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
 

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