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java.lang.Objectgov.nih.nlm.umls.io.RichMRFilesConceptInputStream
gov.nih.nlm.umls.io.RichMRMetathesaurusInputStream
gov.nih.nlm.mms.RichMRMetamorphoSysInputStream
Represents a MetamorphoSysInputStream
that reads content from a
directory containing Rich Release Format Metathesaurus files.
Field Summary | |
protected CuiList |
cui_list
|
protected ApplicationConfiguration |
default_config
|
protected UserConfiguration |
user_configuration
|
protected String |
validate_msg
|
Fields inherited from class gov.nih.nlm.umls.io.RichMRMetathesaurusInputStream |
current_index, index_counter, index_lines, mraui_source, mrcui_source, mrsab_source, mrx_sources |
Fields inherited from class gov.nih.nlm.umls.io.RichMRFilesConceptInputStream |
add_suffix, atom_hm, file_names, from_rsab, from_vsab, install_paths, mrcoc_source, mrconso_counter, mrconso_lines, mrconso_source, mrcxt_source, mrdef_source, mrdoc_source, mrhier_source, mrhist_source, mrmap_source, mrrel_source, mrsat_source, mrsty_source, rel_hm, this_concept, to_rsab, to_vsab, tokens |
Constructor Summary | |
RichMRMetamorphoSysInputStream()
Instantiates an empty RichMRMetamorphoSysInputStream . |
Method Summary | |
void |
addDataChangeListener(DataChangeListener dcl)
Adds a DataChangeListener that will be notified every time a
fireDataChanged() call is made. |
void |
beginInitializeCuiList()
Informs SubsetListener that the Initialize Cui List phase is
starting. |
void |
beginSubsetContent()
Informs SubsetListener that the Subset Content phase is starting. |
void |
close()
Close files opened during RichMRMetathesaurusInputStream.open(String[]) . |
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()
Provides 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 a basic description of how to configure the input stream. |
String |
getValidateMessage()
Returns the message that the user will see if this GUIConfigurable
is invalid. |
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. |
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 data has been changed since the last save. |
void |
resetToDefaults()
Resets the state of the input stream to its default state. |
void |
setConfiguration(ApplicationConfiguration c)
Sets the ApplicationConfiguration representing the default state. |
void |
setConfiguration(UserConfiguration user_configuration)
Sets the UserConfiguration . |
void |
setCuiList(CuiList cui_list)
Sets the CuiList reference. |
void |
setDataChanged(boolean b)
Sets the "has data changed" value. |
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.RichMRMetathesaurusInputStream |
getAmbiguousStringIdentifiers, getAmbiguousStringIdentifiersAsList, getAmbiguousTermIdentifiers, getAmbiguousTermIdentifiersAsList, getIndexProgress, getLineCounts, open, readIndexEntry, readReleaseMetadata |
Methods inherited from class gov.nih.nlm.umls.io.RichMRFilesConceptInputStream |
getAtoms, getAttributes, getComponentHistories, getConceptProgress, getContexts, getCoocurrences, getDefinitions, getMappings, getRelationships, getSemanticTypes, newInstanceFromMRCONSO, newInstanceFromMRHIER, openMRFiles, openSourceFile, setAdditionalSuffix |
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 |
open |
Field Detail |
protected UserConfiguration user_configuration
protected ApplicationConfiguration default_config
protected CuiList cui_list
protected String validate_msg
Constructor Detail |
public RichMRMetamorphoSysInputStream()
RichMRMetamorphoSysInputStream
.
Method Detail |
public void setConfiguration(UserConfiguration user_configuration)
UserConfiguration
.
setConfiguration
in interface Configurable
user_configuration
- the UserConfiguration
.public String getName()
getName
in interface GUIConfigurable
public String getConfigurationDetails()
getConfigurationDetails
in interface Configurable
public void setCuiList(CuiList cui_list)
CuiList
reference.
setCuiList
in interface SubsetListener
cui_list
- CuiList
public Concept readConcept() throws IOException
Concept
containing data from the MR Files. Different from
UMLS objects implementation in that it requires that the Concept
be
present on the CuiList
before reading the Concept
's data
from the MR Files.
readConcept
in interface ConceptInputStream
readConcept
in class RichMRFilesConceptInputStream
Concept
containing data from the MR Files.
