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IMP
2.1.1
The Integrative Modeling Platform
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IMP
2.1.1
The Integrative Modeling Platform
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Common base class for heavy weight IMP objects.
More...
#include <IMP/base/declare_Object.h>
Inherits IMP::base::NonCopyable.
Inherited by IMP::algebra::DynamicNearestNeighbor3D, IMP::algebra::NearestNeighborD< D >, IMP::algebra::VectorKDMetric, IMP::atom::CHARMMResidueTopologyBase, IMP::atom::CHARMMSegmentTopology, IMP::atom::CHARMMTopology, IMP::atom::ForceFieldParameters, IMP::atom::Mol2Selector, IMP::atom::PDBSelector, IMP::atom::SmoothingFunction, IMP::core::ClosePairsFinder, IMP::core::DataObject< Data >, IMP::display::Geometry, IMP::display::Writer, IMP::domino::AssignmentContainer, IMP::domino::AssignmentsTable, IMP::domino::ParticleStates, IMP::domino::ParticleStatesTable, IMP::domino::RestraintCache, IMP::domino::SubsetFilter, IMP::domino::SubsetFilterTable, IMP::em2d::CollisionCrossSection, IMP::em2d::Image, IMP::em2d::ImageReaderWriter, IMP::em2d::ProjectionFinder, IMP::em2d::ScoreFunction, IMP::em::CoarseCC, IMP::em::DensityMap, IMP::em::EnvelopeScore, IMP::em::MapReaderWriter, IMP::em::PCAAligner, IMP::example::ExampleObject, IMP::isd::BivariateFunction, IMP::isd::CrossLinkData, IMP::isd::CysteineCrossLinkData, IMP::isd::FNormal, IMP::isd::FretData, IMP::isd::GaussianProcessInterpolation, IMP::isd::MultivariateFNormalSufficient, IMP::isd::UnivariateFunction, IMP::isd::vonMises, IMP::isd::vonMisesSufficient, IMP::kernel::Configuration, IMP::kernel::ConfigurationSet, IMP::kernel::Model, IMP::kernel::ModelObject, IMP::kernel::PairModifier, IMP::kernel::PairPredicate, IMP::kernel::PairScore, IMP::kernel::QuadModifier, IMP::kernel::QuadPredicate, IMP::kernel::QuadScore, IMP::kernel::Refiner, IMP::kernel::Sampler, IMP::kernel::SingletonModifier, IMP::kernel::SingletonPredicate, IMP::kernel::SingletonScore, IMP::kernel::TripletModifier, IMP::kernel::TripletPredicate, IMP::kernel::TripletScore, IMP::kernel::UnaryFunction, IMP::kernel::Undecorator, IMP::kinematics::DOF, IMP::kinematics::DOFsSampler, IMP::kinematics::Joint, IMP::kinematics::KinematicForest, IMP::kinematics::LocalPlanner, IMP::kmeans::KMeans, IMP::mpi::ReplicaExchange, IMP::multifit::AssemblyHeader, IMP::multifit::ComponentHeader, IMP::multifit::Ensemble, IMP::multifit::FFTFitting, IMP::multifit::FFTFittingOutput, IMP::multifit::ProbabilisticAnchorGraph, IMP::multifit::ProteomicsData, IMP::multifit::ProteomicsEMAlignmentAtomic, IMP::multifit::SettingsData, IMP::rmf::LoadLink, IMP::rmf::SaveLink, IMP::rotamer::RotamerCalculator, IMP::rotamer::RotamerLibrary, IMP::saxs::DerivativeCalculator, IMP::saxs::Profile, IMP::saxs::ProfileFitter< ScoringFunctionT >, IMP::statistics::Embedding, IMP::statistics::Metric, IMP::statistics::PartitionalClustering, log.DummyObject, and IMP::saxs::ProfileFitter< ChiScore >.
Public Member Functions | |
| virtual void | clear_caches () |
| virtual void | do_destroy () |
| CheckLevel | get_check_level () const |
| LogLevel | get_log_level () const |
| virtual VersionInfo | get_version_info () const |
| Get information about the module and version of the object. | |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. More... | |
| void | set_was_used (bool tf) const |
| void | show (std::ostream &out=std::cout) const |
Protected Member Functions | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| Object () | |
The base class for non value-type classes in IMP. Anything inheriting from Object has the following properties:
Types inheriting from Object should always be created using new in C++ and passed using pointers and stored using Pointer objects. Note that you have to be careful of cycles and so must use WeakPointer objects to break cycles. IMP_NEW() can help shorten creating a ref counted pointer. See Pointer for more information.
See example::ExampleObject for a simple example.
Reference counting is a technique for managing memory and automatically freeing memory (destroying objects) when it is no longer needed. In reference counting, each object has a reference count, which tracks how many different places are using the object. When this count goes to 0, the object is freed.
Python internally refence counts everything. C++, on the other hand, requires extra steps be taken to ensure that objects are reference counted properly.
In IMP, reference counting is done through the Pointer, PointerMember and Object classes. The former should be used instead of a raw C++ pointer when storing a pointer to any object inheriting from Object.
Any time one is using reference counting, one needs to be aware of cycles, since if, for example, object A contains an IMP::Pointer to object B and object B contains an Pointer to object A, their reference counts will never go to 0 even if both A and B are no longer used. To avoid this, use an WeakPointer in one of A or B.
Functions that create new objects should follow the following pattern
ObjectType *create_object(arguments) {
IMP_NEW(ObjectType, ret, (args));
do_stuff;
return ret.release();
}
using Pointer::release() to safely return the new object without freeing it.
Definition at line 123 of file base/declare_Object.h.
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An instance of "%1%" in the string will be replaced by a unique index.
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Objects can have internal caches. This method resets them returning the object to its just-initialized state.
Reimplemented in IMP::core::ExcludedVolumeRestraint, and IMP::core::MinimumRestraint.
Definition at line 253 of file base/declare_Object.h.
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Overide this method to take action on destruction.
Reimplemented in IMP::display::BildWriter, IMP::display::PymolWriter, IMP::display::CMMWriter, and IMP::display::ChimeraWriter.
Definition at line 256 of file base/declare_Object.h.
| void IMP::base::Object::set_check_level | ( | CheckLevel | l | ) |
Each object can be assigned a different check level too.
| void IMP::base::Object::set_log_level | ( | LogLevel | l | ) |
Each object can be assigned a different log level in order to, for example, suppress messages for verbose and uninteresting objects. If set to DEFAULT, the global level as returned by IMP::get_log_level() is used, otherwise the local one is used. Methods in classes inheriting from Object should start with IMP_OBJECT_LOG to change the log level to the local one for this object and increase the current indent.
| void IMP::base::Object::set_was_used | ( | bool | tf | ) | const |
IMP provides warnings when objects are never used before they are destroyed. Examples of use include adding an IMP::Restraint to an IMP::kernel::Model. If an object is not properly marked as used, or your code is the one using it, call set_was_used(true) on the object.