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

A

AbstractAnt - Class in biosim.core.body

AbstractAnt() - Constructor for class biosim.core.body.AbstractAnt

AbstractFish - Class in biosim.core.body

AbstractFish() - Constructor for class biosim.core.body.AbstractFish

AbstractFly - Class in biosim.core.body

AbstractFly() - Constructor for class biosim.core.body.AbstractFly

AbstractMonkey - Class in biosim.core.body

This class collects the sensors and actuators for a general body suitible for representing monkeys.

AbstractMonkey() - Constructor for class biosim.core.body.AbstractMonkey

acqTimes - Static variable in class biosim.app.learnedants.LearnedAnts

acqTimes - Static variable in class biosim.app.twostateants.RandomAnt

acqTimes - Static variable in class biosim.app.twostateants.TwoStateAnt

act(double) - Method in class biosim.app.antknn.AntKNN

act(double) - Method in class biosim.app.domworld.DomWorldMonkey

act(double) - Method in class biosim.app.domworld.DomWorldStateMachine

act(double) - Method in class biosim.app.domworld.DomWorldStateMachine.Flee

act(double) - Method in class biosim.app.fishknn.FishKNN

act(double) - Method in class biosim.app.fishknn.FishKNNProx

act(double) - Method in class biosim.app.fishknn.FishKNNZones

act(double) - Method in class biosim.app.fishknn.FishZones

act(double) - Method in class biosim.app.fishlr.FishLR

act(double) - Method in class biosim.app.fishlr.LeaderFish

act(double) - Method in class biosim.app.learnedants.LearnedAnts

act(double) - Method in class biosim.app.tutorial.AvoidAnt

act(double) - Method in class biosim.app.twostateants.LazyFly

act(double) - Method in class biosim.app.twostateants.RandomAnt

act(double) - Method in class biosim.app.twostateants.TwoStateAnt

act(double) - Method in interface biosim.core.agent.Agent

act(double) - Method in class biosim.core.agent.StateMachine

act(double) - Method in interface biosim.core.agent.StateMachine.State

AdaptiveKernelDensityEstimator - Class in biosim.core.util

AdaptiveKernelDensityEstimator(int, Kernel) - Constructor for class biosim.core.util.AdaptiveKernelDensityEstimator

AdaptiveKernelDensityEstimator.NormalKernel - Class in biosim.core.util

AdaptiveKernelDensityEstimator.NormalKernel(double) - Constructor for class biosim.core.util.AdaptiveKernelDensityEstimator.NormalKernel

add(double[]) - Method in class biosim.core.util.AdaptiveKernelDensityEstimator

add(double[]) - Method in class biosim.core.util.annwrapper.SimpleANN

add(double[], double[]) - Method in class biosim.core.util.FastKNN

add(double[], double[], double) - Method in class biosim.core.util.FastKNN

add(double[], double) - Method in class biosim.core.util.kdewrapper.SimpleKDE

add(double[]) - Method in class biosim.core.util.kdewrapper.SimpleKDE

add(double[]) - Method in class biosim.core.util.KernelDensityEstimator

add(double[], double) - Method in class biosim.core.util.KernelDensityEstimator

addBody(Body) - Method in class biosim.core.sim.Environment

addLogger(Logger) - Method in class biosim.core.sim.Simulation

addNoCheck(double[], double) - Method in class biosim.core.util.kdewrapper.SimpleKDE

addObjectsToSim(Simulation) - Method in class biosim.core.sim.Environment

addObstacle(Obstacle, double, double) - Method in class biosim.core.sim.Environment

addStaticPOI(String, double, double) - Method in class biosim.core.sim.Environment

addToKDE(SimpleKDE[], int[]) - Method in class biosim.app.learnedants.BIOHMM

Agent - Interface in biosim.core.agent

agent - Variable in class biosim.core.body.Body

AllVisibleSameType - Interface in biosim.core.body.sensors

This sensor returns a list of all the visible agents of the same kind within a specified field-of-view and range.

AllVisibleSameTypeVecs - Interface in biosim.core.body.sensors

This sensor returns a list of vectors to all the visible agents of the same kind within a specified field-of-view and range.

annwrapper - Class in biosim.core.util.annwrapper

annwrapper() - Constructor for class biosim.core.util.annwrapper.annwrapper

annwrapperJNI - Class in biosim.core.util.annwrapper

annwrapperJNI() - Constructor for class biosim.core.util.annwrapper.annwrapperJNI

antBody - Variable in class biosim.app.twostateants.RandomAnt

antBody - Variable in class biosim.app.twostateants.TwoStateAnt

antboolout - Variable in class biosim.app.tutorial.AvoidAntLogger

antboolout - Variable in class biosim.app.twostateants.TwoStateLogger

antDists - Static variable in class biosim.app.learnedants.LearnedAnts

antDists - Static variable in class biosim.app.twostateants.RandomAnt

antDists - Static variable in class biosim.app.twostateants.TwoStateAnt

AntKNN - Class in biosim.app.antknn

AntKNN(AbstractAnt, FastKNN) - Constructor for class biosim.app.antknn.AntKNN

antout - Variable in class biosim.app.tutorial.AvoidAntLogger

antout - Variable in class biosim.app.twostateants.TwoStateLogger

antTimes - Static variable in class biosim.app.learnedants.LearnedAnts

antVec - Variable in class biosim.app.learnedants.BIOHMMInputParser

antVec - Variable in class biosim.app.learnedants.RealAntInputParser

AphaenogasterCockerelli - Class in biosim.core.body

AphaenogasterCockerelli() - Constructor for class biosim.core.body.AphaenogasterCockerelli

APPROACH_SPEED - Static variable in class biosim.app.domworld.DomWorldMonkey

ATTRACTION_ZONE_IDX - Static variable in class biosim.core.body.NotemigonusCrysoleucas

ATTRACTION_ZONE_RANGE - Static variable in class biosim.core.body.NotemigonusCrysoleucas

atWaypoint(MutableDouble2D) - Method in class biosim.app.domworld.DomWorldStateMachine

AVERAGE_EVENT_TIME - Static variable in class biosim.app.domworld.DomWorldMonkey

AVERAGE_EVENT_TIME - Static variable in class biosim.app.domworld.DomWorldStateMachine

AverageSameTypeVec - Interface in biosim.core.body.sensors

AVOID_RANGE - Static variable in class biosim.app.tutorial.AvoidAnt

AVOID_TIME - Static variable in class biosim.app.twostateants.TwoStateAnt

AvoidAnt - Class in biosim.app.tutorial

AvoidAnt(AbstractAnt) - Constructor for class biosim.app.tutorial.AvoidAnt

AvoidAntLogger - Class in biosim.app.tutorial

AvoidAntLogger() - Constructor for class biosim.app.tutorial.AvoidAntLogger

AvoidAntLogger(File) - Constructor for class biosim.app.tutorial.AvoidAntLogger

B

b - Variable in class biosim.app.learnedants.BIOHMM

BasicBodyPortrayal - Class in biosim.core.gui.portrayals

BasicBodyPortrayal(Simulation, Object) - Constructor for class biosim.core.gui.portrayals.BasicBodyPortrayal

bi - Static variable in class biosim.app.fishknn.FishPortrayal

BIOHMM - Class in biosim.app.learnedants

BIOHMM(int, BIOHMMInputParser) - Constructor for class biosim.app.learnedants.BIOHMM

BIOHMMInputParser - Class in biosim.app.learnedants

BIOHMMInputParser(BTFData) - Constructor for class biosim.app.learnedants.BIOHMMInputParser

biosim.app.antknn - package biosim.app.antknn

biosim.app.btfreplay - package biosim.app.btfreplay

biosim.app.domworld - package biosim.app.domworld

biosim.app.fishknn - package biosim.app.fishknn

biosim.app.fishlr - package biosim.app.fishlr

biosim.app.learnedants - package biosim.app.learnedants

biosim.app.tutorial - package biosim.app.tutorial

biosim.app.twostateants - package biosim.app.twostateants

biosim.core.agent - package biosim.core.agent

biosim.core.body - package biosim.core.body

biosim.core.body.actuators - package biosim.core.body.actuators

biosim.core.body.sensors - package biosim.core.body.sensors

biosim.core.gui - package biosim.core.gui

biosim.core.gui.portrayals - package biosim.core.gui.portrayals

biosim.core.sim - package biosim.core.sim

biosim.core.util - package biosim.core.util

biosim.core.util.annwrapper - package biosim.core.util.annwrapper

biosim.core.util.kdewrapper - package biosim.core.util.kdewrapper

bodies - Variable in class biosim.core.sim.Simulation

body - Variable in class biosim.app.fishknn.FishPortrayal

body - Variable in class biosim.app.twostateants.FoodPortrayal

Body - Class in biosim.core.body

Body() - Constructor for class biosim.core.body.Body

body - Variable in class biosim.core.gui.portrayals.BasicBodyPortrayal

bodyOrientations - Variable in class biosim.core.sim.Simulation

BTFData - Class in biosim.core.util

BTFData() - Constructor for class biosim.core.util.BTFData

BTFLogger - Class in biosim.core.util

BTFLogger() - Constructor for class biosim.core.util.BTFLogger

BTFLogger(File) - Constructor for class biosim.core.util.BTFLogger

BTFMetaData - Class in biosim.core.util

BTFMetaData() - Constructor for class biosim.core.util.BTFMetaData

BTFReplay - Class in biosim.app.btfreplay

BTFReplay() - Constructor for class biosim.app.btfreplay.BTFReplay

buildParameters(File) - Method in class biosim.app.learnedants.LearnedAnts

C

calcGammaFromXi(double[][][], double[][]) - Method in class biosim.app.learnedants.BIOHMM

