A B C D E F G H I L M N O P Q R S T U W

A

addDisease(DiseaseToSymptomMapping) - Method in class org.mitre.midiki.workshop.DiseaseToSymptomMapping

Adds a new matrix entry to the end of the chain for this symptom.

addSymptom(DiseaseToSymptomMapping) - Method in class org.mitre.midiki.workshop.DiseaseToSymptomMapping

Adds a new entry to the end of the chain for this disease.

addSynonym(String) - Method in class org.mitre.midiki.workshop.Synonym

Adds a synonym to the set.

B

buffer - Variable in class org.mitre.midiki.workshop.DiseaseServer

C

compatibleWithSymptoms(String, List, List, List) - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Returns true if the specified disease is compatible with the observed symptoms.

containsIgnoreCase(Collection, String) - Static method in class org.mitre.midiki.workshop.DiseaseServer

Checks the container for a copy of this string, ignoring case.

containsIgnoreCase(Collection, String) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseTest

Checks the container for a copy of this string, ignoring case.

cvtbuf - Variable in class org.mitre.midiki.workshop.DiseaseServer

D

defaultDatabaseName - Static variable in class org.mitre.midiki.workshop.DiseaseServer

defaultDTD - Static variable in class org.mitre.midiki.workshop.DiseaseServer

description - Variable in class org.mitre.midiki.workshop.Disease

A few paragraphs describing the disease.

DiagnosticTest - class org.mitre.midiki.workshop.DiagnosticTest.

Represents a diagnostic test which can be used to confirm the presence or absence of a named symptom, a short text description of a positive test result, and whether the symptom diagnosed by the test must be present or absent.

DiagnosticTest() - Constructor for class org.mitre.midiki.workshop.DiagnosticTest

Empty constructor.

DiagnosticTest(String, String, String, boolean) - Constructor for class org.mitre.midiki.workshop.DiagnosticTest

Creates a new DiagnosticTest instance.

discriminatingHistory - Variable in class org.mitre.midiki.workshop.QueryResponse

Possibly empty list of history which could be added to the last query to reduce the number of diagnosed diseases.

discriminatingHistory(List, List) - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Calculates the history which can be used to discriminate between some of the specified diseases.

discriminatingSymptoms - Variable in class org.mitre.midiki.workshop.QueryResponse

Possibly empty list of symptoms which could be added to the last query to reduce the number of diagnosed diseases.

discriminatingSymptoms(List, List) - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Calculates the symptoms which can be used to discriminate between some of the specified diseases.

discriminatingTests - Variable in class org.mitre.midiki.workshop.QueryResponse

Possibly empty list of tests which could be added to the last query to reduce the number of diagnosed diseases.

discriminatingTests(List, List) - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Calculates the tests which can be used to discriminate between some of the specified diseases.

disease - Variable in class org.mitre.midiki.workshop.DiseaseToSymptomMapping

Name of the diagnosable disease.

Disease - class org.mitre.midiki.workshop.Disease.

Database record containing detailed information about a disease.

Disease() - Constructor for class org.mitre.midiki.workshop.Disease

Empty constructor.

diseaseIndex(String) - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Converts a disease name into a numeric index.

diseaseList - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Unsorted list of disease names.

diseases - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

List of detailed records for diseases.

diseasesByHistory - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Column headers for the sparse matrix.

diseasesBySymptom - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Column headers for the sparse matrix.

diseasesByTest - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Column headers for the sparse matrix.

DiseaseServer - class org.mitre.midiki.workshop.DiseaseServer.

Based on a simple HTTP server, generates XML based on a disease db query in an encoded URL.

DiseaseServer(int, int) - Constructor for class org.mitre.midiki.workshop.DiseaseServer

DiseaseToSymptomMapping - class org.mitre.midiki.workshop.DiseaseToSymptomMapping.

Indicates that the presence of the specified symptom supports a diagnosis of the specified disease.

DiseaseToSymptomMapping() - Constructor for class org.mitre.midiki.workshop.DiseaseToSymptomMapping

No-arg constructor.

