gov.nih.nlm.mms.cxt
Class MRCXTBuilder

java.lang.Object
  gov.nih.nlm.mms.AbstractGUIConfigurable
      gov.nih.nlm.mms.cxt.MRCXTBuilder

All Implemented Interfaces:

Configurable, GUIConfigurable, LocalNullValueSupport, Comparable

public class MRCXTBuilder
extends AbstractGUIConfigurable
implements LocalNullValueSupport

Application for building MRCXT.RRF from MRCONSO.RRF and MRHIER.RRF

Author:

Deborah Shapiro

Field Summary

protected boolean	null_value_flag
protected String	regex_null_value

Fields inherited from class gov.nih.nlm.mms.AbstractGUIConfigurable

data_changed, default_configuration, listeners, user_configuration

Constructor Summary

MRCXTBuilder()
Instantiates a MRCXTBuilder and builds the frame.

Method Summary

void	addSelectedSource(Source source) Indicates that the given Source will be included in the list of sources from which contexts will be built.
void	addSourceToList(Source source) Adds a Source to the full list.
void	buildIndexes() Builds indexes for MRCXT Builder processing if they do not already exist.
void	disableGlassPane() Disable glass pane.
List	disqualifySourcesFromList(List source_candidates) Returns modified List from given list of source candidates.
void	enableGlassPane() Enable glass pane.
boolean	getAddUnicodeBOM() Indicates if the UTF8 Byte Order Mark (BOM) should be prepended to the output MRCXT.RRF.
boolean	getBuildChildren() Indicates if context children should be written to MRCXT.RRF.
boolean	getBuildSiblings() Indicates if context siblings should be written to MRCXT.RRF.
boolean	getComputeXC() Indicates if the XC flag should be computed for MRCXT.RRF.
MRCXTBuilderGUI	getGui() Returns the MRCXTBuilderGUI.
List	getIncludedSources() Returns List of Sources that have been selected to be included in MRCXT.RRF.
boolean	getMaxContexts() Indicates if there is a maximum number of contexts that will be written to MRCXT.RRF for any given atom/sab.
int	getMaxContextsCount() Indicates the maximum number of contexts that will be written to MRCXT.RRF for any given atom/sab assuming that the corresponding checkbox is selected.
String	getNullValue() Returns the null value.
JPanel	getPanel() Returns the GUI panel that will display the user iterface.
Properties	getProperties() Returns the current state of the MRCXTBuilder as a Properties object.
int	getRowForSource(Source source) Returns the index of the row in the table for a given Source
File	getSourceDir() Returns the File where the MRHIER.RRF will be found and the MRCXT.RRF should be written.
List	getSourceList() Returns the full list of sources.
Source[]	getSourceListAsArray() Returns the full list of sources.
JTable	getSourceTable() Returns the JTable that displays the list of sources.
boolean	getVersionedSabs() Indicates if MRCXT.RRF should be written with versioned or versionless source abbreviations.
boolean	getWriteMRCXTFileStatistics() Indicates if statistics should be computed for MRCXT.RRF.
boolean	isEmptyValue(String token) Indicates whether or not the specified token is null or contains a null value as defined by being either zero length or a value equal to the null value.
void	makeMRCXT(ProgressMonitor progress) Calls the MRCXTBuilderOutputStream and instructs it to write the MRCXT.RRF file.
void	removeSelectedSource(Source source) Indicates that the given Source will not have contexts built from it.
void	resetToDefaults() Resets MRCXTBuilder state to default.
protected String	resolveNull(String line) Replaces all "null value" characters in the line.
void	setAddUnicodeBOM(boolean add_unicode_bom) Sets the parameter indicating if the UTF8 Byte Order Mark (BOM) should be prepended to the output MRCXT.RRF.
void	setBuildChildren(boolean build_children) Sets the parameter indicating if children should be built or not
void	setBuildSiblings(boolean build_siblings) Sets the parameter indicating if siblings should be built or not
void	setComputeXC(boolean compute_xc) Sets the parameter indicating if the XC flag should be computed for MRCXT.RRF.
void	setEnableComponents() Logic for control of enabling and disabling gui components.
void	setGui(MRCXTBuilderGUI gui) Sets the MRCXTBuilderGUI.
void	setMaxContexts(boolean max_contexts) Sets if there is a maximum number of contexts that will be written to MRCXT.RRF for any given atom/sab.
void	setMaxContextsCount(int max_contexts_count) Sets the maximum number of contexts that will be written to MRCXT.RRF for any given atom/sab assuming that the corresponding checkbox is selected .
void	setNullValue(String null_value) Sets the null value to use.
void	setPanelSelections() Applies state to panel selections.
void	setProperties(Properties p) Sets the current state of the MRCXTBuilder from a Properties object.
void	setSelectedSourceSet(Set source_set) Supplies the Set of Sources that are selected for inclusion in the built MRCXT.RRF
void	setSourceDir(File source_dir) Sets the File where the MRHIER.RRF will be found and the MRCXT.RRF should be written.
void	setSourceList(List sources) Sets the full list of Sources.
void	setSourceList(Source[] sources) Sets the source list to the given Source[]
void	setVersionedSabs(boolean versioned_sabs) Sets the parameter indicating if MRCXT.RRF should be written with versioned or versionless source abbreviations.
void	setWriteMRCXTFileStatistics(boolean write_mrcxt_file_statistics) Sets the parameter indicating if statistics should be computed for MRCXT.RRF.
void	subsetDirectoryOpened(File source_dir) Handles opening of a source directory.

