gov.nih.nlm.umls.io
Class OriginalMRMetathesaurusInputStream

java.lang.Object
  gov.nih.nlm.umls.io.OriginalMRFilesConceptInputStream
      gov.nih.nlm.umls.io.OriginalMRMetathesaurusInputStream

All Implemented Interfaces:

ConceptInputStream, MetathesaurusInputStream, LocalNullValueSupport

Direct Known Subclasses:

OriginalMRMetamorphoSysInputStream

public class OriginalMRMetathesaurusInputStream
extends OriginalMRFilesConceptInputStream
implements MetathesaurusInputStream

This MetathesaurusInputStream builds IndexEntrys, and ReleaseMetadata from a full set of standard MR files.

Author:

Deborah Shapiro

Field Summary

protected int	current_index
protected int	index_counter
protected int	index_lines
protected BufferedReader	mrcui_source
protected BufferedReader	mrsab_source
protected BufferedReader[]	mrx_sources

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

file_names, mr_dir, mratx_source, mrcoc_source, mrcon_counter, mrcon_lines, mrcon_source, mrcxt_source, mrdef_source, mrlo_source, mrrel_source, mrsat_source, mrso_source, mrsty_source, null_value, this_concept, tokens, warnings

Constructor Summary

OriginalMRMetathesaurusInputStream()
Instantiates an empty OriginalMRMetathesaurusInputStream;

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 to determine the size of the index files.
void	open(String[] install_paths) Opens all target files in the specified directory.
IndexEntry	readIndexEntry() Returns an IndexEntry from one of the index files.
ReleaseMetadata	readReleaseMetadata() Returns the ReleaseMetadata containing data from MRSAB, MRDOC and MRCUI.

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

getAtoms, getAttributes, getConceptProgress, getContexts, getCoocurrences, getDefinitions, getLocators, getMappings, getNullValue, getRelationships, getSemanticTypes, getWarnings, isEmptyValue, openSourceFile, readConcept, 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

Constructor Detail

OriginalMRMetathesaurusInputStream

public OriginalMRMetathesaurusInputStream()

Instantiates an empty OriginalMRMetathesaurusInputStream;

Method Detail

open

public void open(String[] install_paths)
          throws IOException

Opens all target files in the specified directory. The set of target files is the standard MR files.

Specified by:

open in interface ConceptInputStream

Overrides:

open in class OriginalMRFilesConceptInputStream

Parameters:

install_paths - the subset directory

Throws:

IOException - if the files cannot be opened

close

public void close()
           throws IOException

Close files opened during open(String[]).

Specified by:

close in interface ConceptInputStream

Overrides:

close in class OriginalMRFilesConceptInputStream

Throws:

IOException - if files can not be closed

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

getLineCounts

protected Map getLineCounts()
                     throws IOException

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

Overrides:

getLineCounts in class OriginalMRFilesConceptInputStream

Returns:

Map of file names to lines in file

Throws:

IOException - if the file cannot be opened or read

readReleaseMetadata

public ReleaseMetadata readReleaseMetadata()
                                    throws IOException

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

Specified by:

readReleaseMetadata in interface MetathesaurusInputStream

Returns:

the ReleaseMetadata for this input stream

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