This class describes a residue side-chain.
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| SB_DECLARE_DATA (SBMStructuralModelNodeSideChain) |
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| SB_NODE_GETTER_0 (, std::string, GetComment) |
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| SB_NODE_GETTER_0 (, std::string, GetStatusBit) |
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| SB_NODE_GETTER_0 (, int, GetStructuralID) |
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| SB_NODE_PREDICATE_0 (, HasComment) |
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| SB_NODE_PREDICATE_0 (, HasStatusBit) |
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| SB_NODE_PREDICATE_0 (, HasStructuralID) |
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| SB_DECLARE_DATA (SBMStructuralModelNodeGroup) |
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| SBMStructuralModelNodeGroup () |
| Builds a base model.
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| SBMStructuralModelNodeGroup (const std::string &n) |
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virtual | ~SBMStructuralModelNodeGroup () |
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bool | isSerializable () const |
| Returns true.
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virtual void | serialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0)) const |
| Serializes the node.
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virtual void | unserialize (SBCSerializer *serializer, const SBNodeIndexer &nodeIndexer, const SBVersionNumber &sdkVersionNumber=SB_SDK_VERSION_NUMBER, const SBVersionNumber &classVersionNumber=SBVersionNumber(1, 0, 0)) |
| Unserializes the node.
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virtual bool | canAddChild (SBNode *node, SBNode *nextNode=0) const |
| Returns whether this node can add node as a child.
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virtual SBPointerList< SBMStructuralModelNode > const * | getChildren () const |
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virtual void | setName (const std::string &name) |
| Sets the name of the structural group.
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bool | hasComment () const |
| Returns true when the comment is set.
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std::string const & | getComment () const |
| Returns the comment.
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void | setComment (const std::string &comment) |
| Sets the comment.
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void | clearComment () |
| Clears the comment.
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bool | hasStatusBit () const |
| Returns true when the status bit is set.
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std::string const & | getStatusBit () const |
| Returns the status bit.
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void | setStatusBit (const std::string &statusBit) |
| Sets the status bit.
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void | clearStatusBit () |
| Clears the status bit.
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bool | hasStructuralID () const |
| Returns true when the structural group's id is set.
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int const & | getStructuralID () const |
| Returns the structural group's id.
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void | setStructuralID (const int &groupID) |
| Sets the structural group's id.
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void | clearStructuralID () |
| Clears the structural group's id.
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virtual void | onBaseEvent (SBEvent *event) |
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virtual void | getNodes (SBNodeIndexer &nodeIndexer, SBNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const |
| Collects nodes into nodeIndexer , based on a nodeType , a selection status and a visitPredicate , with our without dependencies.
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virtual void | getNodes (SBNodeIndexer &nodeIndexer, const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const |
| Returns some nodes.
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bool | isWater () |
| Returns true if the structural group is a water molecule. More...
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virtual void | forEachNodeDepthFirst (void(*action)(SBDDataGraphNode *node)) |
| Performs an action on each node.
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virtual void | forEachNodeDepthFirst (SBCClass *object, void(SBCClass::*action)(SBDDataGraphNode *node)) |
| Performs an action on each node.
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unsigned int | getNumberOfChains () |
| Returns the number of chains.
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unsigned int | getNumberOfMolecules () |
| Returns the number of molecules.
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unsigned int | getNumberOfResidues () |
| Returns the number of residues.
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unsigned int | getNumberOfSegments () |
| Returns the number of segments.
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unsigned int | getNumberOfStructuralGroups () |
| Returns the number of structural groups.
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unsigned int | getNumberOfAtoms () |
| Returns the number of atoms.
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unsigned int | getNumberOfCarbons () |
| Returns the number of carbons.
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unsigned int | getNumberOfHydrogens () |
| Returns the number of hydrogens.
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unsigned int | getNumberOfNitrogens () |
| Returns the number of nitrogens.
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unsigned int | getNumberOfOxygens () |
| Returns the number of oxygens.
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unsigned int | getNumberOfSulfurs () |
| Returns the number of sulfurs.
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unsigned int | getNumberOfOtherAtoms () |
| Returns the number of other atoms.
