Overview
Package
Class
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
A
B
C
D
E
F
G
H
I
J
L
M
N
O
P
R
S
T
U
V
W
X
G
getAlpha()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate
getAminoAcidId()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.AminoAcid
getAtoms()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.AminoAcid
getBond()
- Method in class uk.ac.ed.simulator_pdb.model.
SimRule
getBondPositions(SimCluster, Matrix4d)
- Method in class uk.ac.ed.simulator_pdb.
SimulationJava3DController.BondPositions
getBondSites()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObjectTemplate
getBondToWorldMatrix(SimBond)
- Method in class uk.ac.ed.simulator_pdb.
SimulationJava3DController.BondPositions
getBondTransforms(SimCluster, Matrix4d)
- Method in class uk.ac.ed.simulator_pdb.
SimulationJava3DController.BondPositions
getBondedAlpha()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate
getBondedColour()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate
getBonds()
- Method in class uk.ac.ed.simulator_pdb.
SimulationJava3DController.BondPositions
getBonds()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFile
getBonds()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObject
getCentreOfMass()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBond
getCentreOfMass()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getChoosenObject()
- Method in class uk.ac.ed.simulator_pdb.
View.ChooserDialog
getCluster()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObject
getCluster()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel.SimulationEvent
getClusterEnergy(SimCluster, Matrix4d)
- Method in class uk.ac.ed.simulator_pdb.
SimulationJava3DController
getClusters()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getCollide()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate
getColour()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate
getConnectedBond()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBond
getContainer()
- Method in class uk.ac.ed.simulator_pdb.
View
Returns the container
getCurrentBondIdNum()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getCurrentObjectIdNum()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getCurrentParticleIdNum()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getCurrentRuleIdNum()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getDeselectedObject()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceBuilderModel.SelectedObjectEvent
getDeselectedObject()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateBuilderModel.SelectedObjectEvent
getDimensions()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate.Shape
getDisplacment()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getDistance(Vector3d, Vector3d)
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getDistanceTesselated(Vector3d, Vector3d)
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getDistanceWalled(Vector3d, Vector3d)
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getElapsedTime()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getEnergy()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getFile()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFile
getFile()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getFrameDelay()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getHalfScale()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFile
getHalfScale()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile
getHalfScale()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getId()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFileObject
getId()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getId()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFileObject
getIfClauses()
- Method in class uk.ac.ed.simulator_pdb.model.
SimRuleTemplate
getInstance(String)
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFile
getInstance()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFileObject.InstanceFileObjectEvent
getInstanceFile()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceBuilderModel.FileEvent
getInstanceFile()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFile.InstanceFileEvent
getInstanceFile()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFileObject
getInstanceFile()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getInstanceFiles()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceBuilderModel
getInstances()
- Method in class uk.ac.ed.simulator_pdb.model.
Model
getInverseScale()
- Method in class uk.ac.ed.simulator_pdb.
Java3DView
getInverseScale()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFile
getInverseTransformationMatrix()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBond
getInverseTransformationMatrix()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getInverseTransformationMatrix()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObject
getInverseTransformationMatrix()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticle
getLandscape()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile
getLandscape()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate
getLikelyhoods()
- Method in class uk.ac.ed.simulator_pdb.model.
SimRuleTemplate
getLoadedTemplateFiles()
- Method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.
NeuroMLHandler
getMass()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.AminoAcid
getMass()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.Atom
getMass()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.Cluster
getMass()
- Method in interface uk.ac.ed.simulator_pdb.model.
PDBFile.DataPoint
getMass()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getMass()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObject
getMass()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObjectTemplate
getMass()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate
getModel()
- Method in class uk.ac.ed.simulator_pdb.
View
Returns the model
getName()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFile
getName()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile
getName()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate.Shape
getName()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getNearbyBonds(Vector3d, double)
- Method in class uk.ac.ed.simulator_pdb.
SimulationJava3DController.BondPositions
getNearbyParticles(Vector3d, double)
- Method in class uk.ac.ed.simulator_pdb.
SimulationJava3DController.ParticlePositions
getNeuroMLHandler()
- Method in class uk.ac.ed.simulator_pdb.model.
Model
getNeuroMLHandler()
- Static method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.
NeuroMLHandler
getNewFrameDelay()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel.SimulationEvent
getNewId()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFileObject.TemplateFileObjectEvent
getNewSimulationState()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel.SimulationEvent
getNewTransformationMatrix()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel.SimulationEvent
getNewValue()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel.SimulationEvent
getNextBondId()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getNextObjectId()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getNextParticleId()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getNextRuleId()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getNumberOfClusters()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile
getNumberOfObjects()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getNumberOfProperties()
- Method in class uk.ac.ed.simulator_pdb.model.
SimLandscapeTemplate
getObject()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBond
getObject()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getObject()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticle
getObjects()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFile
getObjects()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getOldFrameDelay()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel.SimulationEvent
getOldId()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFileObject.TemplateFileObjectEvent
getOldValue()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel.SimulationEvent
getOrientation()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBond
getOrientation()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBondSite
getOrientation()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getOrientation()
- Method in class uk.ac.ed.simulator_pdb.model.
SimSubParticle
getPDBFile()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.PDBEvent
getPDBFile()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateBuilderModel.FileEvent
getPDBFileFilter()
- Static method in class uk.ac.ed.simulator_pdb.model.pdb_handler.
PDBHandler
getPDBHandler()
- Method in class uk.ac.ed.simulator_pdb.model.
Model
getPDBHandler()
- Static method in class uk.ac.ed.simulator_pdb.model.pdb_handler.
PDBHandler
getParent()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBondSite
getParent()
- Method in class uk.ac.ed.simulator_pdb.model.