DiseaseToSymptomMapping(String, String) - Constructor for class org.mitre.midiki.workshop.DiseaseToSymptomMapping

Creates a new DiseaseToSymptomMapping instance.

dtdData - Static variable in class org.mitre.midiki.workshop.DiseaseServer

E

error(SAXParseException) - Method in class org.mitre.midiki.workshop.WorkshopErrorHandler

extractDiseases(NodeList, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseFactory

Generates a master list of all disease names in the database.

extractHistory(NodeList, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseFactory

Compiles a master list of unique history items.

extractSymptoms(NodeList, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseFactory

Compiles a master list of unique symptoms.

extractSynonyms(NodeList, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseFactory

Generates Synonym objects from tags in the database.

extractTests(NodeList, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseFactory

Compiles a master list of unique tests.

F

fatalError(SAXParseException) - Method in class org.mitre.midiki.workshop.WorkshopErrorHandler

fromUrl(String) - Method in class org.mitre.midiki.workshop.DiseaseServer

Decodes %20 hexadecimal codes into spaces and returns the converted string.

G

getAllDiseases() - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Returns a list containing the names of all the diseases in the database.

getAllHistoryItems() - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Returns the list of unique history items in the database.

getAllSymptoms() - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Returns the list of unique symptoms in the database.

getAllSymptomSynonyms() - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Returns all synonym sets specified in the database.

getAllTestNames() - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Returns the names of tests in the database.

getAllTests() - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Returns the list of unique tests in the database.

getApplicableDiseases(List, List, List) - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Searches the database for diseases matching the specified symptoms.

getDataStream() - Method in class org.mitre.midiki.workshop.SocketUtil

getDefault() - Method in class org.mitre.midiki.workshop.Synonym

Returns the first string added to this set.

getDiseaseDescription(String) - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Locates the detailed record for the specified disease.

getPrintStream() - Method in class org.mitre.midiki.workshop.SocketUtil

getUnbufferedDataStream() - Method in class org.mitre.midiki.workshop.SocketUtil

H

handleConnection(Socket) - Method in class org.mitre.midiki.workshop.NetworkServer

This is the method that provides the behavior to the server, since it determines what is done with the resulting socket.

handleConnection(Socket) - Method in class org.mitre.midiki.workshop.DiseaseServer

Overrides the NetworkServer handleConnection to read each line of data received, save it into an array of strings, then send it back embedded inside a PRE element in an HTML page.

handleConnection(Socket) - Method in class org.mitre.midiki.workshop.ThreadedDiseaseServer

The new version of handleConnection starts a thread.

history - Variable in class org.mitre.midiki.workshop.Disease

List of medical history items presented by this disease.

historyByDisease - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Row headers for the sparse matrix.

historyIndex(String) - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Converts a history name to a numeric index.

historyList - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Unsorted list of medical history item names.

I

id - Variable in class org.mitre.midiki.workshop.DiseaseServer

isSynonymFor(String) - Method in class org.mitre.midiki.workshop.Synonym

Returns true if the specified string appears in this synonym set.

iterator() - Method in class org.mitre.midiki.workshop.Synonym

Provides public access to the contents of this synonym set.

L

listen() - Method in class org.mitre.midiki.workshop.NetworkServer

Monitor a port for connections.

loadDatabase(String) - Static method in class org.mitre.midiki.workshop.DiseaseServer

loadDTD(String) - Static method in class org.mitre.midiki.workshop.DiseaseServer

M

main(String[]) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseFactory

Reads the file specified by the first program argument and parses it into a WorkshopDatabase by a call to newDatabase().

main(String[]) - Static method in class org.mitre.midiki.workshop.DiseaseServer

Supply a port number as a command-line argument.

main(String[]) - Static method in class org.mitre.midiki.workshop.ThreadedDiseaseServer

main(String[]) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseTest

Reads arguments and tests queries against the specified database.

mapSymptomsToDiseases(NodeList, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseFactory

Creates a sparse matrix mapping diseases to thier symptoms.

matches(DiagnosticTest) - Method in class org.mitre.midiki.workshop.DiagnosticTest

Returns true if the symptom matches the query.

matches(MedicalHistory) - Method in class org.mitre.midiki.workshop.MedicalHistory

Returns true if the history matches the query.

matches(Symptom) - Method in class org.mitre.midiki.workshop.Symptom

Returns true if the symptom matches the query.

maxConnections - Variable in class org.mitre.midiki.workshop.NetworkServer

maxInputLines - Variable in class org.mitre.midiki.workshop.DiseaseServer

MedicalHistory - class org.mitre.midiki.workshop.MedicalHistory.

Represents an item in the patient's medical history which is suggestive of a particular disease.

MedicalHistory() - Constructor for class org.mitre.midiki.workshop.MedicalHistory

Empty constructor.

