sir.estimate
Class DataFileSpec

java.lang.Object
  extended bysir.estimate.DataFileSpec
All Implemented Interfaces:
DataFileSpecConstants

public class DataFileSpec
extends java.lang.Object
implements DataFileSpecConstants

Used to have plenty of classes here, but for now DataileSpec is all we need It is a JavaCC encoding of the grammar specifying recovery and infection times for each individual individual with such recordings. This is a new format compared to earlier, because we now give event times belonging to each individual instead of just event times. Furthermore, both inf, rec and diag events are specified.

Version:
23 January 2003
Author:
Michael Höhle >hoehle@dina.kvl.dk<

Field Summary
 Token jj_nt
           
 Token token
           
 DataFileSpecTokenManager token_source
           
 
Fields inherited from interface sir.estimate.DataFileSpecConstants
CENSORED, CONSTANT, DEFAULT, DIGIT, EOF, EOL, FLOAT, INTEGER, NA, SIGNEDFLOAT, SINGLE_LINE_COMMENT, tokenImage
 
Constructor Summary
DataFileSpec(DataFileSpecTokenManager tm)
           
DataFileSpec(java.io.InputStream stream)
           
DataFileSpec(java.io.Reader stream)
           
 
Method Summary
 void Beta()
           
 void BetaN()
           
 void CeaseTime()
          In case there is any information about it being a transmission experiment
 void DataFile()
           
 void Diag()
           
 void DiagEventTime()
          Diagnosed events can be censored
 void disable_tracing()
           
 void enable_tracing()
           
 void EventTime()
          Event time - either a double or NA with start value We throw on stack in top: startValue, top-1: t
 ParseException generateParseException()
           
 Data getData()
          Deliver Data object with data read from file
 Token getNextToken()
           
 Token getToken(int index)
           
 void Incu()
           
 void Inf()
           
static void main(java.lang.String[] args)
           
 void ParamStartValue(int paramNo)
           
 void RecTimeList()
          Each individual having events is listed, one per line with format posx posy eventTime eventTime
 void ReInit(DataFileSpecTokenManager tm)
           
 void ReInit(java.io.InputStream stream)
           
 void ReInit(java.io.Reader stream)
           
 void StartValue()
          Start valu of a time
 void Unit()
           
 void UnitList()
           
 void Vaccinated()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

token_source

public DataFileSpecTokenManager token_source

token

public Token token

jj_nt

public Token jj_nt
Constructor Detail

DataFileSpec

public DataFileSpec(java.io.InputStream stream)

DataFileSpec

public DataFileSpec(java.io.Reader stream)

DataFileSpec

public DataFileSpec(DataFileSpecTokenManager tm)
Method Detail

main

public static void main(java.lang.String[] args)
                 throws ParseException
Throws:
ParseException

getData

public Data getData()
Deliver Data object with data read from file


DataFile

public final void DataFile()
                    throws ParseException
Throws:
ParseException

ParamStartValue

public final void ParamStartValue(int paramNo)
                           throws ParseException
Throws:
ParseException

Beta

public final void Beta()
                throws ParseException
Throws:
ParseException

BetaN

public final void BetaN()
                 throws ParseException
Throws:
ParseException

Incu

public final void Incu()
                throws ParseException
Throws:
ParseException

Inf

public final void Inf()
               throws ParseException
Throws:
ParseException

Diag

public final void Diag()
                throws ParseException
Throws:
ParseException

CeaseTime

public final void CeaseTime()
                     throws ParseException
In case there is any information about it being a transmission experiment

Throws:
ParseException

UnitList

public final void UnitList()
                    throws ParseException
Throws:
ParseException

Vaccinated

public final void Vaccinated()
                      throws ParseException
Throws:
ParseException

Unit

public final void Unit()
                throws ParseException
Throws:
ParseException

StartValue

public final void StartValue()
                      throws ParseException
Start valu of a time

Throws:
ParseException

EventTime

public final void EventTime()
                     throws ParseException
Event time - either a double or NA with start value We throw on stack in top: startValue, top-1: t

Throws:
ParseException

DiagEventTime

public final void DiagEventTime()
                         throws ParseException
Diagnosed events can be censored

Throws:
ParseException

RecTimeList

public final void RecTimeList()
                       throws ParseException
Each individual having events is listed, one per line with format posx posy eventTime eventTime

Throws:
ParseException

ReInit

public void ReInit(java.io.InputStream stream)

ReInit

public void ReInit(java.io.Reader stream)

ReInit

public void ReInit(DataFileSpecTokenManager tm)

getNextToken

public final Token getNextToken()

getToken

public final Token getToken(int index)

generateParseException

public final ParseException generateParseException()

enable_tracing

public final void enable_tracing()

disable_tracing

public final void disable_tracing()