// $Id: classes.txt,v 1.29 2004/04/16 11:38:27 amoll Exp $

D documentation deficiencies
E exception qualifier
I interface deficiencies
/ ok
X general deficiencies
Z lacks

name                                class,     test,              notes
------------------------COMMON----------------------------------------------
(exceptions)                        I,          Z
GeneralException
IndexUnderflow
SizeUnderflow
IndexOverflow
InvalidRange
OutOfRange
InvalidFormat
IllegalSelfOperation
NullPointer
InvalidIterator
IncompatibleIterators
NotImplemented
IllegalTreeOperation
OutOfMemory
BufferOverflow
DivisionByZero
OutOfGrid
FileNotFound
GlobalExceptionHandler

Constants                           /           Z
HashFunction                        /           /
Limits                              /           /
LogStreamNotifier                   EI,         X
LogStreamBuf                        EI,         X
LogStream                           EI,         X
Rtti                                /           /
VersionInfo                         /           /
------------------------DATATYPE--------------------------------------------
Bit                                 /           /
BitVector                           /           /
HashGridBox3                        X           Z       HashGridBox3<Item>::set lacks
      DataItem_
      NeighbourBoxItem_
      BoxIteratorTraits_
      DataIteratorTraits_
HashGrid3                           /           X      
      BoxIteratorTraits_
HashMap                             /           /       
      IllegalKey
      IteratorTraits_
HashSet                             X           /       store methods
      IllegalKey
      Node
      IteratorTraits_
List                                /           /
Options                             X           /       isValid
Quadruple                           /           /
RegularData1D                       /           /
RegularData2D                       IX          /				
RegularData3D                       /           /
RegularExpression                   /           /
String                              /           X??
Substring                           /           /
      UnboundSubstring
      InvalidSubstring
StringHashMap                       /           /
TContour                            E           Z
TContourLine                        E           Z
------------------------CONCEPT---------------------------------------------
BaseIterator                        /           Z       
ConstBaseIterator                   /           Z
BidirectionalIterator               /           Z
ConstBidirectionalIterator          /           Z
ForwardIterator                     /           Z
ConstForwardIterator                /           Z

AutoDeletable                       /           /?       Interface so lassen!
Callback                            I           Z
Classtest                           /           /
Comparator                          /           Z
Composite                           /,          /       ausgabe in test
      AncestorIteratorTraits_       I           /
      ChildCompositeIteratorTraits_ I           /
      CompositeIteratorPosition_    I           /
      CompositeIteratorTraits_      I           /
      SubcompositeIteratorTraits_   I           /
Embeddable                          /           X
EnumeratorIndex                     IX          X
      IncompatibleIndex             I,          X
Enumerator                          IX,         X       delete_variants // many methods in test still missing
      IteratorTraits_               IX,         X
NamedProperty                       /           /
PropertyManager                     /           /

NotificationManager_                I,          Z
NotificationTarget_                 I           Z
NotificationSource_                 I           Z
NotificationSlot_                   I           Z
NotificationTarget                  I           Z
NotificationTarget1                 I           Z
NotificationTarget2                 I           Z

Object                              (/)         /       read/write fehlen
PersistenceManager                  I           X       Test is little more than a skeleton! 
PersistentObject                    /           /
RandomAccessIterator                IX          X 
ConstRandomAccessIterator           I           Z
ReverseRandomAccessIterator         I           Z
ConstReverseRandomAccessIterator    I           Z
ReverseBidirectionalIterator        I           Z
ConstReverseBidirectionalIterator   I           Z
Selectable                          /           /
TextPersistenceManager              E           /
TimeStamp                           /           /
PreciseTime                         /           /
Visitor                             I           Z
XDRPersistenceManager               IX          X       many tests missing