calculateAlpha(ArrayList<Integer>, SimpleKDE[], double[][]) - Method in class biosim.app.learnedants.BIOHMM

calculateBeta(ArrayList<Integer>, SimpleKDE[], double[][]) - Method in class biosim.app.learnedants.BIOHMM

calculateLogAlpha(ArrayList<Integer>, SimpleKDE[], double[][]) - Method in class biosim.app.learnedants.BIOHMM

calculateLogBeta(ArrayList<Integer>, SimpleKDE[], double[][]) - Method in class biosim.app.learnedants.BIOHMM

calculateLogGamma(double[][], double[][], double[][]) - Method in class biosim.app.learnedants.BIOHMM

calculateLogXi(ArrayList<Integer>, SimpleKDE[], double[][], double[][], double[][][]) - Method in class biosim.app.learnedants.BIOHMM

calculateScaledAlpha(ArrayList<Integer>, SimpleKDE[], double[][], double[]) - Method in class biosim.app.learnedants.BIOHMM

calculateScaledBeta(ArrayList<Integer>, SimpleKDE[], double[][], double[]) - Method in class biosim.app.learnedants.BIOHMM

calculateSeqLogLikelihood(double[][], double[]) - Method in class biosim.app.learnedants.BIOHMM

calculateSeqLogLikelihood(double[][]) - Method in class biosim.app.learnedants.BIOHMM

calculateXi(ArrayList<Integer>, SimpleKDE[], double[][], double[][], double[][][]) - Method in class biosim.app.learnedants.BIOHMM

calcXiFromScaled(ArrayList<Integer>, SimpleKDE[], double[][], double[][], double[][][]) - Method in class biosim.app.learnedants.BIOHMM

CHASE - Static variable in class biosim.app.domworld.DomWorldStateMachine

CHASE_DIST - Static variable in class biosim.app.domworld.DomWorldStateMachine

CHASE_SPEED - Static variable in class biosim.app.domworld.DomWorldStateMachine

chaseEnd - Variable in class biosim.app.domworld.DomWorldMonkey

chaseLoiterTimeout(double) - Method in class biosim.app.domworld.DomWorldStateMachine

chaseTowards - Variable in class biosim.app.domworld.DomWorldMonkey

CLASSES - Static variable in class biosim.app.fishknn.FishKNN

CLASSES - Static variable in class biosim.app.fishknn.FishKNNProx

CLASSES - Static variable in class biosim.app.fishknn.FishKNNZones

clear() - Method in class biosim.core.util.kdewrapper.SimpleKDE

closeFiles() - Method in class biosim.app.fishknn.FishKNNLogger

closeFiles() - Method in class biosim.app.tutorial.AvoidAntLogger

closeFiles() - Method in class biosim.core.util.BTFLogger

closestPoint(Double2D, Double2D) - Method in interface biosim.core.sim.Obstacle

closestPoint(Double2D, Double2D) - Method in class biosim.core.sim.RectObstacle

collectTimes - Static variable in class biosim.app.learnedants.LearnedAnts

collectTimes - Static variable in class biosim.app.twostateants.RandomAnt

collectTimes - Static variable in class biosim.app.twostateants.TwoStateAnt

collisionCheck(MutableDouble2D, MutableDouble2D) - Method in class biosim.core.body.Body

columns - Variable in class biosim.core.util.BTFData

Compass - Interface in biosim.core.body.sensors

computeNewConfiguration(MutableDouble2D, MutableDouble2D) - Method in class biosim.core.body.AphaenogasterCockerelli

computeNewConfiguration(MutableDouble2D, MutableDouble2D) - Method in class biosim.core.body.Body

computeNewConfiguration(MutableDouble2D, MutableDouble2D) - Method in class biosim.core.body.DrosophilaMelanogaster

computeNewConfiguration(MutableDouble2D, MutableDouble2D) - Method in class biosim.core.body.NotemigonusCrysoleucas

computeNewConfiguration(MutableDouble2D, MutableDouble2D) - Method in class biosim.core.body.ReplayBody

computeNewConfiguration(MutableDouble2D, MutableDouble2D) - Method in class biosim.core.body.RhesusMacaque

config(Properties) - Static method in class biosim.app.domworld.SmallDomWorld

configSim(Simulation) - Method in class biosim.core.sim.Environment

Method which sets up a simulation according to the configuration modeled by this class.

configure(Properties) - Static method in class biosim.app.domworld.DomWorldStateMachine

D

defaultConfig() - Static method in class biosim.app.domworld.SmallDomWorld

delete() - Method in class biosim.core.util.annwrapper.SimpleANN

delete() - Method in class biosim.core.util.kdewrapper.SimpleKDE

delete_SimpleANN(long) - Static method in class biosim.core.util.annwrapper.annwrapperJNI

delete_SimpleKDE(long) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

desiredboolout - Variable in class biosim.app.fishknn.FishKNNLogger

desiredboolout - Variable in class biosim.app.tutorial.AvoidAntLogger

desiredboolout - Variable in class biosim.app.twostateants.TwoStateLogger

desiredout - Variable in class biosim.app.fishknn.FishKNNLogger

desiredout - Variable in class biosim.app.tutorial.AvoidAntLogger

desiredout - Variable in class biosim.app.twostateants.TwoStateLogger

desiredVel - Variable in class biosim.app.learnedants.BIOHMMInputParser

desiredVel - Variable in class biosim.app.learnedants.RealAntInputParser

desiredVelXYT - Variable in class biosim.core.body.AphaenogasterCockerelli

desiredVelXYT - Variable in class biosim.core.body.DrosophilaMelanogaster

desiredVelXYT - Variable in class biosim.core.body.NotemigonusCrysoleucas

DIM - Static variable in class biosim.app.learnedants.BIOHMMInputParser

DIM - Static variable in class biosim.app.learnedants.RealAntInputParser

dimensionality - Variable in class biosim.core.util.KernelDensityEstimator

DirectionToPOI - Interface in biosim.core.body.sensors

display - Variable in class biosim.core.gui.GUISimulation

displayFrame - Variable in class biosim.core.gui.GUISimulation

displayHeightPixels - Variable in class biosim.core.gui.GUISimulation

displayMap - Variable in class biosim.core.gui.GUISimulation

displayWidthPixels - Variable in class biosim.core.gui.GUISimulation

dominanceRank - Variable in class biosim.app.domworld.DomWorldMonkey

DomWorld - Class in biosim.app.domworld

DomWorld() - Constructor for class biosim.app.domworld.DomWorld

DomWorldMonkey - Class in biosim.app.domworld

DomWorldMonkey(AbstractMonkey, double) - Constructor for class biosim.app.domworld.DomWorldMonkey

DomWorldStateMachine - Class in biosim.app.domworld

DomWorldStateMachine(AbstractMonkey, double) - Constructor for class biosim.app.domworld.DomWorldStateMachine

DomWorldStateMachine.Flee - Class in biosim.app.domworld

DomWorldStateMachine.Flee() - Constructor for class biosim.app.domworld.DomWorldStateMachine.Flee

draw(Object, Graphics2D, DrawInfo2D) - Method in class biosim.app.btfreplay.ReplayPortrayal

draw(Object, Graphics2D, DrawInfo2D) - Method in class biosim.app.domworld.StateMachinePortrayal

draw(Object, Graphics2D, DrawInfo2D) - Method in class biosim.app.fishknn.FishPortrayal

draw(Object, Graphics2D, DrawInfo2D) - Method in class biosim.app.twostateants.FoodPortrayal

draw(Object, Graphics2D, DrawInfo2D) - Method in class biosim.core.gui.portrayals.BasicBodyPortrayal

draw(Object, Graphics2D, DrawInfo2D) - Method in class biosim.core.gui.portrayals.RectObstaclePortrayal

DrosophilaMelanogaster - Class in biosim.core.body

DrosophilaMelanogaster() - Constructor for class biosim.core.body.DrosophilaMelanogaster

E

elnsum(double, double) - Static method in class biosim.app.learnedants.BIOHMM

ENCOUNTER - Static variable in class biosim.app.domworld.DomWorldStateMachine

env - Variable in class biosim.core.sim.Simulation

Environment - Class in biosim.core.sim

Environment is a helper class for setting up the initial state of a Simulation before it is run.

