gov.nih.nlm.mms
Class NLMFileMetamorphoSysInputStream

java.lang.Object
  extended bygov.nih.nlm.umls.io.RichMRFilesConceptInputStream
      extended bygov.nih.nlm.umls.io.RichMRMetathesaurusInputStream
          extended bygov.nih.nlm.mms.RichMRMetamorphoSysInputStream
              extended bygov.nih.nlm.mms.NLMFileMetamorphoSysInputStream
All Implemented Interfaces:
Comparable, ConceptInputStream, Configurable, GUIConfigurable, MetamorphoSysInputStream, MetathesaurusInputStream, SubsetListener

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, 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
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, 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, 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
 

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.


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