MedicalHistory(String, boolean) - Constructor for class org.mitre.midiki.workshop.MedicalHistory

Creates a new MedicalHistory instance.

N

name - Variable in class org.mitre.midiki.workshop.MedicalHistory

The name of the history.

name - Variable in class org.mitre.midiki.workshop.DiagnosticTest

The name of the symptom.

name - Variable in class org.mitre.midiki.workshop.Disease

The common name of the disease.

name - Variable in class org.mitre.midiki.workshop.Symptom

The name of the symptom.

NetworkServer - class org.mitre.midiki.workshop.NetworkServer.

A starting point for network servers.

NetworkServer(int, int) - Constructor for class org.mitre.midiki.workshop.NetworkServer

Build a server on specified port.

newDatabase(String) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseFactory

Opens the specified database file and interprets it as an XML file conforming to diseasedb.dtd.

nextDiseaseForSymptom - Variable in class org.mitre.midiki.workshop.DiseaseToSymptomMapping

Reference to the next disease that presents this symptom.

nextId - Static variable in class org.mitre.midiki.workshop.DiseaseServer

nextSymptomForDisease - Variable in class org.mitre.midiki.workshop.DiseaseToSymptomMapping

Reference to the next symptom for this disease.

O

org.mitre.midiki.workshop - package org.mitre.midiki.workshop

P

parseCommand(String) - Method in class org.mitre.midiki.workshop.DiseaseServer

Parses the argument to an HTTP GET into a series of arguments separated by *.

parseHistory(String, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.DiseaseServer

Parses a symptom specification of the form "symptom"/ into a MedicalHistory object.

parseHistory(String, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseTest

Parses a symptom specification of the form "symptom"/ into a MedicalHistory object.

parseSymptom(String, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.DiseaseServer

Parses a symptom specification of the form "symptom"/ into a Symptom object.

parseSymptom(String, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseTest

Parses a symptom specification of the form "symptom"/ into a Symptom object.

parseTest(String, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.DiseaseServer

Parses a symptom specification of the form "symptom"/ into a DiagnosticTest object.

parseTest(String, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseTest

Parses a symptom specification of the form "symptom"/ into a DiagnosticTest object.

port - Variable in class org.mitre.midiki.workshop.NetworkServer

possibleDiagnoses - Variable in class org.mitre.midiki.workshop.QueryResponse

The list of all diseases which could be diagnosed given the symptoms that were presented.

present - Variable in class org.mitre.midiki.workshop.MedicalHistory

true if the history is present.

present - Variable in class org.mitre.midiki.workshop.DiagnosticTest

true if the symptom is present.

present - Variable in class org.mitre.midiki.workshop.Symptom

true if the symptom is present.

prevention - Variable in class org.mitre.midiki.workshop.Disease

Text describing possible measures for preventing infection.

printDiseasesBySymptom() - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Prints a cross-reference listing of diseases by symptom on System.out.

processDocument(Document, WorkshopDatabase) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseFactory

Parses the expected disease database sections.

Q

QueryResponse - class org.mitre.midiki.workshop.QueryResponse.

Wrapper class for the results of a database query.

QueryResponse() - Constructor for class org.mitre.midiki.workshop.QueryResponse

Creates an empty QueryResponse instance.

QueryResponse(List, List, List, List) - Constructor for class org.mitre.midiki.workshop.QueryResponse

Creates a new QueryResponse instance.

R

regions - Variable in class org.mitre.midiki.workshop.Disease

Text identifying regions in which this disease is known to be present.

resolveSynonyms(String) - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Checks all known synonym sets for the specified string.

result - Variable in class org.mitre.midiki.workshop.DiagnosticTest

The description of a positive test result.

run() - Method in class org.mitre.midiki.workshop.ThreadedDiseaseServer

S

serverName - Variable in class org.mitre.midiki.workshop.DiseaseServer

SocketUtil - class org.mitre.midiki.workshop.SocketUtil.

A shorthand way to create PrintStreams and buffered/unbuffered DataInputStreams associated with a socket.

SocketUtil(Socket) - Constructor for class org.mitre.midiki.workshop.SocketUtil

symptom - Variable in class org.mitre.midiki.workshop.DiseaseToSymptomMapping

Name of the presented symptom.

Symptom - class org.mitre.midiki.workshop.Symptom.

Represents a physical symptom, and whether the symptom must be present or absent.

