:

Deborah Shapiro

Field Summary

protected ApplicationConfiguration	default_config
protected UserConfiguration	user_config

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

ancillary_files, atoms, change_files, config, lui_to_cui_set, sui_to_cui_set

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

add_unicode_bom, file_ext, mr_dir, mr_targets, null_value, target_files, target_to_output_stream, versioned_output, warnings

Constructor Summary

RichMRMetamorphoSysOutputStream()
Instantiates an empty RichMRMetamorphoSysOutputStream.

Method Summary

void	addDataChangeListener(DataChangeListener dcl) Adds a DataChangeListener that will be notified every time a fireDataChanged() call is made.
boolean	addUnicodeBom() Indicates whether or not the output stream is configured to prepend the UTF-8 BOM character.
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.
boolean	calculateMD5s() Indicates whether or not the output stream is configured to calculate md5 values for all of the output files.
void	clearValidationErrors() Clears the list of validation errors.
void	clearValidationWarnings() Clears the list of validation warnings.
void	close() Closes source files that were opened by this class's openTargets() method.
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.
Color	getColor() Indicates 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 the GUI panel that will be displayed on one of the tabs on the main GUI window.
Properties	getProperties() Returns the current state of the output stream as a Properties object.
String	getTabDescription() Returns a 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.
void	open(String mr_dir) Opens all target files in the specified directory.
protected BufferedWriter	openTargetFile(String name) Opens the specified file in the directory passed to open(String).
protected void	printLine(String line, String file_name) Prints the given line to the file with the given name.
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.
boolean	removeMTHOnlyConcepts() Indicates whether or not the output stream is configured to remove concepts with only MTH atoms.
boolean	removeUnicode() Indicates whether or not the output stream is configured to remove non-ASCII Unicode lines.
void	resetDataChanged() Resets the data_changed flag to indicate that no data has been changed since the last save.
void	resetToDefaults() Provides a mechanism for resetting the variables on a tab back to their default values.
void	setConfiguration(ApplicationConfiguration c) Sets the ApplicationConfiguration.
void	setConfiguration(UserConfiguration user_config) Sets the UserConfiguration.
void	setCuiList(CuiList cui_list) Sets the CuiList reference.
void	setDataChanged(boolean b) Sets the "has data changed" flag.
void	setPanelSelections() Applies the state of the output stream to the GUI.
void	setProperties(Properties p) Sets the current state of the output 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	validateSubsetDirectory(File subset_directory) Indicates whether or not specified directory is valid.
void	writeIndexEntry(IndexEntry ie) Writes index entries with the "remove utf8" settings in mind.
protected void	writeMRCONSO(Concept concept) Writes MRCONSO.RRF entries for a Concept.
protected void	writeMRCXT(Concept concept) Writes MRCXT entries for a Concept.
protected void	writeMRDEF(Concept concept) Writes MRDEF entries for a Concept.
protected void	writeMRDOC(ReleaseMetadata release_metadata) Write release_info lines to the MRDOC.RRF file, ensuring no duplicates.
protected void	writeMRSAT(Concept concept) Writes MRSAT entries for a Concept.

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

addProgressListener, ambigCheck, fireProgressEvent, getColumnTextFromFileStatistics, getFileTextFromFileStatistics, removeProgressListener, setCandidateAmbiguousStringIdentifiers, setCandidateAmbiguousStringIdentifiers, setCandidateAmbiguousTermIdentifiers, setCandidateAmbiguousTermIdentifiers, writeConcept, writeFileColumnStats, writeMRAUI, writeMRCUI, writeMRRANK, writeMRSAB, writeReleaseMetadata

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

flush, getFilePosition, getNullValue, getWarnings, isEmptyValue, setNullValue, writeMRCOC, writeMRHIER, writeMRHIST, writeMRMAP, writeMRREL, writeMRSMAP, writeMRSTY

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.umls.io.MetathesaurusOutputStream

setCandidateAmbiguousStringIdentifiers, setCandidateAmbiguousStringIdentifiers, setCandidateAmbiguousTermIdentifiers, setCandidateAmbiguousTermIdentifiers, writeReleaseMetadata

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

getWarnings, writeConcept

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

getNullValue, isEmptyValue, setNullValue

Field Detail

user_config

protected UserConfiguration user_config

default_config

protected ApplicationConfiguration default_config

Constructor Detail

RichMRMetamorphoSysOutputStream

public RichMRMetamorphoSysOutputStream()
                                throws IOException

Instantiates an empty RichMRMetamorphoSysOutputStream.

Throws:

IOException

Method Detail

getName

public String getName()

Returns the short name for display purposes.

Specified by:

getName in interface GUIConfigurable

Returns:

the short name for display purposes.

setConfiguration

public void setConfiguration(UserConfiguration user_config)

Sets the UserConfiguration.

Specified by:

setConfiguration in interface Configurable

Parameters:

user_config - the UserConfiguration.

setCuiList

public void setCuiList(CuiList cui_list)

Sets the CuiList reference.

Specified by:

setCuiList in interface SubsetListener

Parameters:

cui_list - the CuiList

setConfiguration

public void setConfiguration(ApplicationConfiguration c)

Sets the ApplicationConfiguration.