Environment(double, double, double) - Constructor for class biosim.core.sim.Environment

EnvironmentSize2D - Interface in biosim.core.body.sensors

EPSILON - Static variable in class biosim.app.domworld.DomWorldStateMachine

estimate(double[], double, int) - Method in class biosim.core.util.AdaptiveKernelDensityEstimator

Estimate f(x) using an adaptive bandwidth.

estimate(double[], double) - Method in class biosim.core.util.kdewrapper.SimpleKDE

estimate(double[], double) - Method in class biosim.core.util.KernelDensityEstimator

ETA - Static variable in class biosim.app.domworld.DomWorldStateMachine

F

FAR_DIST - Static variable in class biosim.app.domworld.DomWorldMonkey

FAR_DIST - Static variable in class biosim.app.domworld.DomWorldStateMachine

FastKNN - Class in biosim.core.util

FastKNN(int, int) - Constructor for class biosim.core.util.FastKNN

FB_BETA - Static variable in class biosim.app.fishlr.FishLR

FEATURE_DIM - Static variable in class biosim.app.antknn.AntKNN

FEATURE_DIM - Static variable in class biosim.app.learnedants.LearnedAnts

FEATURE_WEIGHTS - Static variable in class biosim.app.fishknn.FishKNN

FEATURE_WEIGHTS - Static variable in class biosim.app.fishknn.FishKNNProx

FEATURE_WEIGHTS - Static variable in class biosim.app.fishknn.FishKNNZones

FEATURES - Static variable in class biosim.app.fishknn.FishKNN

FEATURES - Static variable in class biosim.app.fishknn.FishKNNProx

FEATURES - Static variable in class biosim.app.fishknn.FishKNNZones

field2D - Variable in class biosim.core.sim.Simulation

field2DPortrayal - Variable in class biosim.core.gui.GUISimulation

finalize() - Method in class biosim.core.util.annwrapper.SimpleANN

finalize() - Method in class biosim.core.util.kdewrapper.SimpleKDE

finish() - Method in class biosim.app.antknn.AntKNN

finish() - Method in class biosim.app.domworld.DomWorldMonkey

finish() - Method in class biosim.app.domworld.DomWorldStateMachine

finish() - Method in class biosim.app.fishknn.FishKNN

finish() - Method in class biosim.app.fishknn.FishKNNProx

finish() - Method in class biosim.app.fishknn.FishKNNZones

finish() - Method in class biosim.app.fishknn.FishZones

finish() - Method in class biosim.app.fishlr.FishLR

finish() - Method in class biosim.app.fishlr.LeaderFish

finish() - Method in class biosim.app.learnedants.LearnedAnts

finish() - Method in class biosim.app.tutorial.AvoidAnt

finish() - Method in class biosim.app.twostateants.LazyFly

finish() - Method in class biosim.app.twostateants.RandomAnt

finish() - Method in class biosim.app.twostateants.TwoStateAnt

finish() - Method in class biosim.app.twostateants.TwoStateLogger

finish() - Method in interface biosim.core.agent.Agent

finish() - Method in class biosim.core.body.Body

finish() - Method in interface biosim.core.sim.Logger

finish() - Method in class biosim.core.sim.Simulation

finish() - Method in class biosim.core.util.BTFLogger

FishKNN - Class in biosim.app.fishknn

FishKNN(AbstractFish, FastKNN) - Constructor for class biosim.app.fishknn.FishKNN

FishKNNLogger - Class in biosim.app.fishknn

FishKNNLogger() - Constructor for class biosim.app.fishknn.FishKNNLogger

FishKNNLogger(File) - Constructor for class biosim.app.fishknn.FishKNNLogger

FishKNNProx - Class in biosim.app.fishknn

FishKNNProx(AbstractFish, FastKNN) - Constructor for class biosim.app.fishknn.FishKNNProx

FishKNNZones - Class in biosim.app.fishknn

FishKNNZones(AbstractFish, FastKNN) - Constructor for class biosim.app.fishknn.FishKNNZones

FishLR - Class in biosim.app.fishlr

FishLR(AbstractFish) - Constructor for class biosim.app.fishlr.FishLR

FishPortrayal - Class in biosim.app.fishknn

FishPortrayal(Simulation, Object) - Constructor for class biosim.app.fishknn.FishPortrayal

FishZones - Class in biosim.app.fishknn

FishZones(AbstractFish) - Constructor for class biosim.app.fishknn.FishZones

FLEE - Static variable in class biosim.app.domworld.DomWorldStateMachine

FLEE_DIST - Static variable in class biosim.app.domworld.DomWorldStateMachine

FLEE_SPEED - Static variable in class biosim.app.domworld.DomWorldStateMachine

fleeEnd - Variable in class biosim.app.domworld.DomWorldMonkey

fleeFrom - Variable in class biosim.app.domworld.DomWorldMonkey

fleeLoiterTimeout(double) - Method in class biosim.app.domworld.DomWorldStateMachine

foodCounter - Variable in class biosim.app.learnedants.LearnedAnts

foodCounter - Variable in class biosim.app.twostateants.RandomAnt

foodCounter - Variable in class biosim.app.twostateants.TwoStateAnt

foodCounts - Static variable in class biosim.app.learnedants.LearnedAnts

foodCounts - Static variable in class biosim.app.twostateants.RandomAnt

foodCounts - Static variable in class biosim.app.twostateants.TwoStateAnt

foodInGripperOut - Variable in class biosim.app.twostateants.TwoStateLogger

FoodPortrayal - Class in biosim.app.twostateants

FoodPortrayal(Simulation, Object) - Constructor for class biosim.app.twostateants.FoodPortrayal

foodVec - Variable in class biosim.app.learnedants.BIOHMMInputParser

foodVecOut - Variable in class biosim.app.twostateants.TwoStateLogger

FORAGE - Static variable in class biosim.app.twostateants.TwoStateAnt

foundSequences - Variable in class biosim.app.learnedants.BIOHMMInputParser

foundSequences - Variable in class biosim.app.learnedants.RealAntInputParser

FRONTAL_FOV - Static variable in class biosim.app.domworld.DomWorldMonkey

FRONTAL_FOV - Static variable in class biosim.app.domworld.DomWorldStateMachine

G

getAbsoluteOrientation(MutableDouble2D) - Method in class biosim.core.body.RhesusMacaque

getAbsoluteOrientation(MutableDouble2D) - Method in interface biosim.core.body.sensors.Compass

getAbsolutePosition(MutableDouble2D) - Method in class biosim.core.body.RhesusMacaque

getAbsolutePosition(MutableDouble2D) - Method in interface biosim.core.body.sensors.GPS

getAgent() - Method in class biosim.core.body.Body

getAllVisibleSameType(List<Agent>) - Method in class biosim.core.body.RhesusMacaque

getAllVisibleSameType(List<Agent>) - Method in interface biosim.core.body.sensors.AllVisibleSameType

Queries the sensor for visible agents.

getAllVisibleSameTypeSensorFoV() - Method in class biosim.core.body.RhesusMacaque

getAllVisibleSameTypeSensorFoV() - Method in interface biosim.core.body.sensors.AllVisibleSameType

Returns the field-of-view of this sensor.

getAllVisibleSameTypeSensorRange() - Method in class biosim.core.body.RhesusMacaque

getAllVisibleSameTypeSensorRange() - Method in interface biosim.core.body.sensors.AllVisibleSameType

Returns the range of this sensor.

getAllVisibleSameTypeVecs(List<MutableDouble2D>) - Method in class biosim.core.body.RhesusMacaque

getAllVisibleSameTypeVecs(List<MutableDouble2D>) - Method in interface biosim.core.body.sensors.AllVisibleSameTypeVecs

Queries the sensor for visible agents.

getAllVisibleSameTypeVecsSensorFoV() - Method in class biosim.core.body.RhesusMacaque

getAllVisibleSameTypeVecsSensorFoV() - Method in interface biosim.core.body.sensors.AllVisibleSameTypeVecs

Returns the field-of-view of this sensor.

getAllVisibleSameTypeVecsSensorRange() - Method in class biosim.core.body.RhesusMacaque

getAllVisibleSameTypeVecsSensorRange() - Method in interface biosim.core.body.sensors.AllVisibleSameTypeVecs

Returns the range of this sensor.

