scripps.vvm.manager
Class VVM

java.lang.Object
  |
  +--harmonic.mz.data.ModelNode
        |
        +--harmonic.mz.function.Module
              |
              +--scripps.vvm.manager.VVM

All Implemented Interfaces:

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

public class VVM

extends harmonic.mz.function.Module

implements harmonic.mz.event.NodeListener

Nested Class Summary

class

VVM.VVM_Prototype

Field Summary

static java.lang.String	ADD_LABELS
static java.lang.String	ATOM_LABEL_TYPE
static java.util.Hashtable	atomColorTable
static java.util.Hashtable	atomTypes
static java.lang.String	ATTRIB_SSTYPE
static harmonic.mz.data.fields.BooleanField	autoApply
boolean	bAddRemove
static java.lang.String	BAS_BOND_TYPE
boolean	bThreeLetterNames
static java.lang.String	CPK_TYPE
static int	CUBE
static harmonic.mz.data.fields.BooleanField	defaultBAS
static harmonic.mz.data.fields.BooleanField	defaultCPK
static harmonic.mz.data.fields.BooleanField	defaultMetals
static harmonic.mz.data.fields.BooleanField	defaultMolSurface
static harmonic.mz.data.fields.BooleanField	defaultRibbons
static harmonic.mz.data.fields.BooleanField	defaultTubes
static harmonic.mz.data.fields.BooleanField	defaultWire
static int	DODECAHEDRON
static java.lang.String	DOMAIN_ATOMS
static java.lang.String	DOMAIN_BACKBONE
static java.lang.String	DOMAIN_BONDS
static java.lang.String	DOMAIN_CHAINS
static java.lang.String	DOMAIN_MOLECULES
static java.lang.String	DOMAIN_NONE
static java.lang.String	DOMAIN_RESIDUES
static java.lang.String	DOMAIN_SS_ELEMENTS
static harmonic.mz.data.fields.BooleanField	enableToggle
static int	HELIX
static int	HOOP_SPHERE
static int	ICOSOHEDRON
static harmonic.mz.data.fields.BooleanField	keepPropUndos
static harmonic.meshGeom.math.Clr3f	labelColor
static java.awt.Font	labelFont
static java.lang.String	LINES_GEOM
static int	LOOP
static scripps.vvm.gui.MainDialog	mainDlg
static scripps.vvm.gui.MolDialog	molDialog
static VVM	mx
static scripps.vvm.gui.ObjectPropDialog	objectPropDialog
static int	OCTAHEDRON
static java.lang.String	REMOVE_LABELS
static scripps.vvm.gui.RepDialog	repDialog
static java.lang.String	RESIDUE_LABEL_TYPE
static java.util.Hashtable	resTypes
static java.lang.String	RIBBON_TYPE
static harmonic.mz.data.fields.BooleanField	showAllBAS
static harmonic.mz.data.fields.BooleanField	showAllCPK
static harmonic.mz.data.fields.BooleanField	showAllMolSurface
static harmonic.mz.data.fields.BooleanField	showAllRibbons
static harmonic.mz.data.fields.BooleanField	showAllTubes
static harmonic.mz.data.fields.BooleanField	showAllWire
static scripps.vvm.gui.ShowHideDialog	showHideDialog
static VVMSnapSearcher	snaps
static java.lang.String	SOLID_GEOM
static int	SPHERE
static scripps.vvm.gui.RepPropSpreadsheet	spreadsheet
static int	STRAND
static java.lang.String	SURFACE_GEOM
static java.lang.String	SURFACE_TYPE
static int	TETRAHEDRON
static java.lang.String	TUBE_TYPE
static int	TURN
static java.util.Hashtable	typeSetsLists
static java.lang.String	WIRE_BOND_TYPE

Fields inherited from class harmonic.mz.function.Module

bBigImageBad, bigToolbarImage, bInterfaceSettingsInvalid, bPythonDone, className, functionRoot, functionTable, initFile, menu, menuRoot, publicName, pyRef, settings, startCheck, toolbarRoot, vptoolRoot, workingDir

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()

Method Summary

static void	addButton(java.lang.String menuText, java.lang.Object listener, java.lang.String callback, HWHexRectButtons buttons)
void	addResGroup(java.lang.String listName, java.lang.String setName, java.lang.String[] set)
static void	assignIndex(TreeNodeSet treeNode)
static void	createStandaredLists_static(harmonic.mz.data.FileNode file)
void	createStandaredLists(harmonic.mz.data.FileNode file)
static CursorManager	cursors()
static harmonic.mz.data.ModelNode	findMXNode(java.lang.String name)
java.lang.String	getHelpDir()
java.lang.String	getHelpFile(harmonic.mz.gui.Documentable helpMe)
java.lang.String	getResourceDir()
java.lang.String	getWorkingDir()
void	installInFramework()
void	modelLoaded(harmonic.mz.data.FileNode file)
void	modelUnloaded(harmonic.mz.data.FileNode file)
static MoleculeManager	molecules()
void	removeGUI()
static RepManager	reps()
static SetManager	sets()
static HWHexRectButtons	standardMenu()