Specified by:

setConfiguration in interface Configurable

Parameters:

c - the ApplicationConfiguration

getConfigurationDetails

public String getConfigurationDetails()

Returns a message for the log.

Specified by:

getConfigurationDetails in interface Configurable

Returns:

a message for the log

open

public void open(String mr_dir)
          throws IOException

Opens all target files in the specified directory. The set of target files are of the Rich Release Format.

Specified by:

open in interface ConceptOutputStream

Overrides:

open in class RichMRMetathesaurusOutputStream

Parameters:

mr_dir - the subset directory

Throws:

IOException - if the files cannot be opened

close

public void close()
           throws IOException

Closes source files that were opened by this class's openTargets() method.

Specified by:

close in interface ConceptOutputStream

Overrides:

close in class RichMRMetathesaurusOutputStream

Throws:

IOException

openTargetFile

protected BufferedWriter openTargetFile(String name)
                                 throws IOException

Opens the specified file in the directory passed to open(String).

Overrides:

openTargetFile in class RichMRMetathesaurusOutputStream

Parameters:

name - the filename

Returns:

a BufferedWriter for the file

Throws:

IOException - if the file could not be opened.

getPanel

public JPanel getPanel()

Returns the 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 data has changed

getProperties

public Properties getProperties()

Returns the current state of the output 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 output stream from a Properties object.

Specified by:

setProperties in interface Configurable

Parameters:

p - Properties only those directly related to the gui

resetDataChanged

public void resetDataChanged()

Resets the data_changed flag to indicate that no data has been changed 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()

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

Specified by:

getColor in interface GUIConfigurable

Returns:

Color

getTabDescription

public String getTabDescription()

Returns a 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()

Provides a mechanism for resetting 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 state of the output stream to the GUI.

Specified by:

setPanelSelections in interface GUIConfigurable

validateSubsetDirectory

public boolean validateSubsetDirectory(File subset_directory)

Indicates whether or not specified directory is valid.

Returns:

booleantrue if GUIConfigurable is valid false if GUIConfigurable is invalid

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

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.

writeMRDOC

protected void writeMRDOC(ReleaseMetadata release_metadata)
                   throws IOException

Write release_info lines to the MRDOC.RRF file, ensuring no duplicates.

Overrides:

writeMRDOC in class RichMRMetathesaurusOutputStream

Parameters:

release_metadata - the ReleaseMetadata

Throws:

IOException - if anything goes wrong

writeMRDEF

protected void writeMRDEF(Concept concept)
                   throws IOException

Writes MRDEF entries for a Concept. Truncates long fields and/or removes unicode characters as user specifies.

Overrides:

writeMRDEF in class RichMRFilesConceptOutputStream

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRSAT

protected void writeMRSAT(Concept concept)
                   throws IOException

Writes MRSAT entries for a Concept. Truncates long fields and/or removes unicode characters as user specifies.

Overrides:

writeMRSAT in class RichMRFilesConceptOutputStream

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRCXT

protected void writeMRCXT(Concept concept)
                   throws IOException

Writes MRCXT entries for a Concept. Truncates long fields and/or removes unicode characters as user specifies.

Overrides:

writeMRCXT in class RichMRFilesConceptOutputStream

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRCONSO

protected void writeMRCONSO(Concept concept)
                     throws IOException

Writes MRCONSO.RRF entries for a Concept. Also writes modified MRXNW.ENG file that tallies sui word count as well.

Overrides:

writeMRCONSO in class RichMRFilesConceptOutputStream

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

printLine

protected void printLine(String line,
                         String file_name)
                  throws IOException

Prints the given line to the file with the given name.

Overrides:

printLine in class RichMRMetathesaurusOutputStream

Parameters:

line - the line to be printed

file_name - printing destination

Throws:

IOException

writeIndexEntry

public void writeIndexEntry(IndexEntry ie)
                     throws IOException

Writes index entries with the "remove utf8" settings in mind.

Specified by:

writeIndexEntry in interface MetathesaurusOutputStream

Overrides:

writeIndexEntry in class RichMRMetathesaurusOutputStream

Parameters:

ie - IndexEntry to be written

Throws:

IOException - if anything goes wrong

removeUnicode

public boolean removeUnicode()

Indicates whether or not the output stream is configured to remove non-ASCII Unicode lines.

Specified by:

removeUnicode in interface MetamorphoSysOutputStream

Returns:

true if so, false otherwise

addUnicodeBom

public boolean addUnicodeBom()

Indicates whether or not the output stream is configured to prepend the UTF-8 BOM character.

Returns:

true if so, false otherwise

removeMTHOnlyConcepts

public boolean removeMTHOnlyConcepts()

Indicates whether or not the output stream is configured to remove concepts with only MTH atoms.

Specified by:

removeMTHOnlyConcepts in interface MetamorphoSysOutputStream

Returns:

boolean

calculateMD5s

public boolean calculateMD5s()

Indicates whether or not the output stream is configured to calculate md5 values for all of the output files.

Returns:

boolean

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

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 MetamorphoSysOutputStreams.

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.