scripps.vvm.graphics
Class BASShape

java.lang.Object
  |
  +--harmonic.mz.data.ModelNode
        |
        +--harmonic.mz.data.ShapeNode
              |
              +--scripps.vvm.graphics.VVM_Shape
                    |
                    +--scripps.vvm.graphics.VVM_RepShape
                          |
                          +--scripps.vvm.graphics.BASShape

All Implemented Interfaces:

java.awt.event.ActionListener, AtomListener, harmonic.mz.data.DataNode, harmonic.mz.gui.Documentable, java.util.EventListener, harmonic.mz.data.Interpolater, harmonic.meshGeom.math.MarkableObject, harmonic.mz.event.NodeListener, harmonic.viewer3D.ShapeOwner, harmonic.mz.data.Transformable

public class BASShape

extends VVM_RepShape

The Ball and Stick shape definition is the traditional ball and stick visual model. It represents atoms with balls and bonds with sticks.

Field Summary

harmonic.mz.data.TableNode	atomProps Holdes the per element properties for atoms.
harmonic.mz.data.fields.BooleanField	autoBond Renders bonds between all bonded atoms if true
harmonic.mz.data.TableNode	bondProps Holdes the per element properties for bonds.
harmonic.mz.data.fields.ColorField	defaultBondColor Color of auto bonded bonds
harmonic.mz.data.fields.BooleanField	defaultBondHalfness Halfness for auto-bonded bonds
harmonic.mz.data.fields.ScalarField	defaultBondThickness Radius of auto bonded bonds
harmonic.mz.data.fields.IntField	maxBalls Maximum balls to alow
harmonic.mz.data.fields.IntField	sphereDis Fineness of sphere shapes

Fields inherited from class scripps.vvm.graphics.VVM_RepShape

molField, type

Fields inherited from class harmonic.mz.data.ShapeNode

ANY_GEOM, ARRAY_GEOM, ATTRIBUTE_FIELD_TYPE, bAssignMaterialColors, bAttribsValid, bBaseGeometryValid, bSelectionValid, bTSelectionValid, bVisibilityValid, coordSystem, COORDSYSTEM_FIELD_TYPE, existingPainters, fastPainters, GEOMETRY_FIELD_TYPE, LINES_GEOM, localKludge, material, painters, POINT_GEOM, POLYGON_GEOM, REGION_GEOM, SOLID_GEOM, SURFACE_GEOM, transparency, visibility

Fields inherited from class harmonic.mz.data.ModelNode

_fileRoot_, _thread_, ATTRIB_CONTROL_WIDGET, ATTRIB_LISTABLE, ATTRIB_PRESENTABLE, ATTRIB_PRIVATE, ATTRIB_REMOVEABLE, ATTRIB_RENAMEABLE, ATTRIB_SHOW_CONTEXT_MENU, ATTRIB_TYPE_FILTER, ATTRIB_USERGROUP, ATTRIB_VALUE_GROUP, ATTRIB_VE_LISTENER, bCustomCS, bDebug, bValid, name

Constructor Summary

BASShape()
Constructs a BASShape without adding it to database.

BASShape(Molecule mol)
Constructs a BASShape without adding it to database.