Methods inherited from class harmonic.mz.function.Module

addFSFunction, addFunction, addFunction, createStandardLists, execute, getFunction, getFunctionTable, getInstallDir, hasStandardLists, macroGUI, readSettings, writeSettings

Methods inherited from class harmonic.mz.data.ModelNode

actionPerformed, addAll, addAlphaed, addField, addField, addField, addFields, addNetworkInput, addNetworkOutput, addNode, addNodeListener, addNodeListener, addNodes, addNodes, addToCurrent, addToGlobals, addToNetworkEditor, addToTemps, addWithUndo, 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, expectedValidationTime, fileRoot, finalize, findFieldElement, findNode, fromXMLNodes, getAttrib, getBound, getCatagory, getControlWidget, getCurrentNames, getDataTransfer, getDataTransferTypes, 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, getTransformable, getTransformableParent, getTransient, getTreeName, getTypeImage, getTypeURL, getUnfoldedChildren, getUpdateTime, getUserGroup, getValidates, getValue, getXMLNodes, hasDependants, hasExternalRef, hashKey, hasValidationLock, hideControlWidget, indexOf, initControlWidget, insertNode, interpolate_Linear, interpolate_Quadratic, invalidate, isField, isFinal, isInSubtree, isInTree, isLinked, isNotified, isPurged, isSet, isTemporary, isValid, linkedTo, linksChildren, makeContextMenu, makeFixed, makePrototype, makeReferenced, makeUnreferenced, makeVisibleInGUI, markNotified, mayValidate, nodeChanged, notifyListeners, postAssignFromXMLElement, preAssignToXMLElement, printChildren, printTags, printTree, printTree, purge, purgeFinal, pythonString, remove, removeAll, removeAll, removeHandles, removeNetworkInput, removeNetworkOutput, removeNode, removeNode, removeNode, removeNodeListener, replace, selfNodeChanged, 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, setSelect, setSequenced, setSerialNo, setTentativeSelect, setTentativeSelect, setToLink, setTransient, setTransientChildren, setUpdateTime, setUserGroup, setValidates, setValidationLock, setValue, setValueGroup, showControlWidget, showControlWidget, showControlWidget, showHandles, startRename, tag, toString, unlinkListeners, unmarkNotified, untag, updateBindable, valChanged, valChanged, validate, valueString

Methods inherited from class java.lang.Object

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

Methods inherited from interface harmonic.mz.event.NodeListener

nodeChanged

Field Detail

mx

public static VVM mx

atomColorTable

public static java.util.Hashtable atomColorTable

snaps

public static VVMSnapSearcher snaps

resTypes

public static java.util.Hashtable resTypes

atomTypes

public static java.util.Hashtable atomTypes

typeSetsLists

public static java.util.Hashtable typeSetsLists

labelColor

public static harmonic.meshGeom.math.Clr3f labelColor

labelFont

public static java.awt.Font labelFont

RIBBON_TYPE

public static java.lang.String RIBBON_TYPE

TUBE_TYPE

public static java.lang.String TUBE_TYPE

BAS_BOND_TYPE

public static java.lang.String BAS_BOND_TYPE

WIRE_BOND_TYPE

public static java.lang.String WIRE_BOND_TYPE

CPK_TYPE

public static java.lang.String CPK_TYPE

SURFACE_TYPE

public static java.lang.String SURFACE_TYPE

ATOM_LABEL_TYPE

public static java.lang.String ATOM_LABEL_TYPE

RESIDUE_LABEL_TYPE

public static java.lang.String RESIDUE_LABEL_TYPE

ATTRIB_SSTYPE

public static java.lang.String ATTRIB_SSTYPE

DOMAIN_NONE

public static java.lang.String DOMAIN_NONE

DOMAIN_MOLECULES

public static java.lang.String DOMAIN_MOLECULES

DOMAIN_BACKBONE

public static java.lang.String DOMAIN_BACKBONE

DOMAIN_RESIDUES

public static java.lang.String DOMAIN_RESIDUES

DOMAIN_SS_ELEMENTS

public static java.lang.String DOMAIN_SS_ELEMENTS

DOMAIN_BONDS

public static java.lang.String DOMAIN_BONDS

DOMAIN_ATOMS

public static java.lang.String DOMAIN_ATOMS

DOMAIN_CHAINS

public static java.lang.String DOMAIN_CHAINS

SOLID_GEOM

public static java.lang.String SOLID_GEOM

SURFACE_GEOM

public static java.lang.String SURFACE_GEOM

LINES_GEOM

public static java.lang.String LINES_GEOM

SPHERE

public static int SPHERE

CUBE

public static int CUBE

OCTAHEDRON

public static int OCTAHEDRON

TETRAHEDRON

public static int TETRAHEDRON

ICOSOHEDRON

public static int ICOSOHEDRON

DODECAHEDRON

public static int DODECAHEDRON

HOOP_SPHERE

public static int HOOP_SPHERE

HELIX

public static final int HELIX

See Also:

Constant Field Values

STRAND

public static final int STRAND

See Also:

Constant Field Values

TURN

public static final int TURN

See Also:

Constant Field Values

LOOP

public static final int LOOP

See Also:

Constant Field Values

ADD_LABELS

public static final java.lang.String ADD_LABELS

See Also:

Constant Field Values

REMOVE_LABELS

public static final java.lang.String REMOVE_LABELS

See Also:

Constant Field Values

bAddRemove

public boolean bAddRemove

bThreeLetterNames

public boolean bThreeLetterNames

molDialog

public static scripps.vvm.gui.MolDialog molDialog

repDialog

public static scripps.vvm.gui.RepDialog repDialog

spreadsheet

public static scripps.vvm.gui.RepPropSpreadsheet spreadsheet

objectPropDialog

public static scripps.vvm.gui.ObjectPropDialog objectPropDialog

mainDlg

public static scripps.vvm.gui.MainDialog mainDlg

showHideDialog

public static scripps.vvm.gui.ShowHideDialog showHideDialog

autoApply

public static harmonic.mz.data.fields.BooleanField autoApply

enableToggle

public static harmonic.mz.data.fields.BooleanField enableToggle

keepPropUndos

public static harmonic.mz.data.fields.BooleanField keepPropUndos

defaultMetals

public static harmonic.mz.data.fields.BooleanField defaultMetals

defaultCPK

public static harmonic.mz.data.fields.BooleanField defaultCPK

defaultMolSurface

public static harmonic.mz.data.fields.BooleanField defaultMolSurface

defaultBAS

public static harmonic.mz.data.fields.BooleanField defaultBAS

defaultWire

public static harmonic.mz.data.fields.BooleanField defaultWire

defaultTubes

public static harmonic.mz.data.fields.BooleanField defaultTubes

defaultRibbons

public static harmonic.mz.data.fields.BooleanField defaultRibbons

showAllCPK

public static harmonic.mz.data.fields.BooleanField showAllCPK

showAllMolSurface

public static harmonic.mz.data.fields.BooleanField showAllMolSurface

showAllTubes

public static harmonic.mz.data.fields.BooleanField showAllTubes

showAllRibbons

public static harmonic.mz.data.fields.BooleanField showAllRibbons

showAllWire

public static harmonic.mz.data.fields.BooleanField showAllWire

showAllBAS

public static harmonic.mz.data.fields.BooleanField showAllBAS

Constructor Detail

VVM

public VVM()

Method Detail

getResourceDir

public java.lang.String getResourceDir()

Overrides:

getResourceDir in class harmonic.mz.function.Module

getHelpDir

public java.lang.String getHelpDir()

Overrides:

getHelpDir in class harmonic.mz.function.Module

getHelpFile

public java.lang.String getHelpFile(harmonic.mz.gui.Documentable helpMe)

Overrides:

getHelpFile in class harmonic.mz.function.Module

getWorkingDir

public java.lang.String getWorkingDir()

Overrides:

getWorkingDir in class harmonic.mz.function.Module

installInFramework

public void installInFramework()

Overrides:

installInFramework in class harmonic.mz.function.Module

removeGUI

public void removeGUI()

Overrides:

removeGUI in class harmonic.mz.function.Module

modelLoaded

public void modelLoaded(harmonic.mz.data.FileNode file)

Overrides:

modelLoaded in class harmonic.mz.function.Module

modelUnloaded

public void modelUnloaded(harmonic.mz.data.FileNode file)

Overrides:

modelUnloaded in class harmonic.mz.function.Module

createStandaredLists

public void createStandaredLists(harmonic.mz.data.FileNode file)

createStandaredLists_static

public static void createStandaredLists_static(harmonic.mz.data.FileNode file)

cursors

public static CursorManager cursors()

molecules

public static MoleculeManager molecules()

reps

public static RepManager reps()

sets

public static SetManager sets()

findMXNode

public static harmonic.mz.data.ModelNode findMXNode(java.lang.String name)

standardMenu

public static HWHexRectButtons standardMenu()

addButton

public static void addButton(java.lang.String menuText,
                             java.lang.Object listener,
                             java.lang.String callback,
                             HWHexRectButtons buttons)

addResGroup

public void addResGroup(java.lang.String listName,
                        java.lang.String setName,
                        java.lang.String[] set)

assignIndex

public static void assignIndex(TreeNodeSet treeNode)