getAverageSameTypeVec(MutableDouble2D) - Method in class biosim.core.body.NotemigonusCrysoleucas

getAverageSameTypeVec(MutableDouble2D) - Method in interface biosim.core.body.sensors.AverageSameTypeVec

getAverageSameTypeVecSensorRange() - Method in class biosim.core.body.NotemigonusCrysoleucas

getAverageSameTypeVecSensorRange() - Method in interface biosim.core.body.sensors.AverageSameTypeVec

getBodyOrientation(Body, MutableDouble2D) - Method in class biosim.core.sim.Simulation

getCPtr(SimpleANN) - Static method in class biosim.core.util.annwrapper.SimpleANN

getCPtr(SimpleKDE) - Static method in class biosim.core.util.kdewrapper.SimpleKDE

getDataAtIDX(int) - Method in class biosim.app.learnedants.BIOHMMInputParser

getDataAtIDX(int) - Method in class biosim.app.learnedants.RealAntInputParser

getDataAtIDX(int) - Method in class biosim.app.learnedants.SimpleInputParser

getDesiredVel() - Method in class biosim.core.body.AphaenogasterCockerelli

getDim() - Method in class biosim.core.util.kdewrapper.SimpleKDE

getDist(double[], int) - Method in class biosim.core.util.kdewrapper.SimpleKDE

getEnvironmentSize(MutableDouble2D) - Method in class biosim.core.body.RhesusMacaque

getEnvironmentSize(MutableDouble2D) - Method in interface biosim.core.body.sensors.EnvironmentSize2D

getGripped() - Method in class biosim.core.body.AphaenogasterCockerelli

getGripped() - Method in interface biosim.core.body.sensors.GripperSensor

getHomeDir(MutableDouble2D) - Method in class biosim.core.body.AphaenogasterCockerelli

getHomeDir(MutableDouble2D) - Method in interface biosim.core.body.sensors.Homing

getIdx(double[]) - Method in class biosim.core.util.kdewrapper.SimpleKDE

getInfo() - Static method in class biosim.core.gui.GUISimulation

getName() - Static method in class biosim.core.gui.GUISimulation

getNearestObstacleVec(MutableDouble2D) - Method in class biosim.core.body.AphaenogasterCockerelli

getNearestObstacleVec(MutableDouble2D) - Method in class biosim.core.body.DrosophilaMelanogaster

getNearestObstacleVec(MutableDouble2D) - Method in class biosim.core.body.NotemigonusCrysoleucas

getNearestObstacleVec(MutableDouble2D) - Method in class biosim.core.body.RhesusMacaque

getNearestObstacleVec(MutableDouble2D) - Method in interface biosim.core.body.sensors.NearestObstacleVec

getNearestObstacleVecSensorRange() - Method in class biosim.core.body.AphaenogasterCockerelli

getNearestObstacleVecSensorRange() - Method in class biosim.core.body.DrosophilaMelanogaster

getNearestObstacleVecSensorRange() - Method in class biosim.core.body.NotemigonusCrysoleucas

getNearestObstacleVecSensorRange() - Method in class biosim.core.body.RhesusMacaque

getNearestObstacleVecSensorRange() - Method in interface biosim.core.body.sensors.NearestObstacleVec

getNearestPredatorVec(MutableDouble2D) - Method in class biosim.core.body.DrosophilaMelanogaster

getNearestPredatorVec(MutableDouble2D) - Method in interface biosim.core.body.sensors.NearestPredatorVec

getNearestPredatorVecSensorRange() - Method in class biosim.core.body.DrosophilaMelanogaster

getNearestPredatorVecSensorRange() - Method in interface biosim.core.body.sensors.NearestPredatorVec

getNearestPreyVec(MutableDouble2D) - Method in class biosim.core.body.AphaenogasterCockerelli

getNearestPreyVec(MutableDouble2D) - Method in interface biosim.core.body.sensors.NearestPreyVec

getNearestPreyVecSensorRange() - Method in class biosim.core.body.AphaenogasterCockerelli

getNearestPreyVecSensorRange() - Method in interface biosim.core.body.sensors.NearestPreyVec

getNearestSameTypeVec(MutableDouble2D) - Method in class biosim.core.body.AphaenogasterCockerelli

getNearestSameTypeVec(MutableDouble2D) - Method in class biosim.core.body.DrosophilaMelanogaster

getNearestSameTypeVec(MutableDouble2D) - Method in class biosim.core.body.NotemigonusCrysoleucas

getNearestSameTypeVec(MutableDouble2D) - Method in interface biosim.core.body.sensors.NearestSameTypeVec

getNearestSameTypeVecSensorRange() - Method in class biosim.core.body.AphaenogasterCockerelli

getNearestSameTypeVecSensorRange() - Method in class biosim.core.body.DrosophilaMelanogaster

getNearestSameTypeVecSensorRange() - Method in class biosim.core.body.NotemigonusCrysoleucas

getNearestSameTypeVecSensorRange() - Method in interface biosim.core.body.sensors.NearestSameTypeVec

getNumProximitySensors() - Method in class biosim.core.body.NotemigonusCrysoleucas

getNumProximitySensors() - Method in interface biosim.core.body.sensors.Proximity

getNumZones() - Method in class biosim.core.body.NotemigonusCrysoleucas

getNumZones() - Method in interface biosim.core.body.sensors.ZoneCoMVecs

getParams(String) - Static method in class biosim.app.domworld.SmallDomWorld

getPoiDir(MutableDouble2D, String) - Method in class biosim.core.body.AphaenogasterCockerelli

getPoiDir(MutableDouble2D, String) - Method in interface biosim.core.body.sensors.DirectionToPOI

getPoiVec(MutableDouble2D, String) - Method in interface biosim.core.body.sensors.VectorToPOI

getProximity(double[]) - Method in class biosim.core.body.NotemigonusCrysoleucas

getProximity(double[]) - Method in interface biosim.core.body.sensors.Proximity

getProximitySensorRange() - Method in class biosim.core.body.NotemigonusCrysoleucas

getProximitySensorRange() - Method in interface biosim.core.body.sensors.Proximity

getRandom() - Method in class biosim.core.body.AphaenogasterCockerelli

getRandom() - Method in class biosim.core.body.Body

getRandom() - Method in class biosim.core.body.DrosophilaMelanogaster

getRandom() - Method in class biosim.core.body.NotemigonusCrysoleucas

getRandom() - Method in class biosim.core.body.ReplayBody

getRandom() - Method in class biosim.core.body.RhesusMacaque

getSample(double[], int) - Method in class biosim.core.util.kdewrapper.SimpleKDE

getSelfVelXYT(double[]) - Method in class biosim.core.body.AphaenogasterCockerelli

getSelfVelXYT(double[]) - Method in class biosim.core.body.DrosophilaMelanogaster

getSelfVelXYT(double[]) - Method in class biosim.core.body.NotemigonusCrysoleucas

getSelfVelXYT(double[]) - Method in interface biosim.core.body.sensors.SelfVelXYT

getSensors(AbstractAnt) - Static method in class biosim.app.learnedants.BIOHMMInputParser

getSensors(AbstractAnt) - Static method in class biosim.app.learnedants.RealAntInputParser

getSensorsAtIDX(int) - Method in class biosim.app.learnedants.BIOHMMInputParser

getSensorsAtIDX(int) - Method in class biosim.app.learnedants.RealAntInputParser

getSensorsAtIDX(int) - Method in class biosim.app.learnedants.SimpleInputParser

getSequences() - Method in class biosim.app.learnedants.BIOHMMInputParser

getSequences() - Method in class biosim.app.learnedants.RealAntInputParser

getSequences() - Method in class biosim.app.learnedants.SimpleInputParser

getSize() - Method in class biosim.core.body.AphaenogasterCockerelli

getSize() - Method in class biosim.core.body.Body

The size of the body in meters.

getSize() - Method in class biosim.core.body.DrosophilaMelanogaster

getSize() - Method in class biosim.core.body.NotemigonusCrysoleucas

getSize() - Method in class biosim.core.body.ReplayBody

getSize() - Method in class biosim.core.body.RhesusMacaque

getStateAtIDX(int) - Method in class biosim.app.learnedants.BIOHMMInputParser

getStateAtIDX(int) - Method in class biosim.app.learnedants.RealAntInputParser

getSwitch(AbstractAnt) - Static method in class biosim.app.learnedants.BIOHMMInputParser

getSwitch(AbstractAnt) - Static method in class biosim.app.learnedants.RealAntInputParser

getSwitchAtIDX(int) - Method in class biosim.app.learnedants.BIOHMMInputParser

getSwitchAtIDX(int) - Method in class biosim.app.learnedants.RealAntInputParser

getSwitchAtIDX(int) - Method in class biosim.app.learnedants.SimpleInputParser

getTextDisplay() - Method in interface biosim.core.body.actuators.TextDisplay

getTextDisplay() - Method in class biosim.core.body.RhesusMacaque

getVel() - Method in class biosim.core.body.AphaenogasterCockerelli

getWeight(int) - Method in class biosim.core.util.kdewrapper.SimpleKDE

getZoneCoMVecs(MutableDouble2D[]) - Method in class biosim.core.body.NotemigonusCrysoleucas

getZoneCoMVecs(MutableDouble2D[]) - Method in interface biosim.core.body.sensors.ZoneCoMVecs

getZoneRanges(double[]) - Method in class biosim.core.body.NotemigonusCrysoleucas

getZoneRanges(double[]) - Method in interface biosim.core.body.sensors.ZoneCoMVecs

GO_TO_WAYPOINT - Static variable in class biosim.app.domworld.DomWorldStateMachine

GPS - Interface in biosim.core.body.sensors

grabbedBy - Variable in class biosim.core.body.AbstractFly

grabbing - Variable in class biosim.core.body.AbstractAnt

GRIP_RANGE - Static variable in class biosim.core.body.AphaenogasterCockerelli

Gripper - Interface in biosim.core.body.actuators

gripperBool - Variable in class biosim.app.learnedants.BIOHMMInputParser

GripperSensor - Interface in biosim.core.body.sensors

GROUP - Static variable in class biosim.app.domworld.DomWorldStateMachine

GROUP_DIST - Static variable in class biosim.app.domworld.DomWorldStateMachine

GROUP_SPEED - Static variable in class biosim.app.domworld.DomWorldStateMachine

groupLoiterTimeout(double) - Method in class biosim.app.domworld.DomWorldStateMachine