Method Summary

java.lang.String	areFieldsValid()
Atom	atomAtPart(harmonic.viewer3D.PaintStruct p, int iPart, harmonic.meshGeom.math.Pnt3f pickedPoint) Used by the picking system.
void	atomChanged(AtomEvent event)
Bond	bondAtPart(harmonic.viewer3D.PaintStruct p, int iPart, harmonic.meshGeom.math.Pnt3f pickedPoint) Used by the picking system.
void	fullInvalidate()
java.lang.String[]	getDomains() Return a list of domains used by this class
harmonic.mz.data.TableNode	getElementDataTable(java.lang.String domainType) Like getElementProps() except return the ElementListNode object at the domain
java.util.Vector	getElementProps(java.lang.String domainType) Return vector of meta data objects for the domain.
harmonic.mz.data.ModelNode	makePrototype()
void	nodeChanged(harmonic.mz.event.NodeEvent event)
void	setAtomColor(TreeNodeSet set, harmonic.meshGeom.math.Clr3f clr) Set atom color shown by this ball and stick for the given set
void	setAtomColor(TreeNodeSet set, Scheme scheme) Set atom color shown by this ball and stick for the given set
void	setAtomRadius(TreeNodeSet set, float radius) Set atom radius shown by this ball and stick for the given set
void	setAtomRadius(TreeNodeSet set, Scheme scheme) Set atom radius shown by this ball and stick for the given set
void	setBondColor(TreeNodeSet set, harmonic.meshGeom.math.Clr3f clr) Set bond color shown by this ball and stick for the given set
void	setBondColor(TreeNodeSet set, Scheme scheme) Set bond color shown by this ball and stick for the given set
void	setBondHalfness(TreeNodeSet set, boolean bShow) Set bond halfness shown by this ball and stick for the given set
void	setBondHalfness(TreeNodeSet set, Scheme scheme) Set bond halfness shown by this ball and stick for the given set
void	setBondThickness(TreeNodeSet set, float radius) Set bond thickness shown by this ball and stick for the given set
void	setBondThickness(TreeNodeSet set, Scheme scheme) Set bond thickness shown by this ball and stick for the given set
void	validateGeometry() Looking at both bond and atom proporties, incremenetally validate geometry.

Methods inherited from class scripps.vvm.graphics.VVM_RepShape

defineTable, expectedValidationTime, getMol, prop, purge, selfNodeChanged, setDefaultProps, setMol, validateMol

Methods inherited from class scripps.vvm.graphics.VVM_Shape

residueAtPart

Methods inherited from class harmonic.mz.data.ShapeNode

addFastGeometry, addFastGeometry, addFastGeometry, addFastGeometry, addFastPainter, addGeometry, addGeometry, addGeometry, addGeometry, addNetworkOutput, addPainter, addWithUndo, beginTransform, bigValidation, calcGeometricProps, calcSurfaceArea, calcVolume, checkRequirements, clearFastGeometries, clearFastPainters, clearGeometries, clearGeometryCache, clearPainters, defaultPickPriority, endTransform, fastPainterCount, findPointSnaps, getCachedGeometries, getCachedGeometry, getChildRequirements, getCoordSystem, getDataTransfer, getDataTransferTypes, getDragable, getEdges, getFastPainter, getFastPainters, getFitable, getGDIEdges, getGeom, getGeom, getGeomAt, getGeoms, getGeoms, getGeoms, getGlobalPerLocal, getILAEdges, getMoveableCoordSystem, getObjectChildren, getPainter, getPainter, getPainters, getPainters, getPainters, getPaintOnTransient, getPickable, getPointSnaps, getRequirements, getSerializeGeometry, getShapeDefOwner, getTransformable, getTypeImage, getViewpointDependantGeometry, getVisibility, hasFixedCS, hasGeometryLock, hide, hide, invalidate, invalidateAttribs, invalidateCoordSystem, invalidateGeometry, invalidateGeometryDependants, isAttribsValid, isGeomComposite, isGeometryValid, isSelectionValid, isTentativeSelectionValid, isVisibilityValid, makeContextMenu_ShapeFns, makeContextMenu, painterCount, processMouseDragged, processMouseEntered, processMouseExited, processMouseMoved, processMousePressed, processMouseReleased, purgeFinal, removeFastPainter, removePainter, scaleCoordSystem, setDragable, setExclusiveVisibility, setFieldCoordSystems, setFitable, setMoveableCoordSystem, setPaintOnTransient, setPickable, setPickPriority, setSelect, setSerializeGeometry, setTempVisibility, setTentativeSelect, setTransform, setTransient, setViewpointDependantGeometry, setVisibility, shouldSpawnThread, show, show, transferAttributes, transferAttributes, transform, transformFields, translateCoordSystem, validate, validateAttribs, validateSelection, validateTransform