IOException
- if files could not be readpublic void close() throws IOException
RichMRMetathesaurusInputStream.open(String[])
.
close
in interface ConceptInputStream
close
in class RichMRMetathesaurusInputStream
IOException
- if files can not be closedpublic JPanel getPanel()
getPanel
in interface GUIConfigurable
JPanel
that displays graphical interface for a tabpublic boolean hasDataChanged()
hasDataChanged
in interface GUIConfigurable
boolean
true
if data has changed
false
otherwisepublic void setDataChanged(boolean b)
setDataChanged
in interface GUIConfigurable
b
- boolean
indicating whether or not data in the GUI
configuration has changed.public Properties getProperties()
Properties
object.
getProperties
in interface Configurable
Properties
only those directly related to the guipublic void setProperties(Properties p)
Properties
object.
setProperties
in interface Configurable
p
- Properties
pertaining to the guipublic void resetDataChanged()
resetDataChanged
in interface GUIConfigurable
public void addDataChangeListener(DataChangeListener dcl)
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.
addDataChangeListener
in interface GUIConfigurable
dcl
- DataChangeListener
public void removeDataChangeListener(DataChangeListener dcl)
DataChangeListener
so that it will no longer be notified
every time a fireDataChanged()
call is made from this gui.
removeDataChangeListener
in interface GUIConfigurable
dcl
- DataChangeListener
public Color getColor()
Color
that should be used to display the name.
getColor
in interface GUIConfigurable
Color
public String getTabDescription()
getTabDescription
in interface GUIConfigurable
String
text of input stream instructionspublic void resetToDefaults()
resetToDefaults
in interface Configurable
public void showOptions()
showOptions
in interface GUIConfigurable
public boolean hasAdvancedOptions()
hasAdvancedOptions
in interface GUIConfigurable
true
if so; false
otherwisepublic JPanel getHelpPanel()
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.
getHelpPanel
in interface GUIConfigurable
JPanel
to be added to the Help menupublic void setPanelSelections()
setPanelSelections
in interface GUIConfigurable
public boolean validate()
GUIConfigurable
is valid.
validate
in interface GUIConfigurable
boolean
true
if
GUIConfigurable
is valid false
if
GUIConfigurable
is invalidpublic String getValidateMessage()
GUIConfigurable
is invalid.
String
with error messagepublic String[] getValidationErrors()
validate()
returns false
.
getValidationErrors
in interface GUIConfigurable
public String[] getValidationWarnings()
getValidationWarnings
in interface GUIConfigurable
public GUIConfigurable getGUIConfigurableForValidationFailure()
GUIConfigurable
whose tab should next be displayed to
allow the user to correct an error or warning.
getGUIConfigurableForValidationFailure
in interface GUIConfigurable
public boolean validateSourcePaths(String[] source_paths)
validateSourcePaths
in interface MetamorphoSysInputStream
source_paths
- to be validated
true
if validation passes false
otherwisepublic boolean validateSourcePath(String source_path)
validateSourcePath
in interface MetamorphoSysInputStream
source_path
- path to be validated
true
if validation passes false
otherwisepublic boolean validateVersions(String[] paths)
false
is returned.
validateVersions
in interface MetamorphoSysInputStream
paths
- to be validated
true
if validation passes false
otherwisepublic boolean validateVersion(String source_path)
false
is
returned.
validateVersion
in interface MetamorphoSysInputStream
source_path
- to be validated
true
if validation passes false
otherwiseprotected void fireDataChanged()
protected void fireNotUndoableDataChanged()
public int getChooserType()
JFileChooser
.
getChooserType
in interface MetamorphoSysInputStream
String
public void setConfiguration(ApplicationConfiguration c)
ApplicationConfiguration
representing the default state.
setConfiguration
in interface Configurable
c
- ApplicationConfiguration
public void beginInitializeCuiList()
SubsetListener
that the Initialize Cui List phase is
starting.
beginInitializeCuiList
in interface SubsetListener
public void endInitializeCuiList()
SubsetListener
that the Initialize Cui List phase is
ending.
endInitializeCuiList
in interface SubsetListener
public void beginSubsetContent()
SubsetListener
that the Subset Content phase is starting.
beginSubsetContent
in interface SubsetListener
public void endSubsetContent()
SubsetListener
that the Subset Content phase is ending.
endSubsetContent
in interface SubsetListener
public void setEfficientMode(boolean efficient)
setEfficientMode
in interface MetamorphoSysInputStream
efficient
- true
if subsetting should be run in efficient mode
false
if notpublic boolean isEfficientMode()
isEfficientMode
in interface MetamorphoSysInputStream
true
if subsetting will be run in efficent mode
false
otherwisepublic boolean hasFullContextData()
hasFullContextData
in interface MetamorphoSysInputStream
true
if this input source has full context data;
false
otherwise.public int compareTo(Object o)
Required method for implementing
Comparable
interface.
Indicates the means for comparison between two
MetamorphoSysInputStream
s.
compareTo
in interface Comparable
o
- the Object to be compared.
ClassCastException
- if the specified object's type is not
GUIConfigurable
.
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