A C D E F G H I J L M N P R S T V

A

addAbbrs(String, List<ScoredResult>, String, String) - Method in class edu.cornell.med.icb.synonyms.util.SynonymImportTool

Add ArrayList[AbbreviationTerm] to the synonyms list.

addEmptySynonym(EmptySynonym) - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Add a new empty synonym.

addSynonym(Synonym) - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Add a new synonym.

addSynonyms(List<Synonym>) - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Add a new set of synonyms.

ANY_APPLIES_TO - Static variable in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Perform reverseLookup should be false on findSynonym.

ANY_SOURCE - Static variable in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Perform reverseLookup should be false on findSynonym.

APPLIES_TO_ALL - Static variable in class edu.cornell.med.icb.synonyms.entities.Synonym

AppliesTo field value when a synonym applies to all.

C

close(String) - Static method in class edu.cornell.med.icb.persistence.JpaEmFactory

Close a specific EntityManagerFactory that were opened by calling getEmFactory(...).

close() - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Close the synonym engine.

closeAll() - Static method in class edu.cornell.med.icb.persistence.JpaEmFactory

Close all EntityManagerFactory's that were opened by calling getEmFactory(...).

CREATE_INDEX_COMMANDS - Static variable in class edu.cornell.med.icb.synonyms.entities.EmptySynonym

Commands required to index this data.

CREATE_INDEX_COMMANDS - Static variable in class edu.cornell.med.icb.synonyms.entities.Synonym

Commands required to index this data.

D

DONT_INCLUDE_ALL - Static variable in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Include all appliesTo should be false on findSynonym.

DROP_INDEX_COMMANDS - Static variable in class edu.cornell.med.icb.synonyms.entities.EmptySynonym

Commands required to remove the indexes for this data.

DROP_INDEX_COMMANDS - Static variable in class edu.cornell.med.icb.synonyms.entities.Synonym

Commands required to remove the indexes for this data.

dropAll() - Method in class edu.cornell.med.icb.synonyms.util.SynonymImportTool

Drop all synonyms in the SynonymEngine.

dropAllSynonyms() - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Drops all synonyms for a specific source.

dropSource(String) - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Drops all synonyms for a specific source.

dropSource(String) - Method in class edu.cornell.med.icb.synonyms.util.SynonymImportTool

Drop all synonyms for a single source.

E

edu.cornell.med.icb.persistence - package edu.cornell.med.icb.persistence

Classes that deal with Synonym persistence.

edu.cornell.med.icb.synonyms.engine - package edu.cornell.med.icb.synonyms.engine

The engine classes for synonyms

edu.cornell.med.icb.synonyms.entities - package edu.cornell.med.icb.synonyms.entities

The entity classes for synonyms

edu.cornell.med.icb.synonyms.util - package edu.cornell.med.icb.synonyms.util

EmptySynonym - Class in edu.cornell.med.icb.synonyms.entities

The EmptySynonym object, for persistence via JPA.

EmptySynonym(String, String, String) - Constructor for class edu.cornell.med.icb.synonyms.entities.EmptySynonym

General constructor for creating a new synonym.

emptySynonymExists(EmptySynonym) - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Check if an emptySynonym has been persisted emptySynonym.

F

findEmptySynonyms(String, String, String) - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Find a list of synonyms for a specific dinctionary word.

findEmptySynonymsMultiSource(String, String[], String) - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Find a list of synonyms for a specific dinctionary word.

findSynonyms(String, String, String, boolean, boolean) - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Find a list of synonyms for a specific dinctionary word.

findSynonymsMultiSource(String, String[], String, boolean, boolean) - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Find a list of synonyms for a specific dinctionary word.

finished() - Method in class edu.cornell.med.icb.synonyms.util.SynonymImportTool

Call this when you are finished with the ImportTool object if you had import tool create the synonym engine.