GUI - Static variable in class biosim.app.domworld.SmallDomWorld

GUISimulation - Class in biosim.core.gui

GUISimulation(Simulation) - Constructor for class biosim.core.gui.GUISimulation

H

HEIGHT - Static variable in class biosim.app.antknn.AntKNN

HEIGHT - Static variable in class biosim.app.btfreplay.BTFReplay

HEIGHT - Static variable in class biosim.app.domworld.DomWorld

HEIGHT - Static variable in class biosim.app.domworld.SmallDomWorld

HEIGHT - Static variable in class biosim.app.fishknn.FishKNN

HEIGHT - Static variable in class biosim.app.fishknn.FishZones

HEIGHT - Static variable in class biosim.app.fishlr.FishLR

HEIGHT - Static variable in class biosim.app.learnedants.LearnedAnts

HEIGHT - Static variable in class biosim.app.tutorial.Tutorial

HEIGHT - Static variable in class biosim.app.twostateants.RandomAnt

HEIGHT - Static variable in class biosim.app.twostateants.TwoStateAnt

height - Variable in class biosim.core.sim.Environment

height - Variable in class biosim.core.sim.RectObstacle

HIERARCHY_STABILITY - Static variable in class biosim.app.domworld.DomWorldStateMachine

HolonomicDrive - Interface in biosim.core.body.actuators

homeout - Variable in class biosim.app.tutorial.AvoidAntLogger

homeout - Variable in class biosim.app.twostateants.TwoStateLogger

Homing - Interface in biosim.core.body.sensors

I

idout - Variable in class biosim.app.twostateants.TwoStateLogger

idout - Variable in class biosim.core.util.BTFLogger

init() - Method in class biosim.app.antknn.AntKNN

init() - Method in class biosim.app.domworld.DomWorldMonkey

init() - Method in class biosim.app.domworld.DomWorldStateMachine

init() - Method in class biosim.app.fishknn.FishKNN

init() - Method in class biosim.app.fishknn.FishKNNProx

init() - Method in class biosim.app.fishknn.FishKNNZones

init() - Method in class biosim.app.fishknn.FishZones

init() - Method in class biosim.app.fishlr.FishLR

init() - Method in class biosim.app.fishlr.LeaderFish

init() - Method in class biosim.app.learnedants.LearnedAnts

init() - Method in class biosim.app.tutorial.AvoidAnt

init() - Method in class biosim.app.twostateants.LazyFly

init() - Method in class biosim.app.twostateants.RandomAnt

init() - Method in class biosim.app.twostateants.TwoStateAnt

init() - Method in class biosim.app.twostateants.TwoStateLogger

init() - Method in interface biosim.core.agent.Agent

init() - Method in class biosim.core.body.AbstractAnt

init() - Method in class biosim.core.body.AbstractFly

init() - Method in class biosim.core.body.AphaenogasterCockerelli

init() - Method in class biosim.core.body.Body

init(Controller) - Method in class biosim.core.gui.GUISimulation

init() - Method in interface biosim.core.sim.Logger

init() - Method in class biosim.core.util.BTFLogger

initFiles() - Method in class biosim.app.fishknn.FishKNNLogger

initFiles() - Method in class biosim.app.tutorial.AvoidAntLogger

initFiles() - Method in class biosim.core.util.BTFLogger

initialBodies - Variable in class biosim.core.sim.Environment

initParameters(double[][][], double[], int[], SimpleKDE[]) - Method in class biosim.app.learnedants.BIOHMMInputParser

initParameters(double[][][], double[], int[], SimpleKDE[]) - Method in class biosim.app.learnedants.RealAntInputParser

initSimField(Simulation) - Method in class biosim.core.sim.Environment

Method which initializes the Simulation object's internal field2D.

input - Variable in class biosim.app.learnedants.SimpleInputParser

invalidValue(String, String) - Static method in class biosim.app.domworld.DomWorldStateMachine

invalidValue(String, String) - Static method in class biosim.app.domworld.SmallDomWorld

isFarFromGroup(ArrayList<MutableDouble2D>) - Method in class biosim.app.domworld.DomWorldStateMachine

isLeader() - Method in class biosim.core.body.NotemigonusCrysoleucas

isRandomWalking - Variable in class biosim.app.domworld.DomWorldMonkey

K

k(double[]) - Method in class biosim.core.util.AdaptiveKernelDensityEstimator.NormalKernel

k(double[]) - Method in interface biosim.core.util.Kernel

k(double[]) - Method in class biosim.core.util.KernelDensityEstimator.NormalKernel

kdewrapper - Class in biosim.core.util.kdewrapper

kdewrapper() - Constructor for class biosim.core.util.kdewrapper.kdewrapper

kdewrapperJNI - Class in biosim.core.util.kdewrapper

kdewrapperJNI() - Constructor for class biosim.core.util.kdewrapper.kdewrapperJNI

KERN_BANDWIDTH - Static variable in class biosim.app.learnedants.LearnedAnts

Kernel - Interface in biosim.core.util

kernel - Variable in class biosim.core.util.KernelDensityEstimator

KernelDensityEstimator - Class in biosim.core.util

KernelDensityEstimator(int, Kernel) - Constructor for class biosim.core.util.KernelDensityEstimator

KernelDensityEstimator.NormalKernel - Class in biosim.core.util

KernelDensityEstimator.NormalKernel(double) - Constructor for class biosim.core.util.KernelDensityEstimator.NormalKernel

KNN_NEIGHBORS - Static variable in class biosim.app.fishknn.FishKNN

KNN_NEIGHBORS - Static variable in class biosim.app.fishknn.FishKNNProx

KNN_NEIGHBORS - Static variable in class biosim.app.fishknn.FishKNNZones

L

lastTime - Variable in class biosim.app.domworld.DomWorldMonkey

LazyFly - Class in biosim.app.twostateants

LazyFly() - Constructor for class biosim.app.twostateants.LazyFly

LeaderFish - Class in biosim.app.fishlr

LeaderFish(AbstractFish) - Constructor for class biosim.app.fishlr.LeaderFish

learn(double) - Method in class biosim.app.learnedants.BIOHMM

learn(ArrayList<ArrayList<Integer>>, double) - Method in class biosim.app.learnedants.BIOHMM

learn(ArrayList<ArrayList<Integer>>, double, File) - Method in class biosim.app.learnedants.BIOHMM

LearnedAnts - Class in biosim.app.learnedants

LearnedAnts(AbstractAnt, double[], double[][][], FastKNN[]) - Constructor for class biosim.app.learnedants.LearnedAnts

load(SimState) - Method in class biosim.core.gui.GUISimulation

loadAllColumns() - Method in class biosim.core.util.BTFData

loadBTF(BTFData) - Static method in class biosim.app.btfreplay.BTFReplay

loadBTF(File) - Method in class biosim.core.util.BTFData

loadColumn(String) - Method in class biosim.core.util.BTFData

loadDir(File) - Method in class biosim.core.util.BTFData

loadKNN(BTFData) - Static method in class biosim.app.antknn.AntKNN

loadKNN(BTFData) - Static method in class biosim.app.fishknn.FishKNN

loadKNN(BTFData) - Static method in class biosim.app.fishknn.FishKNNProx

loadKNN(BTFData) - Static method in class biosim.app.fishknn.FishKNNZones

loadPrefs() - Static method in class biosim.app.learnedants.BIOHMM

Logger - Interface in biosim.core.sim

loggers - Variable in class biosim.core.sim.Simulation

LOGGING - Static variable in class biosim.app.domworld.SmallDomWorld

loglikeForSeq(double[][]) - Method in class biosim.app.learnedants.BIOHMM

LOITER - Static variable in class biosim.app.domworld.DomWorldStateMachine

loiterRandomWalkTimeout(double) - Method in class biosim.app.domworld.DomWorldStateMachine

lostFight() - Method in class biosim.app.domworld.DomWorldStateMachine

LR_BETA - Static variable in class biosim.app.fishlr.FishLR

M

main(String[]) - Static method in class biosim.app.antknn.AntKNN

main(String[]) - Static method in class biosim.app.btfreplay.BTFReplay

main(String[]) - Static method in class biosim.app.domworld.DomWorld

main(String[]) - Static method in class biosim.app.domworld.SmallDomWorld

main(String[]) - Static method in class biosim.app.fishknn.FishKNN

main(String[]) - Static method in class biosim.app.fishknn.FishZones

main(String[]) - Static method in class biosim.app.fishlr.FishLR

main(String[]) - Static method in class biosim.app.learnedants.BIOHMM

main(String[]) - Static method in class biosim.app.learnedants.LearnedAnts

main(String[]) - Static method in class biosim.app.tutorial.Tutorial

main(String[]) - Static method in class biosim.app.twostateants.RandomAnt

main(String[]) - Static method in class biosim.app.twostateants.TwoStateAnt

main(String[]) - Static method in class biosim.core.util.AdaptiveKernelDensityEstimator

main(String[]) - Static method in class biosim.core.util.BTFData

main(String[]) - Static method in class biosim.core.util.FastKNN

main(String[]) - Static method in class biosim.core.util.kdewrapper.TestSimpleKDE

main(String[]) - Static method in class biosim.core.util.KernelDensityEstimator

MAX_TRACKS - Static variable in class biosim.app.btfreplay.BTFReplay

MAX_VELOCITY_THETA - Static variable in class biosim.core.body.AphaenogasterCockerelli