UnaryFunctor                        /,          Z
BinaryFunctor                       /,          Z
UnaryPredicate                      I           Z
BinaryPredicate                     I           Z
UnaryProcessor                      I           Z
BinaryProcessor                     I           Z
------------------------ENERGY----------------------------------------------
(atomicContactEnergy)               E           /
ComposedEnergyProcessor             /           /
(Coulomb)                           E           Z
(DistanceCoulomb)                   E           Z
EnergyProcessor                     /           /
------------------------FORMAT----------------------------------------------
Bruker1D                            EI,         Z
Bruker2D                            EI,         Z
BrukerParameter                     EIX,        Z       warum in JCAMPFILE?, parameter->getParameter
resourcefile                        E,          X       many tests missing
resourceEntry                       E,          X
GenericMolFile                      /,          /
GenericPDBFile                      EI,         Z
HINFile                             EX,         /
INIFile                             /         	/
LineBasedFile                       /           /
      LineBasedFileError            I           Z
MOLFile                             /           /
MOL2File                            /,          /
NMRStarFile                         /           /
TRRFile                             /?          Z
Parameters                          E           /
ParameterSection                    I,          /
trajectoryFile                      /           X       Test is empty!       
JCAMPFile                           /           Z 
SDFile                              /?          /?    
PDBFile                             /,          /
XYZFile                             /,          /
DCDFile                             X?          X       some tests missing
------------------------KERNEL----------------------------------------------
Atom                                /           /
            BondIteratorTraits_     /           Z
AtomContainer                       /           /
AtomContainerIteratorTraits_        /           Z
AtomIteratorTraits_                 /           Z
Bond                                /           /
            TooManyBonds            I           Z
Chain                               /           /
ChainIteratorTraits_                /           Z
CompositeIteratorTraits_            /           Z
Expression                          X           (X)        attrib doku
ExpressionPredicate                 IX          (X)        attrib doku
ExpressionTree                      IX          (X)        OCI(UnaryPred)
SyntaxTree                          I           (X)        attrib doku
Fragment                            /           / 
FragmentIteratorTraits_             EI          Z
Element                             /           Z
PTE_                                /           /
KernelPredicate                     I           /
Molecule                            /           /
MoleculeIteratorTraits_             EI          Z
NucleicAcid                         I           /
NucleicAcidIteratorTraits_          EI          Z
Nucleotide                          /           /
NucleotideIteratorTraits_           EI          Z
PDBAtom                             /           /          attrib doku
PDBAtomIteratorTraits_              /           Z
Protein                             /           /
ProteinIteratorTraits_              EI          Z
Residue                             /           /
ResidueIteratorTraits_              EI          Z
SecondaryStructure                  /           /
SecondaryStructureIteratorTraits_   EI          Z
Selector                            /           /
System                              /           /