G

getAppliesTo() - Method in class edu.cornell.med.icb.synonyms.entities.EmptySynonym

Getter for AppliesTo.

getAppliesTo() - Method in class edu.cornell.med.icb.synonyms.entities.Synonym

Getter for AppliesTo.

getDictionaryWord() - Method in class edu.cornell.med.icb.synonyms.entities.EmptySynonym

Getter for DictionaryWord.

getDictionaryWord() - Method in class edu.cornell.med.icb.synonyms.entities.Synonym

Getter for DictionaryWord.

getEmFactory(String) - Static method in class edu.cornell.med.icb.persistence.JpaEmFactory

Retrieve an entity manager factory for the persistence-unit.

getEntityManager(String) - Static method in class edu.cornell.med.icb.persistence.JpaEmFactory

Retrieve an EntityManager for the persistence-unit.

getHugoLineCount() - Method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Import value: number of hugo lines processed.

getId() - Method in class edu.cornell.med.icb.synonyms.entities.EmptySynonym

Getter for Id.

getId() - Method in class edu.cornell.med.icb.synonyms.entities.Synonym

Getter for Id.

getImportDate() - Method in class edu.cornell.med.icb.synonyms.entities.EmptySynonym

Getter for ImportDate.

getImportDate() - Method in class edu.cornell.med.icb.synonyms.entities.Synonym

Getter for ImportDate.

getMeshBaseTermsCount() - Method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Import value: number of mesh base terms processed.

getScore() - Method in class edu.cornell.med.icb.synonyms.entities.Synonym

Getter for Score.

getSource() - Method in class edu.cornell.med.icb.synonyms.entities.EmptySynonym

Getter for Source.

getSource() - Method in class edu.cornell.med.icb.synonyms.entities.Synonym

Getter for Source.

getSynonymEngine() - Method in class edu.cornell.med.icb.synonyms.util.SynonymImportTool

getSynonymImportTool() - Method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

getSynonymWord() - Method in class edu.cornell.med.icb.synonyms.entities.Synonym

Getter for SynonymWord.

getTweaseImportBadParseCount() - Method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Import value: number of twease queries that couldn't be parsed.

getTweaseImportQueryCount() - Method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Import value: number of twease queries imported.

getTweaseImportTermCount() - Method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Import value: number of twease terms found.

getTweaseImportTermRepeatCount() - Method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Import value: number of twease repeat terms found.

getWordReader() - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Get the TextractorWordReader to use.

H

HUGO_ALIASES - Static variable in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Hugo_Aliases are stored in this position of the array.

HUGO_MIN_SYMBOL_LENGTH - Static variable in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

The minimum length acceptable for Hugo symbols.

HUGO_NAME - Static variable in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Hugo_Name are stored in this position of the array.

HUGO_PREVSYMBOLS - Static variable in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Hugo_PrevSymbols are stored in this position of the array.

HUGO_SYMBOL - Static variable in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Hugo_Symbol are stored in this position of the array.

hugoImport(String) - Method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Import a Hugo TSV file.

I

INCLUDE_ALL - Static variable in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Include all appliesTo should be true on findSynonym.

initializeQueryExecutor() - Method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Initialze the QueryExecutor.

isEquivalent(EmptySynonym) - Method in class edu.cornell.med.icb.synonyms.entities.EmptySynonym

Returns true if this synonym and the suggested on are the same, ignoring the id and the import date.

isEquivalent(Synonym) - Method in class edu.cornell.med.icb.synonyms.entities.Synonym

Returns true if this synonym and the suggested on are the same, ignoring the id and the import date.

J

JpaEmFactory - Class in edu.cornell.med.icb.persistence

Factory for JPA Entity Managers for multiple (or one) persistence-unit names.

L

listContainsDictionaryWord(List<Synonym>, String) - Static method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Searches a list of synonyms.

listContainsSynonym(List<Synonym>, Synonym) - Static method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Searches a list of synonyms.

listContainsSynonym(List<Synonym>, Synonym) - Static method in class edu.cornell.med.icb.synonyms.entities.Synonym

Searches a list of synonyms.