MAX_VELOCITY_THETA - Static variable in class biosim.core.body.DrosophilaMelanogaster

MAX_VELOCITY_THETA - Static variable in class biosim.core.body.NotemigonusCrysoleucas

MAX_VELOCITY_THETA - Static variable in class biosim.core.body.RhesusMacaque

MAX_VELOCITY_X - Static variable in class biosim.core.body.NotemigonusCrysoleucas

MAX_VELOCITY_X - Static variable in class biosim.core.body.RhesusMacaque

MAX_VELOCITY_XY - Static variable in class biosim.core.body.AphaenogasterCockerelli

MAX_VELOCITY_XY - Static variable in class biosim.core.body.DrosophilaMelanogaster

MAX_VELOCITY_Y - Static variable in class biosim.core.body.NotemigonusCrysoleucas

MAX_VELOCITY_Y - Static variable in class biosim.core.body.RhesusMacaque

MIN_OTHERS - Static variable in class biosim.app.domworld.DomWorldMonkey

MIN_OTHERS - Static variable in class biosim.app.domworld.DomWorldStateMachine

MIRROR_TRAINING_DATA - Static variable in class biosim.app.fishknn.FishKNN

MIRROR_TRAINING_DATA - Static variable in class biosim.app.fishknn.FishKNNProx

MIRROR_TRAINING_DATA - Static variable in class biosim.app.fishknn.FishKNNZones

missingPropsError(String) - Static method in class biosim.app.domworld.SmallDomWorld

move(MutableDouble2D, MutableDouble2D) - Method in class biosim.core.body.Body

N

NEAR_DIST - Static variable in class biosim.app.domworld.DomWorldMonkey

NEAR_DIST - Static variable in class biosim.app.domworld.DomWorldStateMachine

NEAR_THRESH - Static variable in class biosim.app.learnedants.RealAntInputParser

NearestObstacleVec - Interface in biosim.core.body.sensors

NearestPredatorVec - Interface in biosim.core.body.sensors

NearestPreyVec - Interface in biosim.core.body.sensors

NearestSameTypeVec - Interface in biosim.core.body.sensors

nearFoodBool - Variable in class biosim.app.learnedants.BIOHMMInputParser

nearNestBool - Variable in class biosim.app.learnedants.BIOHMMInputParser

nearNestOut - Variable in class biosim.app.twostateants.TwoStateLogger

nearPOI(String) - Method in class biosim.core.body.AphaenogasterCockerelli

NearPOI - Interface in biosim.core.body.sensors

nearPOI(String) - Method in interface biosim.core.body.sensors.NearPOI

nestTimes - Static variable in class biosim.app.learnedants.LearnedAnts

nestVec - Variable in class biosim.app.learnedants.BIOHMMInputParser

nestVec - Variable in class biosim.app.learnedants.RealAntInputParser

new_SimpleANN__SWIG_0(long, SimpleANN) - Static method in class biosim.core.util.annwrapper.annwrapperJNI

new_SimpleANN__SWIG_1(int) - Static method in class biosim.core.util.annwrapper.annwrapperJNI

new_SimpleKDE__SWIG_0(int, double) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

new_SimpleKDE__SWIG_1(long, SimpleKDE) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

newInstance(long, String[]) - Method in class biosim.core.sim.Environment

newSimulation() - Method in class biosim.core.sim.Environment

newSimulation(long) - Method in class biosim.core.sim.Environment

Convenience method for generating Simulation objects.

nextAction - Variable in class biosim.app.tutorial.AvoidAnt

nextState - Variable in class biosim.core.agent.StateMachine

nextTime - Variable in class biosim.app.domworld.DomWorldMonkey

NotemigonusCrysoleucas - Class in biosim.core.body

NotemigonusCrysoleucas() - Constructor for class biosim.core.body.NotemigonusCrysoleucas

notFinished - Variable in class biosim.core.body.Body

nullFiles() - Method in class biosim.app.fishknn.FishKNNLogger

nullFiles() - Method in class biosim.app.tutorial.AvoidAntLogger

nullFiles() - Method in class biosim.core.util.BTFLogger

NUM_NEIGHBORS - Static variable in class biosim.app.learnedants.LearnedAnts

NUM_SENSORS - Static variable in class biosim.app.learnedants.BIOHMMInputParser

NUM_SENSORS - Static variable in class biosim.app.learnedants.RealAntInputParser

NUM_STATES - Static variable in class biosim.app.domworld.DomWorldStateMachine

NUM_SWITCHES - Static variable in class biosim.app.learnedants.BIOHMMInputParser

NUM_SWITCHES - Static variable in class biosim.app.learnedants.LearnedAnts

NUM_SWITCHES - Static variable in class biosim.app.learnedants.RealAntInputParser

NUM_ZONES - Static variable in class biosim.core.body.NotemigonusCrysoleucas

numSamples() - Method in class biosim.core.util.AdaptiveKernelDensityEstimator

numSamples() - Method in class biosim.core.util.FastKNN

numSamples() - Method in class biosim.core.util.kdewrapper.SimpleKDE

numSamples() - Method in class biosim.core.util.KernelDensityEstimator

numSwitches() - Static method in class biosim.app.learnedants.BIOHMMInputParser

numSwitches() - Static method in class biosim.app.learnedants.RealAntInputParser

numSwitches() - Static method in class biosim.app.learnedants.SimpleInputParser

numTrackPoints - Variable in class biosim.app.learnedants.BIOHMMInputParser

numTrackPoints - Variable in class biosim.app.learnedants.RealAntInputParser

O

obst - Variable in class biosim.core.gui.portrayals.RectObstaclePortrayal

Obstacle - Interface in biosim.core.sim

obstacleLocations - Variable in class biosim.core.sim.Environment

obstacles - Variable in class biosim.core.sim.Environment

obstacles - Variable in class biosim.core.sim.Simulation

oldTime - Variable in class biosim.app.fishlr.FishLR

orientation2D() - Method in class biosim.app.fishknn.FishPortrayal

orientation2D() - Method in class biosim.app.twostateants.FoodPortrayal

orientation2D() - Method in class biosim.core.gui.portrayals.BasicBodyPortrayal

ORIENTATION_ZONE_IDX - Static variable in class biosim.core.body.NotemigonusCrysoleucas

ORIENTATION_ZONE_RANGE - Static variable in class biosim.core.body.NotemigonusCrysoleucas

output - Variable in class biosim.app.learnedants.SimpleInputParser

outputDim() - Static method in class biosim.app.learnedants.BIOHMMInputParser

outputDim() - Static method in class biosim.app.learnedants.RealAntInputParser

outputDim() - Static method in class biosim.app.learnedants.SimpleInputParser

outputLogProbAtIDX(int, int) - Method in class biosim.app.learnedants.BIOHMM

P

parentDirectory - Variable in class biosim.app.twostateants.TwoStateLogger

parentDirectory - Variable in class biosim.core.util.BTFLogger

partition - Variable in class biosim.app.learnedants.BIOHMM

partSize() - Method in class biosim.app.learnedants.BIOHMMInputParser

partSize() - Method in class biosim.app.learnedants.RealAntInputParser

partSize() - Method in class biosim.app.learnedants.SimpleInputParser

PERSONAL_DIST - Static variable in class biosim.app.domworld.DomWorldMonkey

PERSONAL_DIST - Static variable in class biosim.app.domworld.DomWorldStateMachine

poi - Variable in class biosim.core.sim.Environment

poi - Variable in class biosim.core.sim.Simulation

poiLocations - Variable in class biosim.core.sim.Environment

prevboolout - Variable in class biosim.app.tutorial.AvoidAntLogger

prevboolout - Variable in class biosim.app.twostateants.TwoStateLogger

previousVelXYT - Variable in class biosim.core.body.AphaenogasterCockerelli

prevout - Variable in class biosim.app.tutorial.AvoidAntLogger

prevout - Variable in class biosim.app.twostateants.TwoStateLogger

prevVec - Variable in class biosim.app.learnedants.BIOHMMInputParser

PRINT_ITERATIONS - Static variable in class biosim.app.learnedants.BIOHMM

printEverything() - Method in class biosim.core.util.FastKNN

printMat(double[][], DecimalFormat) - Static method in class biosim.app.domworld.SmallDomWorld

prior - Variable in class biosim.app.learnedants.BIOHMM

PROX_RANGE - Static variable in class biosim.core.body.NotemigonusCrysoleucas

PROX_RANGE - Static variable in class biosim.core.body.RhesusMacaque

PROX_SENSORS - Static variable in class biosim.core.body.NotemigonusCrysoleucas

PROX_SENSORS - Static variable in class biosim.core.body.RhesusMacaque

Proximity - Interface in biosim.core.body.sensors

Q

query(double[], int[], int) - Method in class biosim.core.util.annwrapper.SimpleANN

query(double[], double[][]) - Method in class biosim.core.util.FastKNN

query(double[], double[][], double[], double[][]) - Method in class biosim.core.util.FastKNN