Methods inherited from class harmonic.mz.data.ModelNode

actionPerformed, addAll, addAlphaed, addField, addField, addField, addFields, addNetworkInput, addNode, addNodeListener, addNodeListener, addNodes, addNodes, addToCurrent, addToGlobals, addToNetworkEditor, addToTemps, allFieldsAreFinal, applyDataTransfer, assignFromMetaFields, assignFromXMLAttributes, assignFromXMLString, assignToMetaFields, assignToXMLAttributes, assignToXMLString, at, bind, canSelect, castSelection, checkFileRead, checkNetworkInput, childCount, clean, clearAttrib, clearNotified, compare, copyFrom, createControlWidget, createCopy, createXMLElement, deepCopy, defeatNodeEvents, disableEvents, enableEvents, fileRoot, finalize, findFieldElement, findNode, fromXMLNodes, getAttrib, getBound, getCatagory, getControlWidget, getCurrentNames, getDeleted, getDirectInputs, getDirectOutputs, getEffectors, getEntryListener, getErrorState, getFilterType, getFullName, getHandles, getInstanceURL, getInterpolater, getIsLeaf, getListable, getMark, getMetaFields, getName, getNodeChildren_V, getNodeChildren, getNodeID, getNodeParent, getObjectRep, getPresentable, getPrivate, getReferencePoolName, getRemoteOwner, getRemoveable, getRenameable, getSaveable, getSavedChildren, getSelect, getSeparateDirectInputs, getSeparateDirectOutputs, getSequenced, getSerialNo, getTags, getTentativeSelect, getTransformableParent, getTransient, getTreeName, getTypeURL, getUnfoldedChildren, getUpdateTime, getUserGroup, getValidates, getValue, getXMLNodes, hasDependants, hasExternalRef, hashKey, hasValidationLock, hideControlWidget, indexOf, initControlWidget, insertNode, interpolate_Linear, interpolate_Quadratic, isField, isFinal, isInSubtree, isInTree, isLinked, isNotified, isPurged, isSet, isTemporary, isValid, linkedTo, linksChildren, makeFixed, makeReferenced, makeUnreferenced, makeVisibleInGUI, markNotified, mayValidate, notifyListeners, postAssignFromXMLElement, preAssignToXMLElement, printChildren, printTags, printTree, printTree, pythonString, remove, removeAll, removeAll, removeHandles, removeNetworkInput, removeNetworkOutput, removeNode, removeNode, removeNode, removeNodeListener, replace, set, setActualName, setAttrib, setBound, setCatagory, setChildrenExcept, setCoordSystem, setCurrentControlWidget, setCurrentNames, setDeleted, setEntryListener, setErrorState, setFromPrototype, setIsField, setIsLeaf, setIsSet, setListable, setMark, setMetaFields, setName, setNodeParent, setPresentable, setPrivate, setRemoteOwner, setRemoveable, setRenameable, setSaveable, setSelect, setSequenced, setSerialNo, setTentativeSelect, setToLink, setTransientChildren, setUpdateTime, setUserGroup, setValidates, setValidationLock, setValue, setValueGroup, showControlWidget, showControlWidget, showControlWidget, showHandles, startRename, tag, toString, unlinkListeners, unmarkNotified, untag, updateBindable, valChanged, valChanged, valueString

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

bondProps

public harmonic.mz.data.TableNode bondProps

Holdes the per element properties for bonds. These include:
BondColorProp
BondThicknessProp
BondHalfnessProp

atomProps

public harmonic.mz.data.TableNode atomProps

Holdes the per element properties for atoms. These include:
AtomColorProp
AtomRadiusProp

maxBalls

public harmonic.mz.data.fields.IntField maxBalls

Maximum balls to alow

sphereDis

public harmonic.mz.data.fields.IntField sphereDis

Fineness of sphere shapes

autoBond

public harmonic.mz.data.fields.BooleanField autoBond

Renders bonds between all bonded atoms if true

defaultBondHalfness

public harmonic.mz.data.fields.BooleanField defaultBondHalfness

Halfness for auto-bonded bonds

defaultBondColor

public harmonic.mz.data.fields.ColorField defaultBondColor

Color of auto bonded bonds

defaultBondThickness

public harmonic.mz.data.fields.ScalarField defaultBondThickness

Radius of auto bonded bonds

Constructor Detail

BASShape

public BASShape(Molecule mol)

Constructs a BASShape without adding it to database.

BASShape

public BASShape()

Constructs a BASShape without adding it to database. The super classes 'mol' field needs to be set to a loaded Molecule. No atoms or bonds are shown by default.

