gov.nih.nlm.umls.io
Class RichMRMetathesaurusInputStream

java.lang.Object
  gov.nih.nlm.umls.io.RichMRFilesConceptInputStream
      gov.nih.nlm.umls.io.RichMRMetathesaurusInputStream

All Implemented Interfaces:

ConceptInputStream, MetathesaurusInputStream, LocalNullValueSupport

Direct Known Subclasses:

RichMRMetamorphoSysInputStream

public class RichMRMetathesaurusInputStream
extends RichMRFilesConceptInputStream
implements MetathesaurusInputStream

This ConceptInputStream builds objects from a full set of "Rich Release Format" MR files.

Author:

Deborah Shapiro

Field Summary

protected int	current_index
protected int	index_counter
protected int	index_lines
protected BufferedReader	mraui_source
protected BufferedReader	mrcui_source
protected BufferedReader	mrrank_source
protected BufferedReader	mrsab_source
protected BufferedReader[]	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

RichMRMetathesaurusInputStream()
Instantiates an empty RichMRMetathesaurusInputStream;

Method Summary

void	close() Close files opened during open(String[]).
String[]	getAmbiguousStringIdentifiers() Returns the complete list of suis from the AMBIGSUI list.
List	getAmbiguousStringIdentifiersAsList() Returns the complete list of suis from the AMBIGSUI list.
String[]	getAmbiguousTermIdentifiers() Returns the complete list of terms from the AMBIGLUI list.
List	getAmbiguousTermIdentifiersAsList() Returns the complete list of terms from the AMBIGLUI list.
int	getIndexProgress() Returns the percentage of the index file lines that have been processed.
protected Map	getLineCounts() Reads through MRFILES.RRF to determine the size of the index files.
void	open(String[] install_paths) Opens all of the MR Files in preparation for subsetting.
IndexEntry	readIndexEntry() Returns an IndexEntry from one of the index files.
ReleaseMetadata	readReleaseMetadata() Returns the ReleaseMetadata containing data from MRSAB.RRF, MRCUI.RRF, MRAUI.RRF, and MRDOC.RRF.

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, readConcept, 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.umls.io.ConceptInputStream

getConceptProgress, getWarnings, readConcept

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

getNullValue, isEmptyValue, setNullValue

Field Detail

current_index

protected int current_index

index_lines

protected int index_lines

index_counter

protected int index_counter

mrx_sources

protected BufferedReader[] mrx_sources

mrcui_source

protected BufferedReader mrcui_source

mrsab_source

protected BufferedReader mrsab_source

mraui_source

protected BufferedReader mraui_source

mrrank_source

protected BufferedReader mrrank_source

Constructor Detail

RichMRMetathesaurusInputStream

public RichMRMetathesaurusInputStream()

Instantiates an empty RichMRMetathesaurusInputStream;

Method Detail

open

public void open(String[] install_paths)
          throws IOException

Opens all of the MR Files in preparation for subsetting.

Specified by:

open in interface ConceptInputStream

Overrides:

open in class RichMRFilesConceptInputStream

Parameters:

install_paths - the directory containing the files

Throws:

IOException - if any files can not be opened

close

public void close()
           throws IOException

Close files opened during open(String[]).

Specified by:

close in interface ConceptInputStream

Overrides:

close in class RichMRFilesConceptInputStream

Throws:

IOException - if files can not be closed

getLineCounts

protected Map getLineCounts()
                     throws IOException

Reads through MRFILES.RRF to determine the size of the index files. This is used in the getIndexProgress() method.

Overrides:

getLineCounts in class RichMRFilesConceptInputStream

Returns:

Map of file names to lines in file

Throws:

IOException - if the file cannot be opened or read

readIndexEntry

public IndexEntry readIndexEntry()
                          throws IOException

Returns an IndexEntry from one of the index files. We read through the index files one at a time, returning all of the entries.

Specified by:

readIndexEntry in interface MetathesaurusInputStream

Returns:

an IndexEntry from one of the index files

Throws:

IOException - if the files cannot be read

getIndexProgress

public int getIndexProgress()

Returns the percentage of the index file lines that have been processed.

Specified by:

getIndexProgress in interface MetathesaurusInputStream

Returns:

the percentage of the index file lines that have been processed

readReleaseMetadata

public ReleaseMetadata readReleaseMetadata()
                                    throws IOException

Returns the ReleaseMetadata containing data from MRSAB.RRF, MRCUI.RRF, MRAUI.RRF, and MRDOC.RRF.

Specified by:

readReleaseMetadata in interface MetathesaurusInputStream

Returns:

the ReleaseMetadata

Throws:

IOException - if the files could not be read

getAmbiguousStringIdentifiers

public String[] getAmbiguousStringIdentifiers()
                                       throws IOException

Returns the complete list of suis from the AMBIGSUI list. They will be used in calculating entries for the output AMBIGSUI list.

Specified by:

getAmbiguousStringIdentifiers in interface MetathesaurusInputStream

Returns:

list of suis

Throws:

IOException

getAmbiguousStringIdentifiersAsList

public List getAmbiguousStringIdentifiersAsList()
                                         throws IOException

Returns the complete list of suis from the AMBIGSUI list. They will be used in calculating entries for the output AMBIGSUI list.

Specified by:

getAmbiguousStringIdentifiersAsList in interface MetathesaurusInputStream

Returns:

list of suis

Throws:

IOException

getAmbiguousTermIdentifiers

public String[] getAmbiguousTermIdentifiers()
                                     throws IOException

Returns the complete list of terms from the AMBIGLUI list. They will be used in calculating entries for the output AMBIGLUI list.

Specified by:

getAmbiguousTermIdentifiers in interface MetathesaurusInputStream

Returns:

list of terms

Throws:

IOException

getAmbiguousTermIdentifiersAsList

public List getAmbiguousTermIdentifiersAsList()
                                       throws IOException

Returns the complete list of terms from the AMBIGLUI list. They will be used in calculating entries for the output AMBIGLUI list.

Specified by:

getAmbiguousTermIdentifiersAsList in interface MetathesaurusInputStream

Returns:

list of terms

Throws:

IOException