R

random - Variable in class biosim.app.learnedants.BIOHMMInputParser

random - Variable in class biosim.app.learnedants.RealAntInputParser

RANDOM_WALK_DIST - Static variable in class biosim.app.domworld.DomWorldStateMachine

RANDOM_WALK_SPEED - Static variable in class biosim.app.domworld.DomWorldStateMachine

RandomAnt - Class in biosim.app.twostateants

RandomAnt(AbstractAnt) - Constructor for class biosim.app.twostateants.RandomAnt

randomTieStrength(MersenneTwisterFast, int) - Static method in class biosim.app.domworld.DomWorld

randomTieStrength(MersenneTwisterFast, int) - Static method in class biosim.app.domworld.SmallDomWorld

randomTurnSpeed - Variable in class biosim.app.domworld.DomWorldMonkey

randomWalkLoiterTimeout(double) - Method in class biosim.app.domworld.DomWorldStateMachine

RANGE - Static variable in class biosim.core.body.AphaenogasterCockerelli

RANGE - Static variable in class biosim.core.body.DrosophilaMelanogaster

RANGE - Static variable in class biosim.core.body.NotemigonusCrysoleucas

readParameters(File) - Method in class biosim.app.learnedants.BIOHMM

readPrefFile(File) - Static method in class biosim.app.learnedants.BIOHMM

RealAntInputParser - Class in biosim.app.learnedants

RealAntInputParser(BTFData) - Constructor for class biosim.app.learnedants.RealAntInputParser

RectObstacle - Class in biosim.core.sim

RectObstacle(double, double) - Constructor for class biosim.core.sim.RectObstacle

RectObstaclePortrayal - Class in biosim.core.gui.portrayals

RectObstaclePortrayal(RectObstacle) - Constructor for class biosim.core.gui.portrayals.RectObstaclePortrayal

ReplayBody - Class in biosim.core.body

ReplayBody() - Constructor for class biosim.core.body.ReplayBody

ReplayPortrayal - Class in biosim.app.btfreplay

ReplayPortrayal(Simulation, Object) - Constructor for class biosim.app.btfreplay.ReplayPortrayal

REPULSION_ZONE_IDX - Static variable in class biosim.core.body.NotemigonusCrysoleucas

REPULSION_ZONE_RANGE - Static variable in class biosim.core.body.NotemigonusCrysoleucas

RESOLUTION - Static variable in class biosim.app.domworld.SmallDomWorld

resolution - Variable in class biosim.core.sim.Environment

resolution - Variable in class biosim.core.sim.Simulation

RETURN - Static variable in class biosim.app.twostateants.TwoStateAnt

RhesusMacaque - Class in biosim.core.body

RhesusMacaque() - Constructor for class biosim.core.body.RhesusMacaque

ROAM - Static variable in class biosim.app.domworld.DomWorldStateMachine

ROAM_DIST - Static variable in class biosim.app.domworld.DomWorldStateMachine

ROAM_OBST_DIST - Static variable in class biosim.app.domworld.DomWorldStateMachine

ROAM_SPEED - Static variable in class biosim.app.domworld.DomWorldStateMachine

roamLoiterTimeout(double) - Method in class biosim.app.domworld.DomWorldStateMachine

runCtr - Variable in class biosim.core.util.BTFLogger

runSimulation(String[]) - Method in class biosim.core.sim.Environment

S

samples - Variable in class biosim.core.util.KernelDensityEstimator

savePrefs(File) - Static method in class biosim.app.learnedants.BIOHMM

SelfVelXYT - Interface in biosim.core.body.sensors

SENSOR_FOV - Static variable in class biosim.core.body.RhesusMacaque

SENSOR_RANGE - Static variable in class biosim.core.body.RhesusMacaque

sensorDim() - Static method in class biosim.app.learnedants.BIOHMMInputParser

sensorDim() - Static method in class biosim.app.learnedants.RealAntInputParser

sensorDim() - Static method in class biosim.app.learnedants.SimpleInputParser

sensors - Variable in class biosim.app.learnedants.BIOHMM

SEQMAX - Static variable in class biosim.app.learnedants.SimpleInputParser

setAgent(Agent) - Method in class biosim.core.body.Body

setAngularVelocity() - Method in interface biosim.core.body.actuators.TricycleDrive

setDesiredVelocity(double, double, double) - Method in interface biosim.core.body.actuators.HolonomicDrive

setDesiredVelocity(double, double, double) - Method in class biosim.core.body.AphaenogasterCockerelli

setDesiredVelocity(double, double, double) - Method in class biosim.core.body.DrosophilaMelanogaster

setDesiredVelocity(double, double, double) - Method in class biosim.core.body.NotemigonusCrysoleucas

setDesiredVelocity(double, double, double) - Method in class biosim.core.body.RhesusMacaque

setDisplaySize(int, int) - Method in class biosim.core.gui.GUISimulation

setEps(double) - Method in class biosim.core.util.FastKNN

setEpsilon(double) - Method in class biosim.core.util.annwrapper.SimpleANN

setFeatureWeights(double[]) - Method in class biosim.core.util.FastKNN

setFieldDiscretizationSize(double) - Method in class biosim.core.sim.Environment

setForwardVelocity() - Method in interface biosim.core.body.actuators.TricycleDrive

setLeader(boolean) - Method in class biosim.core.body.NotemigonusCrysoleucas

setObjectLocation(Object, Double2D) - Method in class biosim.core.sim.Simulation

setPortrayalClass(Class<?>, Class<? extends Portrayal>) - Method in class biosim.core.gui.GUISimulation

setSize(double) - Method in class biosim.core.body.ReplayBody

setTextDisplay(String) - Method in interface biosim.core.body.actuators.TextDisplay

setTextDisplay(String) - Method in class biosim.core.body.RhesusMacaque

setTieStrengths(HashMap<DomWorldStateMachine, Double>) - Method in class biosim.app.domworld.DomWorldStateMachine

setToroidal(boolean) - Method in class biosim.core.sim.Environment

setupPortrayals() - Method in class biosim.core.gui.GUISimulation

setWeight(int, double) - Method in class biosim.core.util.kdewrapper.SimpleKDE

setWeight(double[], double) - Method in class biosim.core.util.KernelDensityEstimator

sigmaNormalize() - Method in class biosim.core.util.FastKNN

sim - Variable in class biosim.app.fishknn.FishPortrayal

sim - Variable in class biosim.app.twostateants.FoodPortrayal

sim - Variable in class biosim.core.body.Body

sim - Variable in class biosim.core.gui.portrayals.BasicBodyPortrayal

SimpleANN - Class in biosim.core.util.annwrapper

SimpleANN(long, boolean) - Constructor for class biosim.core.util.annwrapper.SimpleANN

SimpleANN(SimpleANN) - Constructor for class biosim.core.util.annwrapper.SimpleANN

SimpleANN(int) - Constructor for class biosim.core.util.annwrapper.SimpleANN

SimpleANN_add(long, SimpleANN, double[]) - Static method in class biosim.core.util.annwrapper.annwrapperJNI

SimpleANN_query(long, SimpleANN, double[], int[], int) - Static method in class biosim.core.util.annwrapper.annwrapperJNI

SimpleANN_setEpsilon(long, SimpleANN, double) - Static method in class biosim.core.util.annwrapper.annwrapperJNI

SimpleInputParser - Class in biosim.app.learnedants

SimpleInputParser(BTFData) - Constructor for class biosim.app.learnedants.SimpleInputParser

SimpleKDE - Class in biosim.core.util.kdewrapper

SimpleKDE(long, boolean) - Constructor for class biosim.core.util.kdewrapper.SimpleKDE

SimpleKDE(int, double) - Constructor for class biosim.core.util.kdewrapper.SimpleKDE

SimpleKDE(SimpleKDE) - Constructor for class biosim.core.util.kdewrapper.SimpleKDE

SimpleKDE_add__SWIG_0(long, SimpleKDE, double[], double) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

SimpleKDE_add__SWIG_1(long, SimpleKDE, double[]) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

SimpleKDE_addNoCheck(long, SimpleKDE, double[], double) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

SimpleKDE_clear(long, SimpleKDE) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

SimpleKDE_estimate(long, SimpleKDE, double[], double) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

SimpleKDE_getDim(long, SimpleKDE) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

SimpleKDE_getDist(long, SimpleKDE, double[], int) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

SimpleKDE_getIdx(long, SimpleKDE, double[]) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

SimpleKDE_getSample(long, SimpleKDE, double[], int) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

SimpleKDE_getWeight(long, SimpleKDE, int) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

SimpleKDE_numSamples(long, SimpleKDE) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

SimpleKDE_setWeight(long, SimpleKDE, int, double) - Static method in class biosim.core.util.kdewrapper.kdewrapperJNI

