scripps.vvm.graphics
Class VVM_RepShape

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

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

Direct Known Subclasses:

AtomLabelShape, BASShape, CPKShape, MolSurfaceShape, ResidueLabelShape, RibbonBackboneShape, TubeBackboneShape, WireShape

public class VVM_RepShape

extends VVM_Shape

implements AtomListener

Base class for shapes that represend a molecule

Field Summary

harmonic.mz.data.fields.NodeSetField	molField
java.lang.String	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

VVM_RepShape(java.lang.String s)

Method Summary

void	atomChanged(AtomEvent event)
void	defineTable(harmonic.mz.data.TableNode table, java.util.Vector metaProperties)
int	expectedValidationTime()
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 domainName) Return vector of meta data objects for the domain.
Molecule	getMol()
void	nodeChanged(harmonic.mz.event.NodeEvent e)
scripps.vvm.data.ElementProperty	prop(java.lang.String name, java.util.Vector list)
void	purge()
void	selfNodeChanged(harmonic.mz.event.NodeEvent event)
void	setDefaultProps() Override to fill the the per element props with default properties
void	setMol(Molecule mol)
void	validateMol() Sub classes may call this to make sure the molecule has been read in.

Methods inherited from class scripps.vvm.graphics.VVM_Shape

atomAtPart, bondAtPart, 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, validateGeometry, 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, areFieldsValid, 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, makePrototype, 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

molField

public harmonic.mz.data.fields.NodeSetField molField

type

public java.lang.String type

Constructor Detail

VVM_RepShape

public VVM_RepShape(java.lang.String s)

Method Detail

expectedValidationTime

public int expectedValidationTime()

Overrides:

expectedValidationTime in class harmonic.mz.data.ShapeNode

nodeChanged

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

Specified by:

nodeChanged in interface harmonic.mz.event.NodeListener

Overrides:

nodeChanged in class harmonic.mz.data.ShapeNode

atomChanged

public void atomChanged(AtomEvent event)

Specified by:

atomChanged in interface AtomListener

setMol

public void setMol(Molecule mol)

getMol

public Molecule getMol()

validateMol

public void validateMol()

Sub classes may call this to make sure the molecule has been read in.

defineTable

public void defineTable(harmonic.mz.data.TableNode table,
                        java.util.Vector metaProperties)
                 throws java.lang.Exception

java.lang.Exception

setDefaultProps

public void setDefaultProps()

Override to fill the the per element props with default properties

getElementProps

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

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

getElementDataTable

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

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

getDomains

public java.lang.String[] getDomains()

Return a list of domains used by this class

selfNodeChanged

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

Overrides:

selfNodeChanged in class harmonic.mz.data.ShapeNode

purge

public void purge()

Specified by:

purge in interface harmonic.mz.data.DataNode

Overrides:

purge in class harmonic.mz.data.ShapeNode

fullInvalidate

public void fullInvalidate()

prop

public scripps.vvm.data.ElementProperty prop(java.lang.String name,
                                             java.util.Vector list)