Symptom() - Constructor for class org.mitre.midiki.workshop.Symptom

Empty constructor.

Symptom(String, boolean) - Constructor for class org.mitre.midiki.workshop.Symptom

Creates a new Symptom instance.

symptomIndex(String) - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Converts a symptom name to a numeric index.

symptomList - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Unsorted list of resolved symptom names.

symptoms - Variable in class org.mitre.midiki.workshop.Disease

List of symptoms presented by this disease.

symptomsByDisease - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Row headers for the sparse matrix.

Synonym - class org.mitre.midiki.workshop.Synonym.

Identifies a list of symptom names which are considered to be identical.

Synonym() - Constructor for class org.mitre.midiki.workshop.Synonym

Creates a new Synonym instance.

synonymList - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

List of synonym sets.

T

test - Variable in class org.mitre.midiki.workshop.DiagnosticTest

The name of the appropriate test.

testIndex(String) - Method in class org.mitre.midiki.workshop.WorkshopDatabase

Converts a test name to a numeric index.

testList - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Unsorted list of test names.

tests - Variable in class org.mitre.midiki.workshop.Disease

List of tests presented by this disease.

testsByDisease - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Row headers for the sparse matrix.

textChild(Node) - Static method in class org.mitre.midiki.workshop.WorkshopDatabaseFactory

Finds the first "#text" child of the specified node and returns its value.

ThreadedDiseaseServer - class org.mitre.midiki.workshop.ThreadedDiseaseServer.

A multi-threaded variation of DiseaseServer.
Adapted from code that appears in Core Web Programming from Prentice Hall Publishers, and may be freely used or adapted.

ThreadedDiseaseServer(int, int) - Constructor for class org.mitre.midiki.workshop.ThreadedDiseaseServer

toString() - Method in class org.mitre.midiki.workshop.MedicalHistory

Generates a string representation of the history.

toString() - Method in class org.mitre.midiki.workshop.DiagnosticTest

Generates a string representation of the symptom.

toString() - Method in class org.mitre.midiki.workshop.Disease

Generates a string representation of this object.

toString() - Method in class org.mitre.midiki.workshop.Symptom

Generates a string representation of the symptom.

toString() - Method in class org.mitre.midiki.workshop.QueryResponse

Generates a string representation of the query result.

toString() - Method in class org.mitre.midiki.workshop.Synonym

Generate a string representation of this set.

toUrl(String) - Method in class org.mitre.midiki.workshop.DiseaseServer

Encodes spaces in a string into %20 hexadecimal encoding, so that the string can be passed as part of a URL.

treatment - Variable in class org.mitre.midiki.workshop.Disease

Text describing available treatments for this disease.

U

uniqueHistory - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Maps resolved names of all history to the appropriate record.

uniqueSymptoms - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Maps resolved names of all symptoms to the appropriate record.

uniqueTests - Variable in class org.mitre.midiki.workshop.WorkshopDatabase

Maps resolved names of all tests to the appropriate record.

W

warning(SAXParseException) - Method in class org.mitre.midiki.workshop.WorkshopErrorHandler

wd - Static variable in class org.mitre.midiki.workshop.DiseaseServer

WorkshopDatabase - class org.mitre.midiki.workshop.WorkshopDatabase.

Simple medical diagnosis database to support the MITRE Dialogue Workshop.

WorkshopDatabase() - Constructor for class org.mitre.midiki.workshop.WorkshopDatabase

Creates an empty WorkshopDatabase instance.

WorkshopDatabaseFactory - class org.mitre.midiki.workshop.WorkshopDatabaseFactory.

Factory class for parsing XML files conforming to the diseasedb.dtd into WorkshopDatabase objects.

WorkshopDatabaseFactory() - Constructor for class org.mitre.midiki.workshop.WorkshopDatabaseFactory

WorkshopDatabaseTest - class org.mitre.midiki.workshop.WorkshopDatabaseTest.

Simple test class for dialogue workshop backend.

WorkshopDatabaseTest() - Constructor for class org.mitre.midiki.workshop.WorkshopDatabaseTest

WorkshopErrorHandler - class org.mitre.midiki.workshop.WorkshopErrorHandler.

Error handler for use by XML document parser.

WorkshopErrorHandler() - Constructor for class org.mitre.midiki.workshop.WorkshopErrorHandler

A B C D E F G H I L M N O P Q R S T U W