gov.nih.nlm.mms
Class NLMFileMetamorphoSysInputStream

java.lang.Object
  gov.nih.nlm.umls.io.RichMRFilesConceptInputStream
      gov.nih.nlm.umls.io.RichMRMetathesaurusInputStream
          gov.nih.nlm.mms.RichMRMetamorphoSysInputStream
              gov.nih.nlm.mms.NLMFileMetamorphoSysInputStream

All Implemented Interfaces:

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

public class NLMFileMetamorphoSysInputStream
extends RichMRMetamorphoSysInputStream

Represents a MetamorphoSysInputStream which are file(s) in the "NLM data file" format.

Author:

Deborah Shapiro

Field Summary

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

cui_list, default_config, user_configuration, validate_msg

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

current_index, index_counter, index_lines, mraui_source, mrcui_source, mrrank_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, null_value, rel_hm, this_concept, to_rsab, to_vsab, tokens, warnings

Constructor Summary

NLMFileMetamorphoSysInputStream()
Instantiates an empty NLMFileMetamorphoSysInputStream.

Method Summary

String	getConfigurationDetails() Returns a message for the log.
String	getName() Returns the short name for display purposes.
boolean	hasFullContextData() Indicates whether this input source has full context data, such as that included in a MRCXT file.
boolean	validateSourcePath(String source_path) Validates the source path.
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.

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

addDataChangeListener, beginInitializeCuiList, beginSubsetContent, close, compareTo, endInitializeCuiList, endSubsetContent, fireDataChanged, fireNotUndoableDataChanged, getChooserType, getColor, getGUIConfigurableForValidationFailure, getHelpPanel, getPanel, getProperties, getTabDescription, getValidateMessage, getValidationErrors, getValidationWarnings, hasAdvancedOptions, hasDataChanged, isEfficientMode, open, readConcept, removeDataChangeListener, resetDataChanged, resetToDefaults, setConfiguration, setConfiguration, setCuiList, setDataChanged, setEfficientMode, setPanelSelections, setProperties, showOptions, validate, validateSourcePaths, validateVersions

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

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

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

getAtoms, getAttributes, getComponentHistories, getConceptProgress, getContexts, getCoocurrences, getDefinitions, getMappings, getNullValue, getRelationships, getSemanticTypes, getWarnings, isEmptyValue, newInstanceFromMRCONSO, newInstanceFromMRHIER, openMRFiles, openSourceFile, setAdditionalSuffix, 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

getWarnings

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

getNullValue, isEmptyValue, setNullValue

Constructor Detail

NLMFileMetamorphoSysInputStream

public NLMFileMetamorphoSysInputStream()

Instantiates an empty NLMFileMetamorphoSysInputStream.

Method Detail

getName

public String getName()

Returns the short name for display purposes.

Specified by:

getName in interface GUIConfigurable

Overrides:

getName in class RichMRMetamorphoSysInputStream

Returns:

the short name for display purposes

getConfigurationDetails

public String getConfigurationDetails()

Returns a message for the log.

Specified by:

getConfigurationDetails in interface Configurable

Overrides:

getConfigurationDetails in class RichMRMetamorphoSysInputStream

Returns:

a message for the log

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

Overrides:

validateSourcePath in class RichMRMetamorphoSysInputStream

Parameters:

source_path - path 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

Overrides:

validateVersion in class RichMRMetamorphoSysInputStream

Parameters:

source_path - to be validated

Returns:

true if validation passes 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

Overrides:

hasFullContextData in class RichMRMetamorphoSysInputStream

Returns:

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