gov.nih.nlm.umls.io
Class RichMRFilesIndexLookup

java.lang.Object
  gov.nih.nlm.umls.io.RichMRFilesIndexLookup

All Implemented Interfaces:

LocalNullValueSupport

public class RichMRFilesIndexLookup
extends Object
implements LocalNullValueSupport

Peforms a lookup in the index files to locate the Concepts that contain given words.

Author:

Deborah Shapiro

Field Summary

protected boolean	null_value_flag
protected String	regex_null_value

Constructor Summary

RichMRFilesIndexLookup(String dir)
Instantiates an RichMRFilesIndexLookup from the specified input directory.

Method Summary

void	close() Release resources being used by this class.
int	countChildContexts(Context cxt) Looks up the given Context in the appropriate index files and returns the count of Contexts whose ptr matches the given one + the aui.
int	countSiblingContexts(Context cxt) Looks up the given Context in the appropriate index files and returns the count of Contexts whose ptr matches the given one.
Context	findAncestorContext(Context cxt, String ptr) Looks up the given ptr in the appropriate index files and returns the matching ancestor.
Atom	findAtomByAui(String aui) Looks up the given aui in the AUI_MRCONSO.x index file and returns the Atom that contains the given aui.
Context[]	findChildContexts(Context cxt) Looks up the given Context's ptr + aui in the appropriate index files and returns the Contexts with matching ptrs.
Concept	findConceptByAui(String aui) Looks up the given aui in the AUI_MRCONSO.x index file and returns the Concept that contains the given aui.
Concept	findConceptByCui(String cui) Looks up the given cui in MRCONSO and returns the Concept associated with the given cui.
Context[]	findSiblingContexts(Context cxt) Looks up the given Context's ptr in the appropriate index files and returns the Contexts with matching ptrs.
String	getLanguage() Returns the language of the index file that should be searched.
String	getNullValue() Returns the null value.
int	getPreviousTotalResultCount() Returns the total number of concept matches found on the previous search.
double	getThreshold() Returns the rank threshold value for searching.
int	getWordCountThreshold() Returns the rank threshold value for searching.
boolean	isEmptyValue(String token) Indicates whether or not the specified token is null or contains a null value as defined by being either zero length or a value equal to the null value.
protected String	resolveNull(String line) Replaces all "null value" characters in the line.
void	setLanguage(String lat) Sets the language of the index file that should be searched.
void	setMaxResults(int max_results) Sets the maximum number of results that should be returned.
void	setNullValue(String null_value) Sets the null value to use.
void	setThreshold(double threshold) Sets the rank threshold value for searching.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

regex_null_value

protected String regex_null_value

null_value_flag

protected boolean null_value_flag

Constructor Detail

RichMRFilesIndexLookup

public RichMRFilesIndexLookup(String dir)
                       throws IOException

Instantiates an RichMRFilesIndexLookup from the specified input directory.

Parameters:

dir - subset directory where index files can be found

Throws:

IOException

Method Detail

setNullValue

public void setNullValue(String null_value)

Sets the null value to use. This is needed if release.dat specifies some non-standard null value char sequence.

Specified by:

setNullValue in interface LocalNullValueSupport

Parameters:

null_value - the new null string value

getNullValue

public String getNullValue()

Returns the null value. This is needed if release.dat specifies some non-standard null value char sequence.

Specified by:

getNullValue in interface LocalNullValueSupport

Returns:

the string value for "null"

isEmptyValue

public boolean isEmptyValue(String token)

Indicates whether or not the specified token is null or contains a null value as defined by being either zero length or a value equal to the null value.

Specified by:

isEmptyValue in interface LocalNullValueSupport

resolveNull

protected String resolveNull(String line)

Replaces all "null value" characters in the line.

Parameters:

line - input line

Returns:

output line

close

public void close()
           throws IOException

Release resources being used by this class.

Throws:

IOException

getPreviousTotalResultCount

public int getPreviousTotalResultCount()

Returns the total number of concept matches found on the previous search.

Returns:

int number of concepts found on previous search

findChildContexts

public Context[] findChildContexts(Context cxt)
                            throws IOException

Looks up the given Context's ptr + aui in the appropriate index files and returns the Contexts with matching ptrs.

Parameters:

cxt - Context

Returns:

Context[] children

Throws:

IOException

findSiblingContexts

public Context[] findSiblingContexts(Context cxt)
                              throws IOException

Looks up the given Context's ptr in the appropriate index files and returns the Contexts with matching ptrs.

Parameters:

cxt - Context

Returns:

Context[] children

Throws:

IOException

findAncestorContext

public Context findAncestorContext(Context cxt,
                                   String ptr)
                            throws IOException

Looks up the given ptr in the appropriate index files and returns the matching ancestor.

Parameters:

cxt - Context

ptr - String

Returns:

Context[]

Throws:

IOException

countChildContexts

public int countChildContexts(Context cxt)
                       throws IOException

Looks up the given Context in the appropriate index files and returns the count of Contexts whose ptr matches the given one + the aui.

Parameters:

cxt - Context parent

Returns:

int children

Throws:

IOException

countSiblingContexts

public int countSiblingContexts(Context cxt)
                         throws IOException

Looks up the given Context in the appropriate index files and returns the count of Contexts whose ptr matches the given one.

Parameters:

cxt - Context parent

Returns:

int siblings

Throws:

IOException

findConceptByCui

public Concept findConceptByCui(String cui)
                         throws IOException

Looks up the given cui in MRCONSO and returns the Concept associated with the given cui.

Parameters:

cui - to be searched for

Returns:

Concept

Throws:

IOException

findConceptByAui

public Concept findConceptByAui(String aui)
                         throws IOException

Looks up the given aui in the AUI_MRCONSO.x index file and returns the Concept that contains the given aui.

Parameters:

aui - to be searched for

Returns:

Concept containing the aui

Throws:

IOException

findAtomByAui

public Atom findAtomByAui(String aui)
                   throws IOException

Looks up the given aui in the AUI_MRCONSO.x index file and returns the Atom that contains the given aui.

Parameters:

aui - to be searched for

Returns:

Atom containing the aui

Throws:

IOException

setLanguage

public void setLanguage(String lat)

Sets the language of the index file that should be searched.

Parameters:

lat - language abbreviation

getLanguage

public String getLanguage()

Returns the language of the index file that should be searched.

Returns:

the language of the index file that should be searched

setMaxResults

public void setMaxResults(int max_results)

Sets the maximum number of results that should be returned.

Parameters:

max_results - number of results

setThreshold

public void setThreshold(double threshold)

Sets the rank threshold value for searching.

Parameters:

threshold - the rank threshold valud for searching

getThreshold

public double getThreshold()

Returns the rank threshold value for searching.

Returns:

the rank threshold value for searching

getWordCountThreshold

public int getWordCountThreshold()

Returns the rank threshold value for searching.

Returns:

the rank threshold value for searching