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int | getSumOfFormalCharges () |
| Returns the sum of formal charges.
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float | getSumOfPartialCharges () |
| Returns the sum of partial charges.
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SBQuantity::mass | getMolecularWeight () |
| Returns the molecular weight. More...
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virtual void | print (unsigned int offset=0) const |
| Prints debugging information.
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| SB_NODE_GETTER_0 (, bool, GetMobilityFlag) |
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| SB_DECLARE_DATA (SBMStructuralModelNode) |
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virtual | ~SBMStructuralModelNode () |
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SBMStructuralModelNode * | getNextStructuralNode () const |
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SBMStructuralModelNode * | getPreviousStructuralNode () const |
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virtual bool | isLocked () const |
| Returns whether the node is locked (because of the model)
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virtual bool | getLockedFlag () const |
| Returns the locked flag of the model.
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SBMStructuralModel * | getModel () const |
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bool | getMobilityFlag () const |
| Returns the mobility flag.
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void | setMobilityFlag (bool flag) |
| Sets the mobility flag to flag .
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virtual unsigned int | getOpacity () const |
| Returns the opacity.
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virtual unsigned int | getMinimumOpacity () const |
| Returns the minimum opacity.
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virtual unsigned int | getTransparency () const |
| Returns the transparency.
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virtual unsigned int | getMaximumTransparency () const |
| Returns the maximum transparency.
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void | connectStructuralSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *), SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBStructuralEvent *)=0) |
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bool | structuralSignalIsConnectedToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *)) const |
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void | disconnectStructuralSignalFromSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBStructuralEvent *)) |
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void | getAllStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
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void | getInternalStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
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void | getLeafStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
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void | getStructuralNodesBreadthFirstTopDown (std::vector< SBMStructuralModelNode *> &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *)) |
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void | getAllStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
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void | getInternalStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
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void | getLeafStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
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void | getStructuralNodesBreadthFirstBottomUp (std::vector< SBMStructuralModelNode *> &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *)) |
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void | getAllStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
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void | getInternalStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
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void | getLeafStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer) |
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void | getStructuralNodesDepthFirst (std::vector< SBMStructuralModelNode *> &nodeIndexer, bool(*selectionRule)(SBMStructuralModelNode *)) |
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void | getStructuralNodesBreadthFirst (std::vector< SBMStructuralModelNode *> &nodeVectorTopDown, std::vector< SBMStructuralModelNode *> &nodeVectorBottomUp, bool(*selectionRule)(SBMStructuralModelNode *)) |
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void | forEachStructuralNodeBreadthFirst (void(*action)(SBMStructuralModelNode *node)) |
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void | forEachStructuralNodeDepthFirst (void(*action)(SBMStructuralModelNode *node)) |
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void | forEachStructuralNodeBreadthFirst (SBCClass *object, void(SBCClass::*action)(SBMStructuralModelNode *node)) |
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void | forEachStructuralNodeDepthFirst (SBCClass *object, void(SBCClass::*action)(SBMStructuralModelNode *node)) |
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| SB_DECLARE_DATA (SBMModelNode) |
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| SB_DECLARE_DATA (SBDDataGraphNode) |
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SBDDataGraphNode * | getParent () const |
| Returns the parent of the node. More...
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SBDDataGraphNode * | getThisNode () const |
| Returns the pointer to this node. More...
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SBDDataGraphNode * | getNextNode () const |
| Returns the pointer to the next node in the children of the node's parent. More...
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SBDDataGraphNode * | getPreviousNode () const |
| Returns the pointer to the previous node in the children of the node's parent. More...
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SBDDataGraphNode * | getNextNode (SBDDataGraphNode::Type nodeType) const |
| Returns the pointer to the next node with type nodeType in the children of the node's parent. More...
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SBDDataGraphNode * | getPreviousNode (SBDDataGraphNode::Type nodeType) const |
| Returns the pointer to the previous node with type nodeType in the children of the node's parent. More...
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SBDDocument * | getDocument () const |
| Returns the document the node belongs to. More...