SimSubParticle
getParticleCentreOfMass(SimParticle)
- Method in class uk.ac.ed.simulator_pdb.
SimulationJava3DController.ParticlePositions
getParticleOrientation(SimParticle)
- Method in class uk.ac.ed.simulator_pdb.
SimulationJava3DController.ParticlePositions
getParticlePositions(SimCluster, Matrix4d)
- Method in class uk.ac.ed.simulator_pdb.
SimulationJava3DController.ParticlePositions
getParticleTemplate()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.Atom
getParticleToWorldMatrix(SimParticle)
- Method in class uk.ac.ed.simulator_pdb.
SimulationJava3DController.ParticlePositions
getParticleTransforms(SimCluster, Matrix4d)
- Method in class uk.ac.ed.simulator_pdb.
SimulationJava3DController.ParticlePositions
getParticles()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFile
getParticles()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getParticles()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObject
getPosition()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.AminoAcid
getPosition()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.Atom
getPosition()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.Cluster
getPosition()
- Method in interface uk.ac.ed.simulator_pdb.model.
PDBFile.DataPoint
getPosition()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBondSite
getPosition()
- Method in class uk.ac.ed.simulator_pdb.model.
SimSubParticle
getPosition(Vector3d)
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getPositionTesselated(Vector3d)
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getProbabilityAtTime(double)
- Method in class uk.ac.ed.simulator_pdb.model.
SimRuleTemplate
getPropertyName(int)
- Method in class uk.ac.ed.simulator_pdb.model.
SimLandscapeTemplate
getPropertyValue(int)
- Method in class uk.ac.ed.simulator_pdb.model.
SimLandscapeTemplate
getRadius()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.AminoAcid
getRadius()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.Atom
getRadius()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.Cluster
getRadius()
- Method in interface uk.ac.ed.simulator_pdb.model.
PDBFile.DataPoint
getRadius()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getRadius()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObjectTemplate
getRadius()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate.Shape
getRadius()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate
getRuleTemplates()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBondTemplate
getRules()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFile
getRules()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBond
getScale()
- Method in class uk.ac.ed.simulator_pdb.
Java3DView
getScale()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFile.InstanceFileEvent
getScale()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceFile
getScale()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.PDBEvent
getScale()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile
getScale()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile.TemplateFileEvent
getScale()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getSelectedObject()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceBuilderModel.SelectedObjectEvent
getSelectedObject()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceBuilderModel
getSelectedObject()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateBuilderModel.SelectedObjectEvent
getSelectedObject()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateBuilderModel
getShapeDimensions()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate
getShapeName()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate
getShortName()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile
getSimBondSite()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObjectTemplate.SimObjectTemplateEvent
getSimBondTemplate(String)
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getSimBondTemplates()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getSimInstanceFileFilter()
- Static method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.
NeuroMLHandler
getSimLandscapeTemplates()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getSimObjectTemplate(String)
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getSimObjectTemplates()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getSimParticleTemplate(String)
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getSimParticleTemplates()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getSimRuleTemplate(String)
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getSimRuleTemplates()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getSimSubParticle()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObjectTemplate.SimObjectTemplateEvent
getSimTemplateFileFilter()
- Static method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.
NeuroMLHandler
getSimulation()
- Method in class uk.ac.ed.simulator_pdb.model.
Model
getSimulationSize()
- Method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.
XMLParams
getSquaredDistance(Vector3d, Vector3d)
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getSquaredDistanceTesselated(Vector3d, Vector3d)
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getSquaredDistanceWalled(Vector3d, Vector3d)
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getState()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getSubParticles()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile
getSubParticles()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObjectTemplate
getTempateFiles()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateBuilderModel
getTemplate()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile.PDBEvent
getTemplate()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBond
getTemplate()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBondSite
getTemplate()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObject
getTemplate()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObjectTemplate.SimObjectTemplateEvent
getTemplate()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticle
getTemplate()
- Method in class uk.ac.ed.simulator_pdb.model.
SimRule
getTemplate()
- Method in class uk.ac.ed.simulator_pdb.model.
SimSubParticle
getTemplate()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile.TemplateFileEvent
getTemplate(String)
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFile
getTemplate()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFileObject.TemplateFileObjectEvent
getTemplateFile()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateBuilderModel.FileEvent
getTemplateFile()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateFileObject
getTemplates()
- Method in class uk.ac.ed.simulator_pdb.model.
Model
getTimeStep()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getTimeUnit()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getTimeValue()
- Method in class uk.ac.ed.simulator_pdb.model.
SimulatorModel
getTransformationMatrix()
- Method in class uk.ac.ed.simulator_pdb.model.
InstanceBuilderModel.SelectedObjectEvent
getTransformationMatrix()
- Method in class uk.ac.ed.simulator_pdb.model.
SimBond
getTransformationMatrix()
- Method in class uk.ac.ed.simulator_pdb.model.
SimCluster
getTransformationMatrix()
- Method in class uk.ac.ed.simulator_pdb.model.
SimObject
getTransformationMatrix()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticle
getTransformationMatrix()
- Method in class uk.ac.ed.simulator_pdb.model.
TemplateBuilderModel.SelectedObjectEvent
getType()
- Method in class uk.ac.ed.simulator_pdb.model.
PDBFile
getType()
- Method in class uk.ac.ed.simulator_pdb.model.
SimLandscapeTemplate
getType()
- Method in class uk.ac.ed.simulator_pdb.model.
SimRuleTemplate
getVolume()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate.Shape
getVolume()
- Method in class uk.ac.ed.simulator_pdb.model.
SimParticleTemplate
Overview
Package
Class
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
A
B
C
D
E
F
G
H
I
J
L
M
N
O
P
R
S
T
U
V
W
X