Methods inherited from class gov.nih.nlm.mms.AbstractGUIConfigurable

addDataChangeListener, addValidationError, addValidationWarning, clearValidationErrors, clearValidationWarnings, compareTo, fireDataChanged, getColor, getConfigurationDetails, getGUIConfigurableForValidationFailure, getHelpPanel, getName, getTabDescription, getValidationErrors, getValidationWarnings, hasAdvancedOptions, hasDataChanged, removeDataChangeListener, resetDataChanged, setConfiguration, setConfiguration, setDataChanged, showOptions, validate

Methods inherited from class java.lang.Object

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

Field Detail

regex_null_value

protected String regex_null_value

null_value_flag

protected boolean null_value_flag

Constructor Detail

MRCXTBuilder

public MRCXTBuilder()

Instantiates a MRCXTBuilder and builds the frame.

Method Detail

getPanel

public JPanel getPanel()

Returns the GUI panel that will display the user iterface.

Specified by:

getPanel in interface GUIConfigurable

Overrides:

getPanel in class AbstractGUIConfigurable

Returns:

JPanel that displays graphical interface for the application.

subsetDirectoryOpened

public void subsetDirectoryOpened(File source_dir)

Handles opening of a source directory. Should be called from a separate thread.

Parameters:

source_dir - the source directory

disqualifySourcesFromList

public List disqualifySourcesFromList(List source_candidates)

Returns modified List from given list of source candidates. Sources are removed if their concept count = 0 or they are without contexts or they are not in the current subset

Parameters:

source_candidates -

Returns:

qualified subset

getSourceList

public List getSourceList()

Returns the full list of sources.

Returns:

List of sources

getSourceListAsArray

public Source[] getSourceListAsArray()

Returns the full list of sources.

Returns:

Source[] of sources

getSourceTable

public JTable getSourceTable()

Returns the JTable that displays the list of sources.

Returns:

JTable

getRowForSource

public int getRowForSource(Source source)

Returns the index of the row in the table for a given Source

Parameters:

source - Source

Returns:

int

setSourceList

public void setSourceList(Source[] sources)

Sets the source list to the given Source[]

Parameters:

sources - array

addSourceToList

public void addSourceToList(Source source)

Adds a Source to the full list.

Parameters:

source - Source

setSourceList

public void setSourceList(List sources)

Sets the full list of Sources.

Parameters:

sources - List

addSelectedSource

public void addSelectedSource(Source source)

Indicates that the given Source will be included in the list of sources from which contexts will be built.

Parameters:

source - Source to be included in context building

removeSelectedSource

public void removeSelectedSource(Source source)

Indicates that the given Source will not have contexts built from it.

Parameters:

source - Source to be excluded from context building

setSelectedSourceSet

public void setSelectedSourceSet(Set source_set)

Supplies the Set of Sources that are selected for inclusion in the built MRCXT.RRF

Parameters:

source_set -

buildIndexes

public void buildIndexes()

Builds indexes for MRCXT Builder processing if they do not already exist.

getBuildSiblings

public boolean getBuildSiblings()

Indicates if context siblings should be written to MRCXT.RRF.

Returns:

true if siblings should be built false otherwise

setBuildSiblings

public void setBuildSiblings(boolean build_siblings)

Sets the parameter indicating if siblings should be built or not

Parameters:

build_siblings -

getBuildChildren

public boolean getBuildChildren()

Indicates if context children should be written to MRCXT.RRF.

Returns:

true if children should be built false otherwise

setBuildChildren

public void setBuildChildren(boolean build_children)

Sets the parameter indicating if children should be built or not

Parameters:

build_children -

getComputeXC

public boolean getComputeXC()

Indicates if the XC flag should be computed for MRCXT.RRF.

Returns:

true if yes false otherwise

setComputeXC

public void setComputeXC(boolean compute_xc)

Sets the parameter indicating if the XC flag should be computed for MRCXT.RRF.

Parameters:

compute_xc -

getMaxContextsCount

public int getMaxContextsCount()

Indicates the maximum number of contexts that will be written to MRCXT.RRF for any given atom/sab assuming that the corresponding checkbox is selected.

Returns:

int maximum contexts

getMaxContexts

public boolean getMaxContexts()

Indicates if there is a maximum number of contexts that will be written to MRCXT.RRF for any given atom/sab.