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virtual bool | canAddChild (SBDDataGraphNode *node, SBDDataGraphNode *nextNode=0) const |
| Returns whether this node can add node as a child. More...
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virtual bool | addChild (SBDDataGraphNode *node, SBDDataGraphNode *nextNode=0) |
| Adds a child to the node. More...
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virtual bool | removeChild (SBDDataGraphNode *node) |
| Removes a child from the node. More...
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bool | hasOneOf (const SBNodeIndexer &nodeIndexer) const |
| Returns true if and only if this node is one of the nodes of the nodeIndexer , or is the ancestor of one of them. More...
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bool | descendsFrom (SBDDataGraphNode *node) const |
| Returns true if and only if this node is node , or descends from it. More...
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bool | descendsFrom (const SBNodeIndexer &nodeIndexer) const |
| Returns true if and only if this node is one of the nodes of the nodeIndexer , or descends from one of them. More...
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bool | descendsFrom (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const |
| Returns true if and only if this node is one of the nodes of the nodePointerIndexer , or descends from one of them. More...
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bool | isIn (SBDDataGraphNode *node) const |
| Returns true if and only if this node is node , or descends from it, or belongs to a group stored in node . More...
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bool | isIn (const SBNodeIndexer &nodeIndexer) const |
| Returns true if and only if this node is one of the nodes of the nodeIndexer , or descends from one of them, or belongs to a group stored in one of the nodes of the nodeIndexer . More...
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bool | isIn (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const |
| Returns true if and only if this node is one of the nodes of the nodePointerIndexer , or descends from one of them, or belongs to a group stored in of the nodes of the nodePointerIndexer . More...
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bool | isOneOf (const SBNodeIndexer &nodeIndexer) const |
| Returns true if and only if this node is one of the nodes of the nodeIndexer . More...
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bool | isOneOf (SBPointerIndexer< SBDDataGraphNode > *nodePointerIndexer) const |
| Returns true if and only if this node is one of the nodes of the nodePointerIndexer . More...
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SBDDataGraphNode * | getRoot () const |
| Returns the root of the hierarchy the node belongs to. More...
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unsigned int | getNodeIndex () const |
| Returns the node index (unique in the whole data graph, but non-persistent) More...
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std::string | getTypeString (bool humanReadable=false) const |
| Returns a string describing the type of the data graph node. More...
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virtual std::string const & | getName () const |
| Returns the name of the node.
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bool | isType (Type type) const |
| Returns true when the type of the node corresponds to type .
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bool | isModel () const |
| Returns true when the node is a model.
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bool | isStructuralNode () const |
| Returns true when the node is a structural node.
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bool | isStructuralModel () const |
| Returns true when the node is a structural model.
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bool | isVisualModel () const |
| Returns true when the node is a visual model.
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bool | isDynamicalModel () const |
| Returns true when the node is a dynamical model.
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bool | isInteractionModel () const |
| Returns true when the node is a interaction model.
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bool | isPropertyModel () const |
| Returns true when the node is a property model.
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bool | isMesh () const |
| Returns true when the node is a mesh.
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bool | isSimulator () const |
| Returns true when the node is a simulator.
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bool | isStructuralParticle () const |
| Returns true when the node is a structural particle (an atom or a pseudo-atom)
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virtual void | setLockedFlag (bool flag) |
| Sets the locked flag.
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bool | isCreated () const |
| Returns true if and only if the node is created. More...
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void | create () |
| Creates the node. More...
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bool | isErased () const |
| Returns true if and only if the node is erased. More...
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void | erase () |
| Erases the node. More...
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unsigned int | getFlags () const |
| Returns the flags. More...
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unsigned int | getInheritedFlags () const |
| Returns the inherited flags. More...
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bool | isSelected () const |
| Returns whether the node is selected. More...
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bool | getSelected () const |
| Returns whether the node is selected.
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bool | getSelectionFlag () const |
| Returns the selection flag. More...
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void | setSelectionFlag (bool flag) |
| Sets the selection flag. More...
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bool | isVisible () const |
| Returns whether the node is visible. More...
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bool | getVisible () const |
| Returns whether the node is visible.