Method Detail

setAtomColor

public void setAtomColor(TreeNodeSet set,
                         harmonic.meshGeom.math.Clr3f clr)

Set atom color shown by this ball and stick for the given set

setAtomColor

public void setAtomColor(TreeNodeSet set,
                         Scheme scheme)

Set atom color shown by this ball and stick for the given set

setAtomRadius

public void setAtomRadius(TreeNodeSet set,
                          float radius)

Set atom radius shown by this ball and stick for the given set

setAtomRadius

public void setAtomRadius(TreeNodeSet set,
                          Scheme scheme)

Set atom radius shown by this ball and stick for the given set

setBondColor

public void setBondColor(TreeNodeSet set,
                         harmonic.meshGeom.math.Clr3f clr)

Set bond color shown by this ball and stick for the given set

setBondColor

public void setBondColor(TreeNodeSet set,
                         Scheme scheme)

Set bond color shown by this ball and stick for the given set

setBondThickness

public void setBondThickness(TreeNodeSet set,
                             float radius)

Set bond thickness shown by this ball and stick for the given set

setBondThickness

public void setBondThickness(TreeNodeSet set,
                             Scheme scheme)

Set bond thickness shown by this ball and stick for the given set

setBondHalfness

public void setBondHalfness(TreeNodeSet set,
                            boolean bShow)

Set bond halfness shown by this ball and stick for the given set

setBondHalfness

public void setBondHalfness(TreeNodeSet set,
                            Scheme scheme)

Set bond halfness shown by this ball and stick for the given set

areFieldsValid

public java.lang.String areFieldsValid()

Overrides:

areFieldsValid in class harmonic.mz.data.ModelNode

makePrototype

public harmonic.mz.data.ModelNode makePrototype()

Overrides:

makePrototype in class harmonic.mz.data.ModelNode

fullInvalidate

public void fullInvalidate()

Overrides:

fullInvalidate in class VVM_RepShape

nodeChanged

public void nodeChanged(harmonic.mz.event.NodeEvent event)

Specified by:

nodeChanged in interface harmonic.mz.event.NodeListener

Overrides:

nodeChanged in class VVM_RepShape

atomChanged

public void atomChanged(AtomEvent event)

Specified by:

atomChanged in interface AtomListener

Overrides:

atomChanged in class VVM_RepShape

validateGeometry

public void validateGeometry()

Looking at both bond and atom proporties, incremenetally validate geometry. A bond may need to be replaced if the bond or either surrounding atom property has changed. An atom may need to be replace if the color or radius changed. Loop over bonds, and for each bond consider redoing the bond section and either atom. Need to check if an atom has already been done by this call of the function, by another bond. Make sure to not get confused and compare against previous calls to this function. To do this, mark all atoms as 0 to start, mark as 1 when it handled.

Overrides:

validateGeometry in class harmonic.mz.data.ShapeNode

atomAtPart

public Atom atomAtPart(harmonic.viewer3D.PaintStruct p,
                       int iPart,
                       harmonic.meshGeom.math.Pnt3f pickedPoint)

Description copied from class: VVM_Shape

Used by the picking system. Return atom reference or null

Overrides:

atomAtPart in class VVM_Shape

bondAtPart

public Bond bondAtPart(harmonic.viewer3D.PaintStruct p,
                       int iPart,
                       harmonic.meshGeom.math.Pnt3f pickedPoint)

Description copied from class: VVM_Shape

Used by the picking system. Return bond reference or null

Overrides:

bondAtPart in class VVM_Shape

getDomains

public java.lang.String[] getDomains()

Description copied from class: VVM_RepShape

Return a list of domains used by this class

Overrides:

getDomains in class VVM_RepShape

getElementProps

public java.util.Vector getElementProps(java.lang.String domainType)

Description copied from class: VVM_RepShape

Return vector of meta data objects for the domain. The meta data objects are sub classes of the ElementProperty class

Overrides:

getElementProps in class VVM_RepShape

getElementDataTable

public harmonic.mz.data.TableNode getElementDataTable(java.lang.String domainType)

Description copied from class: VVM_RepShape

Like getElementProps() except return the ElementListNode object at the domain

Overrides:

getElementDataTable in class VVM_RepShape