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java.lang.Objectgov.nih.nlm.umls.io.RichMRFilesConceptInputStream
gov.nih.nlm.umls.io.RichMRMetathesaurusInputStream
This ConceptInputStream
builds objects from a full set of
"Rich Release Format" MR files.
Field Summary | |
protected int |
current_index
|
protected int |
index_counter
|
protected int |
index_lines
|
protected BufferedReader |
mraui_source
|
protected BufferedReader |
mrcui_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, rel_hm, this_concept, to_rsab, to_vsab, tokens |
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, getRelationships, getSemanticTypes, newInstanceFromMRCONSO, newInstanceFromMRHIER, openMRFiles, openSourceFile, readConcept, 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.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
protected BufferedReader mraui_source
Constructor Detail |
public RichMRMetathesaurusInputStream()
RichMRMetathesaurusInputStream
;
Method Detail |
public void open(String[] install_paths) throws IOException
open
in interface ConceptInputStream
open
in class RichMRFilesConceptInputStream
install_paths
- the directory containing the files
IOException
- if any files can not be openedpublic void close() throws IOException
open(String[])
.
close
in interface ConceptInputStream
close
in class RichMRFilesConceptInputStream
IOException
- if files can not be closedprotected Map getLineCounts() throws IOException
MRFILES.RRF
to determine the size of the index files.
This is used in the getIndexProgress()
method.
getLineCounts
in class RichMRFilesConceptInputStream
Map
of file names to lines in file
IOException
- if the file cannot be opened or readpublic 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
public ReleaseMetadata readReleaseMetadata() throws IOException
ReleaseMetadata
containing data from
MRSAB.RRF
, MRCUI.RRF
, MRAUI.RRF
,
and MRDOC.RRF
.
readReleaseMetadata
in interface MetathesaurusInputStream
ReleaseMetadata
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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