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bool | getVisibilityFlag () const |
| Returns the visibility flag. More...
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void | setVisibilityFlag (bool flag) |
| Sets the visibility flag. More...
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bool | isHighlighted () const |
| Returns whether the node is highlighted. More...
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bool | getHighlightingFlag () const |
| Returns the highlighting flag. More...
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void | setHighlightingFlag (bool flag) |
| Sets the highlighting flag. More...
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virtual void | display (RenderingPass renderingPass) |
| Displays the node. More...
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virtual void | display () |
| Displays the node (deprecated) More...
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virtual void | displayForShadow () |
| Displays the node for shadowing purposes (deprecated) More...
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virtual void | displayForSelection () |
| Displays the node for selection purposes (deprecated) More...
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virtual void | setOpacity (unsigned int opacity) |
| Sets the opacity.
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virtual bool | hasOpacityRange () const |
| Returns whether the node has the opacity range.
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virtual unsigned int | getDefaultOpacity () const |
| Returns the default opacity.
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virtual unsigned int | getMaximumOpacity () const |
| Returns the maximum opacity.
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virtual unsigned int | getOpacitySingleStep () const |
| Returns the opacity single step.
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virtual std::string | getOpacitySuffix () const |
| Returns the opacity suffix.
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virtual void | setTransparency (unsigned int transparency) |
| Sets the transparency.
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virtual bool | hasTransparencyRange () const |
| Returns whether the node has the transparency range.
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virtual unsigned int | getDefaultTransparency () const |
| Returns the default transparency.
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virtual unsigned int | getMinimumTransparency () const |
| Returns the minimum transparency.
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virtual unsigned int | getTransparencySingleStep () const |
| Returns the transparency single step.
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virtual std::string | getTransparencySuffix () const |
| Returns the transparency suffix.
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float | getInheritedOpacity () const |
| Returns the cumulative opacity, when taking into account the ascendants.
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float | getInheritedTransparency () const |
| Returns the cumulative transparency, when taking into account the ascendants.
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bool | addMaterial (SBDDataGraphNodeMaterial *material) |
| Adds a material. More...
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bool | removeMaterial () |
| Removes the material. More...
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bool | hasMaterial () const |
| Returns whether the node has a material (by itself, or inherited)
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bool | ownsMaterial () const |
| Returns whether the node owns a material.
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SBDDataGraphNodeMaterial * | getMaterial () const |
| Returns the material. More...
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SBDDataGraphNode * | getMaterialOwner () const |
| Returns the node whose material is inherited. More...
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void | connectBaseSignalToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *), SBCReferenceTarget *nextReferenceTarget=0, void(SBCReferenceTarget::*nextFunctionPointer)(SBBaseEvent *)=0) |
| Connects the base signal to a slot. More...
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bool | baseSignalIsConnectedToSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *)) const |
| Returns true when the base signal is connected to a slot.
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void | disconnectBaseSignalFromSlot (SBCReferenceTarget *referenceTarget, void(SBCReferenceTarget::*functionPointer)(SBBaseEvent *)) |
| Disconnects the base signal from a slot.
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unsigned int | countNodes (SBDDataGraphNode::Type nodeType, bool selectedNodesOnly=false, const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const |
| Collects nodes into nodeIndexer , based on a nodeType , a selection status and a visitPredicate , with our without dependencies. More...
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unsigned int | countNodes (const SBNodePredicate &selectionPredicate=SBDDataGraphNode::All(), const SBNodePredicate &visitPredicate=SBDDataGraphNode::All(), bool includeDependencies=false) const |
| Collects nodes into nodeIndexer , based on a selectionPredicate and a visitPredicate , with our without dependencies. More...
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virtual std::string | getHierarchyString (const std::string &separator=" / ", bool includeNodeType=false) const |
| Returns a string with hierarchical information on the node and its parents names. More...
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virtual unsigned int | getNumberOfStructuralModels () |
| Returns the number of structural models.
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| SBCReferenceTarget () |
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virtual | ~SBCReferenceTarget () |
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unsigned int | getMemoryFootprint () const |
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void | printReferencesToOwners () const |
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