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java.lang.Objectgov.nih.nlm.umls.io.OriginalMRFilesConceptInputStream
gov.nih.nlm.umls.io.OriginalMRMetathesaurusInputStream
This MetathesaurusInputStream
builds
IndexEntry
s, and ReleaseMetadata
from a full set of standard
MR files.
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, this_concept, tokens |
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, getRelationships, getSemanticTypes, openSourceFile, readConcept |
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, readConcept |
Field Detail |
protected int current_index
protected int index_lines
protected int index_counter
protected BufferedReader[] mrx_sources
protected BufferedReader mrcui_source
protected BufferedReader mrsab_source
Constructor Detail |
public OriginalMRMetathesaurusInputStream()
OriginalMRMetathesaurusInputStream
;
Method Detail |
public void open(String[] install_paths) throws IOException
open
in interface ConceptInputStream
open
in class OriginalMRFilesConceptInputStream
install_paths
- the subset directory
IOException
- if the files cannot be openedpublic void close() throws IOException
open(String[])
.
close
in interface ConceptInputStream
close
in class OriginalMRFilesConceptInputStream
IOException
- if files can not be closedpublic IndexEntry readIndexEntry() throws IOException
IndexEntry
from one of the index files.
We read through the index files one at a time, returning
all of the entries.
readIndexEntry
in interface MetathesaurusInputStream
IndexEntry
from one of the index files
IOException
- if the files cannot be readpublic int getIndexProgress()
getIndexProgress
in interface MetathesaurusInputStream
protected Map getLineCounts() throws IOException
MRFILES
to determine the size of the index files.
This is used in the getIndexProgress()
method.
getLineCounts
in class OriginalMRFilesConceptInputStream
Map
of file names to lines in file
IOException
- if the file cannot be opened or readpublic ReleaseMetadata readReleaseMetadata() throws IOException
ReleaseMetadata
containing data from
MRSAB, MRDOC and MRCUI.
readReleaseMetadata
in interface MetathesaurusInputStream
ReleaseMetadata
for this input stream
IOException
- if the files could not be readpublic String[] getAmbiguousStringIdentifiers() throws IOException
getAmbiguousStringIdentifiers
in interface MetathesaurusInputStream
IOException
public List getAmbiguousStringIdentifiersAsList() throws IOException
getAmbiguousStringIdentifiersAsList
in interface MetathesaurusInputStream
IOException
public String[] getAmbiguousTermIdentifiers() throws IOException
getAmbiguousTermIdentifiers
in interface MetathesaurusInputStream
IOException
public List getAmbiguousTermIdentifiersAsList() throws IOException
getAmbiguousTermIdentifiersAsList
in interface MetathesaurusInputStream
IOException
|
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