 AromaticBondsPredicate             /           /           OCI nicht notwendig
 AtomNamePredicate                  /           /           OCI nicht notwendig
 AtomTypePredicate                  /           /           OCI nicht notwendig
 BackBonePredicate                  /           /           OCI nicht notwendig
 ChainPredicate                     /           /           OCI nicht notwendig
 ConnectedToPredicate               (X)         /           OCI nicht notwendig
 DoubleBondsPredicate               /           /           OCI nicht notwendig
 ElementPredicate                   /           /           OCI nicht notwendig
 InRingPredicate                    /           /           OCI nicht notwendig
 MoleculePredicate                  /           /           OCI nicht notwendig
 NucleicAcidPredicate               /           /           OCI nicht notwendig
 NucleotidePredicate                /           /           OCI nicht notwendig
 NumberOfBondsPredicate             /           /           OCI nicht notwendig
 ProteinPredicate                   /           /           OCI nicht notwendig
 ResidueIDPredicate                 /           /           OCI nicht notwendig
 ResiduePredicate                   /           /           OCI nicht notwendig
 SecondaryStructurePredicate        /           /           OCI nicht notwendig
 SelectedPredicate                  /           /           OCI nicht notwendig
 SingleBondsPredicate               /           /           OCI nicht notwendig
 SolventPredicate                   /           Z           OCI nicht notwendig
 Sp2HybridizedPredicate             /           /           OCI nicht notwendig
 Sp3HybridizedPredicate             /           /           OCI nicht notwendig
 SpHybridizedPredicate              /           /           OCI nicht notwendig
 TripleBondsPredicate               /           /           OCI nicht notwendig
 TruePredicate                      /           /           OCI nicht notwendig
------------------------MATHS-----------------------------------------------    
AnalyticalGeometry                  /           /
MathsCommon                         /           /
TAngle                              /           /
TBox3                               /           /
TCircle3                            /           /
TLine3                              /           /
TMatrix4x4                          /           /
PiecewiseFunction                   X           X
PiecewisePolynomial                 X           X       tests for special cases missing        
RombergIntegrator                   /           Z  
TPlane3                             /           /
TQuaternion                         /           /
TSphere3                            /           /
TSurface                            /           /    
TVector2                            /           /
TVector3                            /           /
TVector4                            /           /
Function                            I           /
NumericalIntegrator                 /           /
------------------------MOLMEC----------------------------------------------
                        ---------AMBER-----
amberBend                           EI          Z
AmberFF                             EI          /
AmberNonBonded                      EI          Z
AmberTorsion                        EI          Z
AmberStretch                        EI          Z
                        --------CHARM------
CharmmBend                          EI          Z
CharmmImproperTorsion               EI          Z
CharmmFF                            EI          /
CharmmStretch                       EI          Z
CharmmTorsion                       EIX         Z
CharmmNonBonded                     EI          Z
                        --------COMMON-----
AtomVector                          EX          /       problem in docu with "using" keyword
	AtomConstVector             EI 	        Z
AssignTypeProcessor                 EI          Z
  AssignTypeNameProcessor
ChargeRuleProcessor                 EI          Z
ForceField                          E           Z
ForceFieldComponent                 EI          Z
Gradient                            EI          /
PeriodicBoundary                    /           Z
RadiusRuleProcessor                 EI          Z
RuleEvaluator                       X           X       ruleEvaluator::dump missing // some tests missing
RuleProcessor                       EIX         Z       ::set and ::dump not implemented
SnapShot                            EI          X       problems with operator >> // test empty!
SnapShotManager                     EIX         X       ::clear and ::applyFirstSnapShot // test empty!
TypeRuleProcessor                   EI          Z
TypenameRuleProcessor               EI          Z
(support)                           EI          Z
                        -----MDSIMULATION--
CanonicalMD                         EX          Z
MicroCanonicalMD                    EX          Z
MolecularDynamics                   E           Z
                        -----MINIMIZATION--
ConjugateGradientMinimizer          EIX         Z       copy constructor and operator =
EnergyMinimizer                     EIX         X       copy constructor, assignment op = and ::setMaximalNumberOfIterations
LineSearch                          E           Z
SteepestDescentMinimizer            EI          Z
                        -----PARAMETER-----
AtomTypes                           (/)         Z
CharmmEEF1                          /           Z
CosineTorsion                       /           Z
            SingleValues            EI          Z
            Values                  EI          Z
ForceFieldParameters                IX          Z       ::clear() and operator ==
ResidueTorsions                     (/)         Z
Templates                           EI          Z
QuadraticAngleBend                  E           Z
QuadraticBondStretch                E           Z
QuadraticImproperTorsion            /           Z
LennardJones                        X           Z       ::extractSection
Potential1210                       (/)         Z
------------------------VIEW---------------------------------------------
                        -----COMMON-------
Common                              /           Z
                        -----FUNCTOR------
AddVanDerWaalsModel                 I           Z
AtomBondModelBaseProcessor          I           Z
AddBallAndStickModel                I           Z
AddLineModel                        I           Z
BaseModelProcessor                  I           Z
BackboneModel                       E           Z
ColorCalculator                     I           Z
StandardColorCalculator             I           Z
  ElementColorCalculator
  ResidueNameColorCalculator      
  AtomChargeColorCalculator
  AtomDistanceColorCalculator 
FindGeometricObjects                I           Z
MolecularInformation                I           Z
                        -------GUI-------
LabelProperties                     /           Z
DisplayProperties                   /           Z
AddSurfaceModel                   	/           Z
AddBallAndStickModel              	/           Z
AddLineModel                      	/           Z
AddVanDerWaalsModel               	/           Z
Control                             EI          Z
MolecularControl                    I           Z
MolecularStructure                  /           Z
                        -----KERNEL------
                        -----PRIMITV-----
Backbone                            EI?         Z
TwoColoredLine                      /           Z
TwoColoredTube                      /           Z
------------------------NMR-------------------------------------------------
AnisotropyShiftProcessor            X           /
AssignShiftProcessor                I           /
ClearShiftProcessor                 I           /
CreateSpectrumProcessor             X           X       operator << not implemented // a few tests missing
EFShiftProcessor                    I           X       many tests missing
Experiment                          X	        Z
HaighMallionShiftProcessor          X           X       
HBondShiftProcessor                 X           Z
JohnsonBoveyShiftProcessor          X           /
MakeSpectrumProcessor               EI          X
Spectrum  		            X           X
Peak1D                              EI          /
PeakList                            /           /
RandomCoilShiftProcessor            EI          X       some tests missing
ShiftModel                          I           /
ShiftModule                         I           /
------------------------PYTHON----------------------------------------------
(extractors)                        /           Z
PyAtomContainerList                 E           Z
PyAtomList                          E           Z
PyBALLSipHelper                     /           Z
PyBondList                          E           Z
PyChainList                         E           Z
PyConstant                          /           Z
PyFragmentList                      E           Z
PyInterpreter                       E           Z
PyNucleotideList                    E           Z
PyNucleicAcidList                   E           Z
PyMoleculeList                      E           Z
PyPDBAtomList                       E           Z
PyProteinList                       E           Z
PyResidueList                       E           Z
PySecondaryStructureList            E           Z
------------------------QSAR------------------------------------------------
Descriptor                          /           X?
SimpleDescriptors                   /           X?
------------------------SOLVATION-------------------------------------------
ClaverieParameter                   /           /
FDPB                                IX          X
(molecularSurfaceGrid)              /           Z
OoiEnergy                           /           /
Pair6_12InteractionEnergyProcessor  IX          X
Pair6_12RDFIntegrator               EIX         X
PairExpRDFIntegrator                IX          X       options::clear
PairExpInteractionEnergyProcessor   IX          X
PCMCavFreeEnergyProcessor           I           /
PierottiCavFreeEnergyProcessor      /           /
PoissonBoltzmann                    X           X       setupSASGrid implementation missing
ReissCavFreeEnergyProcessor         /           /
SolventParameter                    X           X       ::operator == and extraxtSextion
SolventDescriptor                   X           X       test: const and muteable methods
UhligCavFreeEnergyProcessor         /           /
------------------------STRUCTURE-------------------------------------------
analyticalSES                       EI          /
AssignChargeProcessor               I           /
AssignRadiusProcessor               I           /
GeometricCenterProcessor            EI          /
FragmentDistanceCollector           EI          /

