gov.nih.nlm.mms
Class OriginalMRMetamorphoSysOutputStream

java.lang.Object
  gov.nih.nlm.umls.io.OriginalMRFilesConceptOutputStream
      gov.nih.nlm.umls.io.OriginalMRMetathesaurusOutputStream
          gov.nih.nlm.mms.OriginalMRMetamorphoSysOutputStream

All Implemented Interfaces:

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

public class OriginalMRMetamorphoSysOutputStream
extends OriginalMRMetathesaurusOutputStream
implements MetamorphoSysOutputStream

Represents a MetamorphoSysOutputStream that writes a directory containing Original Release Format Metathesaurus files.

Author:

Deborah Shapiro

Field Summary

protected boolean	data_changed
protected ApplicationConfiguration	default_config
protected List	listeners
protected UserConfiguration	user_config

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

ancillary_files, change_files, config, lui_to_cui_set, sui_to_cui_set

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

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

Constructor Summary

OriginalMRMetamorphoSysOutputStream()
Instantiates an empty OriginalMRMetamorphoSysOutputStream.

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.
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 target 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 details of the configuration for use in a 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 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() Indicates whether or not the values on this gui have changed.
protected boolean	isLuiSuppressible(String lui, Atom[] atoms) Returns true if the specified LUI is suppressible.
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 "has 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 used for default settings.
void	setConfiguration(UserConfiguration user_config) Sets the UserConfiguration.
void	setCuiList(CuiList cui_list) Provides output stream access to the cui list.
void	setDataChanged(boolean b) Sets the "has data changed" flag.
void	setPanelSelections() Method makes selections on the panel.
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() This method indicates whether or not the GUIConfigurable is valid.
void	writeIndexEntry(IndexEntry ie) Writes index entries with the "remove utf8" settings in mind.
protected void	writeMRCXT(Concept concept) Writes MRCXT entries for a Concept.
protected void	writeMRDEF(Concept concept) Writes MRDEF entries for a Concept.
protected void	writeMRSAT(Concept concept) Writes MRSAT entries for a Concept.

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

ambigCheck, getColumnTextFromFileStatistics, getFileTextFromFileStatistics, setCandidateAmbiguousStringIdentifiers, setCandidateAmbiguousStringIdentifiers, setCandidateAmbiguousTermIdentifiers, setCandidateAmbiguousTermIdentifiers, writeConcept, writeFileColumnStats, writeMRCUI, writeMRRANK, writeMRSAB, writeReleaseMetadata

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

assignLrl, getNullValue, getWarnings, isEmptyValue, setNullValue, writeMRCON, writeMRSO

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

data_changed

protected boolean data_changed

listeners

protected List listeners

Constructor Detail

OriginalMRMetamorphoSysOutputStream

public OriginalMRMetamorphoSysOutputStream()
                                    throws IOException

Instantiates an empty OriginalMRMetamorphoSysOutputStream.

Throws:

IOException - if anything goes wrong

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)

Provides output stream access to the cui list.

Specified by:

setCuiList in interface SubsetListener

Parameters:

cui_list - CuiList

setConfiguration

public void setConfiguration(ApplicationConfiguration c)

Sets the ApplicationConfiguration used for default settings.

Specified by:

setConfiguration in interface Configurable

Parameters:

c - the ApplicationConfiguration

getConfigurationDetails

public String getConfigurationDetails()

Returns details of the configuration for use in a log.

Specified by:

getConfigurationDetails in interface Configurable

Returns:

details of the configuration for use in a log.

open

public void open(String mr_dir)
          throws IOException

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

Specified by:

open in interface ConceptOutputStream

Overrides:

open in class OriginalMRMetathesaurusOutputStream

Parameters:

mr_dir - the subset directory

Throws:

IOException - if the files cannot be opened

close

public void close()
           throws IOException

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

Specified by:

close in interface ConceptOutputStream

Overrides:

close in class OriginalMRMetathesaurusOutputStream

Throws:

IOException - if any files cannot be closed, or if the release.dat file or DB load scripts cannot be written.

isLuiSuppressible

protected boolean isLuiSuppressible(String lui,
                                    Atom[] atoms)

Returns true if the specified LUI is suppressible.

Overrides:

isLuiSuppressible in class OriginalMRFilesConceptOutputStream

Parameters:

lui - the LUI value to check

atoms - the Atoms

Returns:

true if the LUI is suppressible, false otherwise

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 OriginalMRFilesConceptOutputStream

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 OriginalMRFilesConceptOutputStream

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 OriginalMRFilesConceptOutputStream

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

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 OriginalMRMetathesaurusOutputStream

Parameters:

ie - IndexEntry to be written

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 OriginalMRMetathesaurusOutputStream

Parameters:

line - the line to be printed

file_name - printing destination

Throws:

IOException

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

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

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

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

hasDataChanged

public boolean hasDataChanged()

Indicates 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

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 "has 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 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()

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()

Method makes selections on the panel.

Specified by:

setPanelSelections in interface GUIConfigurable

validate

public boolean validate()

This method 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.

openTargetFile

protected BufferedWriter openTargetFile(String name)
                                 throws IOException

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

Overrides:

openTargetFile in class OriginalMRMetathesaurusOutputStream

Parameters:

name - the filename

Returns:

a BufferedWriter for the file

Throws:

IOException - if the file could not 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 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.