Returns:

boolean true if limited false false otherwise

setMaxContextsCount

public void setMaxContextsCount(int max_contexts_count)

Sets the maximum number of contexts that will be written to MRCXT.RRF for any given atom/sab assuming that the corresponding checkbox is selected .

Parameters:

max_contexts_count -

setMaxContexts

public void setMaxContexts(boolean max_contexts)

Sets if there is a maximum number of contexts that will be written to MRCXT.RRF for any given atom/sab.

Parameters:

max_contexts - true if limited false false otherwise

setNullValue

public void setNullValue(String null_value)

Sets the null value to use. This is needed if release.dat specifies some non-standard null value char sequence.

Specified by:

setNullValue in interface LocalNullValueSupport

Parameters:

null_value - the new null string value

getNullValue

public String getNullValue()

Returns the null value. This is needed if release.dat specifies some non-standard null value char sequence.

Specified by:

getNullValue in interface LocalNullValueSupport

Returns:

the string value for "null"

isEmptyValue

public boolean isEmptyValue(String token)

Indicates whether or not the specified token is null or contains a null value as defined by being either zero length or a value equal to the null value.

Specified by:

isEmptyValue in interface LocalNullValueSupport

resolveNull

protected String resolveNull(String line)

Replaces all "null value" characters in the line.

Parameters:

line - input line

Returns:

output line

setAddUnicodeBOM

public void setAddUnicodeBOM(boolean add_unicode_bom)

Sets the parameter indicating if the UTF8 Byte Order Mark (BOM) should be prepended to the output MRCXT.RRF.

Parameters:

add_unicode_bom -

getAddUnicodeBOM

public boolean getAddUnicodeBOM()

Indicates if the UTF8 Byte Order Mark (BOM) should be prepended to the output MRCXT.RRF.

Returns:

true if BOM is required false if not

setWriteMRCXTFileStatistics

public void setWriteMRCXTFileStatistics(boolean write_mrcxt_file_statistics)

Sets the parameter indicating if statistics should be computed for MRCXT.RRF.

Parameters:

write_mrcxt_file_statistics -

getWriteMRCXTFileStatistics

public boolean getWriteMRCXTFileStatistics()

Indicates if statistics should be computed for MRCXT.RRF.

Returns:

true if statistics should be computed false if not

setVersionedSabs

public void setVersionedSabs(boolean versioned_sabs)

Sets the parameter indicating if MRCXT.RRF should be written with versioned or versionless source abbreviations.

Parameters:

versioned_sabs -

getVersionedSabs

public boolean getVersionedSabs()

Indicates if MRCXT.RRF should be written with versioned or versionless source abbreviations.

Returns:

true if versioned false if versionless

getSourceDir

public File getSourceDir()

Returns the File where the MRHIER.RRF will be found and the MRCXT.RRF should be written.

Returns:

File directory

setSourceDir

public void setSourceDir(File source_dir)
                  throws IOException

Sets the File where the MRHIER.RRF will be found and the MRCXT.RRF should be written.

Parameters:

source_dir - File directory

Throws:

IOException

getIncludedSources

public List getIncludedSources()

Returns List of Sources that have been selected to be included in MRCXT.RRF.

Returns:

List of included Sources

makeMRCXT

public void makeMRCXT(ProgressMonitor progress)

Calls the MRCXTBuilderOutputStream and instructs it to write the MRCXT.RRF file.

Parameters:

progress -

setGui

public void setGui(MRCXTBuilderGUI gui)

Sets the MRCXTBuilderGUI.

Parameters:

gui -

getGui

public MRCXTBuilderGUI getGui()

Returns the MRCXTBuilderGUI.

Returns:

gui

setEnableComponents

public void setEnableComponents()

Logic for control of enabling and disabling gui components.

resetToDefaults

public void resetToDefaults()

Resets MRCXTBuilder state to default.

Specified by:

resetToDefaults in interface Configurable

Overrides:

resetToDefaults in class AbstractGUIConfigurable

setPanelSelections

public void setPanelSelections()

Applies state to panel selections.

Specified by:

setPanelSelections in interface GUIConfigurable

Overrides:

setPanelSelections in class AbstractGUIConfigurable

getProperties

public Properties getProperties()

Returns the current state of the MRCXTBuilder as a Properties object.

Specified by:

getProperties in interface Configurable

Overrides:

getProperties in class AbstractGUIConfigurable

Returns:

Properties only those directly related to the gui

setProperties

public void setProperties(Properties p)

Sets the current state of the MRCXTBuilder from a Properties object.

Specified by:

setProperties in interface Configurable

Overrides:

setProperties in class AbstractGUIConfigurable

Parameters:

p - Properties only those directly related to the gui

enableGlassPane

public void enableGlassPane()

Enable glass pane.

disableGlassPane

public void disableGlassPane()

Disable glass pane.