Simulation - Class in biosim.core.sim

Simulation(long) - Constructor for class biosim.core.sim.Simulation

simulationClass() - Method in class biosim.core.sim.Environment

SIZE - Static variable in class biosim.app.btfreplay.BTFReplay

SIZE - Static variable in class biosim.core.body.AphaenogasterCockerelli

SIZE - Static variable in class biosim.core.body.DrosophilaMelanogaster

SIZE - Static variable in class biosim.core.body.NotemigonusCrysoleucas

size - Variable in class biosim.core.body.ReplayBody

SIZE - Static variable in class biosim.core.body.RhesusMacaque

SmallDomWorld - Class in biosim.app.domworld

SmallDomWorld() - Constructor for class biosim.app.domworld.SmallDomWorld

start() - Method in class biosim.core.gui.GUISimulation

start() - Method in class biosim.core.sim.Simulation

state - Variable in class biosim.app.learnedants.SimpleInputParser

state - Variable in class biosim.app.twostateants.TwoStateAnt

StateMachine - Class in biosim.core.agent

StateMachine() - Constructor for class biosim.core.agent.StateMachine

StateMachine.State - Interface in biosim.core.agent

StateMachinePortrayal - Class in biosim.app.domworld

StateMachinePortrayal(Simulation, Object) - Constructor for class biosim.app.domworld.StateMachinePortrayal

stateout - Variable in class biosim.app.twostateants.TwoStateLogger

states - Variable in class biosim.core.agent.StateMachine

stateVec - Variable in class biosim.app.learnedants.BIOHMMInputParser

step(SimState) - Method in class biosim.app.fishknn.FishKNNLogger

step(SimState) - Method in class biosim.app.tutorial.AvoidAntLogger

step(SimState) - Method in class biosim.app.twostateants.TwoStateLogger

step(SimState) - Method in class biosim.core.body.Body

step(SimState) - Method in class biosim.core.body.ReplayBody

step(SimState) - Method in interface biosim.core.sim.Logger

step(SimState) - Method in class biosim.core.util.BTFLogger

swigCMemOwn - Variable in class biosim.core.util.annwrapper.SimpleANN

swigCMemOwn - Variable in class biosim.core.util.kdewrapper.SimpleKDE

switching - Variable in class biosim.app.learnedants.SimpleInputParser

T

target - Variable in class biosim.app.domworld.DomWorldMonkey

targetDist - Variable in class biosim.app.domworld.DomWorldMonkey

TestSimpleKDE - Class in biosim.core.util.kdewrapper

TestSimpleKDE() - Constructor for class biosim.core.util.kdewrapper.TestSimpleKDE

TextDisplay - Interface in biosim.core.body.actuators

tieStrengthFromFile(String) - Static method in class biosim.app.domworld.SmallDomWorld

timeAvg(ArrayList<Double>) - Static method in class biosim.app.learnedants.LearnedAnts

timeAvoiding - Variable in class biosim.app.twostateants.TwoStateAnt

timeNearAnt - Variable in class biosim.app.twostateants.TwoStateAnt

timeout - Variable in class biosim.app.twostateants.TwoStateLogger

timeout - Variable in class biosim.core.util.BTFLogger

timeStdDev(ArrayList<Double>, double) - Static method in class biosim.app.learnedants.LearnedAnts

timgout - Variable in class biosim.app.twostateants.TwoStateLogger

timgout - Variable in class biosim.core.util.BTFLogger

tmpDir - Variable in class biosim.core.util.BTFLogger

tmpFilePrefix - Variable in class biosim.core.util.BTFLogger

tooClose(ArrayList<MutableDouble2D>, ArrayList<Agent>) - Method in class biosim.app.domworld.DomWorldStateMachine

TOROIDAL - Static variable in class biosim.app.domworld.SmallDomWorld

toroidal - Variable in class biosim.core.sim.Simulation

toroidalClosestPoint(Double2D, Double2D, Continuous2D) - Method in interface biosim.core.sim.Obstacle

toroidalClosestPoint(Double2D, Double2D, Continuous2D) - Method in class biosim.core.sim.RectObstacle

toString() - Method in class biosim.app.domworld.DomWorldStateMachine.Flee

track - Variable in class biosim.core.body.ReplayBody

trackID - Variable in class biosim.core.body.ReplayBody

transitionFunction - Variable in class biosim.app.learnedants.BIOHMM

TricycleDrive - Interface in biosim.core.body.actuators

tryToDrop() - Method in interface biosim.core.body.actuators.Gripper

tryToDrop() - Method in class biosim.core.body.AphaenogasterCockerelli

tryToGrab() - Method in interface biosim.core.body.actuators.Gripper

tryToGrab() - Method in class biosim.core.body.AphaenogasterCockerelli

Tutorial - Class in biosim.app.tutorial

Tutorial() - Constructor for class biosim.app.tutorial.Tutorial

TwoStateAnt - Class in biosim.app.twostateants

TwoStateAnt(AbstractAnt) - Constructor for class biosim.app.twostateants.TwoStateAnt

TwoStateLogger - Class in biosim.app.twostateants

TwoStateLogger() - Constructor for class biosim.app.twostateants.TwoStateLogger

TwoStateLogger(File) - Constructor for class biosim.app.twostateants.TwoStateLogger

U

updateCompleteLLGamma(ArrayList<Integer>, double[][]) - Method in class biosim.app.learnedants.BIOHMM

updatePartition(ArrayList<Integer>, double[][], int[]) - Method in class biosim.app.learnedants.BIOHMM

updatePartition(ArrayList<Integer>, SimpleKDE[], int[]) - Method in class biosim.app.learnedants.BIOHMM

updatePartitionLog(ArrayList<Integer>, SimpleKDE[], int[]) - Method in class biosim.app.learnedants.BIOHMM

updatePrior(double[], double[][], int) - Method in class biosim.app.learnedants.BIOHMM

updatePriorLog(double[], double[][], int) - Method in class biosim.app.learnedants.BIOHMM

updateTransitions(ArrayList<Integer>, double[][][], double[][][], double[][][], double[][]) - Method in class biosim.app.learnedants.BIOHMM

updateTransitionsLog(ArrayList<Integer>, double[][][], double[][][], double[][][], double[][]) - Method in class biosim.app.learnedants.BIOHMM

USE_WEIGHTS - Static variable in class biosim.app.fishknn.FishKNN

USE_WEIGHTS - Static variable in class biosim.app.fishknn.FishKNNProx

USE_WEIGHTS - Static variable in class biosim.app.fishknn.FishKNNZones

V

validSimState(SimState) - Method in class biosim.core.gui.GUISimulation

VectorToPOI - Interface in biosim.core.body.sensors

velXYT - Variable in class biosim.core.body.DrosophilaMelanogaster

visible - Variable in class biosim.core.body.ReplayBody

VISIT_RANGE - Static variable in class biosim.app.twostateants.TwoStateAnt

VISIT_TIME - Static variable in class biosim.app.twostateants.TwoStateAnt

W

wallboolout - Variable in class biosim.app.fishknn.FishKNNLogger

wallboolout - Variable in class biosim.app.tutorial.AvoidAntLogger

wallboolout - Variable in class biosim.app.twostateants.TwoStateLogger

wallDists - Static variable in class biosim.app.learnedants.LearnedAnts

wallDists - Static variable in class biosim.app.twostateants.RandomAnt

wallDists - Static variable in class biosim.app.twostateants.TwoStateAnt

wallout - Variable in class biosim.app.fishknn.FishKNNLogger

wallout - Variable in class biosim.app.tutorial.AvoidAntLogger

wallout - Variable in class biosim.app.twostateants.TwoStateLogger

WALLS - Static variable in class biosim.app.fishknn.FishKNN

wallTimes - Static variable in class biosim.app.learnedants.LearnedAnts

wallVec - Variable in class biosim.app.learnedants.BIOHMMInputParser

wallVec - Variable in class biosim.app.learnedants.RealAntInputParser

weights - Variable in class biosim.core.util.KernelDensityEstimator

WIDTH - Static variable in class biosim.app.antknn.AntKNN

WIDTH - Static variable in class biosim.app.btfreplay.BTFReplay

WIDTH - Static variable in class biosim.app.domworld.DomWorld

WIDTH - Static variable in class biosim.app.domworld.SmallDomWorld

WIDTH - Static variable in class biosim.app.fishknn.FishKNN

WIDTH - Static variable in class biosim.app.fishknn.FishZones

WIDTH - Static variable in class biosim.app.fishlr.FishLR

WIDTH - Static variable in class biosim.app.learnedants.LearnedAnts

WIDTH - Static variable in class biosim.app.tutorial.Tutorial

WIDTH - Static variable in class biosim.app.twostateants.RandomAnt

WIDTH - Static variable in class biosim.app.twostateants.TwoStateAnt

width - Variable in class biosim.core.sim.Environment

width - Variable in class biosim.core.sim.RectObstacle

wonFight() - Method in class biosim.app.domworld.DomWorldStateMachine

writeParameters(File) - Method in class biosim.app.learnedants.BIOHMM

writeParameters(File, BigDecimal) - Method in class biosim.app.learnedants.BIOHMM

X

ximgout - Variable in class biosim.app.twostateants.TwoStateLogger

ximgout - Variable in class biosim.core.util.BTFLogger

Y

yimgout - Variable in class biosim.app.twostateants.TwoStateLogger

yimgout - Variable in class biosim.core.util.BTFLogger

yummy - Variable in class biosim.core.body.AbstractFly

Z

zoneboolout - Variable in class biosim.app.fishknn.FishKNNLogger

ZoneCoMVecs - Interface in biosim.core.body.sensors

zoneout - Variable in class biosim.app.fishknn.FishKNNLogger

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