M

main(String[]) - Static method in class edu.cornell.med.icb.synonyms.util.MeshDiseaseReader

main(String[]) - Static method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Command line interface to SynonymImportTool.

MeshDiseaseReader - Class in edu.cornell.med.icb.synonyms.util

Read a Mesh XML file and output the list of diseases.

MeshDiseaseReader() - Constructor for class edu.cornell.med.icb.synonyms.util.MeshDiseaseReader

meshImport(String) - Method in class edu.cornell.med.icb.synonyms.util.MeshDiseaseReader

Import the MeSH data.

meshImport(String) - Method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Import the MeSH data.

N

NO_REVERSE_LOOKUP - Static variable in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Perform reverseLookup should be false on findSynonym.

P

PERSISTENCE_UNIT_DEFAULT - Static variable in class edu.cornell.med.icb.synonyms.util.SynonymImportTool

The default persistenceUnit as defined by textractor.properties.

processHugoDataLine(String, int[], int) - Method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Process a Hugo data line for synonyms.

processTerm(String) - Static method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Use the term processor to process the term or phrase.

R

recreateIndexes() - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Create or re-create the synonym indexes.

recreateIndexes() - Method in class edu.cornell.med.icb.synonyms.util.SynonymImportTool

Recreate the indexes.

removeEmptySynonym(EmptySynonym) - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Remove the empty synonym as described here.

removeSynonymWord(List<Synonym>, String) - Static method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Remove all synonyms from the list where the synonymWord is synToExclude.

REVERSE_LOOKUP - Static variable in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Perform reverseLookup should be true on findSynonym.

S

setWordReader(TextractorWordReader) - Method in class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Set the TextractorWordReader to use.

Synonym - Class in edu.cornell.med.icb.synonyms.entities

The Synonym object, for persistence via JPA.

Synonym(String, String, double, String, String) - Constructor for class edu.cornell.med.icb.synonyms.entities.Synonym

General constructor for creating a new synonym.

SynonymClImportTool - Class in edu.cornell.med.icb.synonyms.util

Import abbreviations and DYMs from twease query logs using the command line.

SynonymClImportTool(String) - Constructor for class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Constructor.

SynonymClImportTool() - Constructor for class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Constructor.

SynonymEngine - Class in edu.cornell.med.icb.synonyms.engine

Enging for persisting and recalling Synonyms.

SynonymEngine(String) - Constructor for class edu.cornell.med.icb.synonyms.engine.SynonymEngine

Create a new synonym engine for a specific persistence-unit name.

SynonymImportTool - Class in edu.cornell.med.icb.synonyms.util

Import abbreviations and DYMs from twease query logs.

SynonymImportTool() - Constructor for class edu.cornell.med.icb.synonyms.util.SynonymImportTool

Constructor.

SynonymImportTool(String) - Constructor for class edu.cornell.med.icb.synonyms.util.SynonymImportTool

Constructor.

SynonymImportTool(SynonymEngine) - Constructor for class edu.cornell.med.icb.synonyms.util.SynonymImportTool

Constructor to use if you created the SynonymEngine elsewhere.

T

toString() - Method in class edu.cornell.med.icb.synonyms.entities.EmptySynonym

Human readable version of this object.

toString() - Method in class edu.cornell.med.icb.synonyms.entities.Synonym

Human readable version of this object.

tweaseQueryLogImport(String, boolean, boolean, boolean) - Method in class edu.cornell.med.icb.synonyms.util.SynonymClImportTool

Import the abbreviations and DYM's for all the phrases and terms in the specified twease query logs.

V

viewWord(String) - Method in class edu.cornell.med.icb.synonyms.util.SynonymImportTool

View all synonyms (with details) for a single dictionary word.

A C D E F G H I J L M N P R S T V