ClearChargeProcessor                I           /
ClearRadiusProcessor                I           /
(connolly)                          EIX         /           der code ist furchtbar!
BoundingBoxProcessor                EI          Z
GeometricCenterProcessor            IX          Z           angle-calculation should be done somewhere else
GraphEdge                           ?           Z
GraphFace                           ?           Z
GraphVertex                         ?           Z

FragmentDB                          IX          X               
            NoFragmentNode          I           Z
            NormalizeNamesProcessor I           Z
            AddHydrogensProcessor   I           Z
            BuildBondsProcessor     I           /

(numericalSAS)                      EI          /           der code ist furchtbar!
RadialDistributionFunction          /           /
ResidueChecker                      E           Z
RDFIntegrator                       /           X
RDFParameter                        /           X       test is empty!         
RDFSection                          /           X       test is empty!
Rotamer                             EI          Z
ResidueRotamerSet                   EI          Z
RotamerLibrary                      E           Z
RuleProcessor                       EI          Z
singularities                       (D)         Z
SmilesParser                        X?          /?
SurfaceProcessor                    /           Z
StructureMapper                     EIX         X
TranslationProcessor                EI          X
TransformationProcessor             EI          X
TReducedSurface                     EIX         Z
TBSDTree                            EIX         Z
TRSEdge                             EIX         Z
TRSFace                             EIX         Z
TRSVertex                           EIX         Z
TSESVertex                          EIX         Z
TSESFace                            EIX         Z
TSESEdge                            EIX         Z
TSESEdge                            EIX         Z
TSESEdge                            EIX         Z
TSESEdge                            EIX         Z
TSolventExcludedSurface             EIX         Z
(triangulation)                     EIX         Z
TTriangulatedSurface                EIX         Z          
  Triangle
  Edge
  Point
------------------------SYSTEM----------------------------------------------
Directory                           E           /
File                                /           /
FileSystem                          /           /
Path                                EI          /
ISockStream                         EI          Z
IOSockStream                        EI          Z
IOStreamSocket                      EI          Z
OSockStream                         EI          Z
SockAddr                            EI          Z
SocketBuf                           EI          Z
SockInetAddr                        EI          Z
SockInetBuf                         EI          Z
Timer                               I           /
TCPTransfer                         /           /
-------------------------VIEW-----------------------------------------------
                        -------DATATYPE----
Color                               /           Z
ColorUnitHue                        E           Z
ColorRGBA                           E           Z
ColorHSV                            E           Z
ColorUnit                           E           Z
ColorTable                          EI          Z
                        -------FUNCTOR-----
Filter                              /           Z
GeometricCollector                  E           Z
Information                         /           Z
                        ---------GUI-------
GLLabel                             /           Z
GLPoint                             /           Z
GLSimpleBox                         E           Z
GLMesh                              E           Z
GLLine                              E           Z
GLSphere                            /           Z
GLTube                              E           Z

FileDialog                          /           Z
Preferences                         /           Z

DlgmoveOverlay                      /?          Z
GLObjectCollector                   E           Z
GLDisplayList                       /           Z
CompositeDescriptor                 EX          Z
GLQuadricObject                     E           Z
GLPrimitiveManager                  /           Z
  GLDisplayListObject_              
  GLSphereDisplayLists_
  GLTubeDisplayLists_
  GLSimpleBoxDisplayLists_
GLObject                            E           Z
Server                              /           Z
GLEntityDescriptor                  E           Z
MainControl                         EIX         Z
ObjectCreator                       E           Z

Sphere                              EI          Z
  Box
  Cone
  Tube
Events                              E           Z
PyWidget                            /           Z
Control                             E           Z
MainControlPreferences              /           Z
ModularWidget                       /           Z
RegularData1DWidget                 /           Z
RegularData2DWidget                 /           Z
Scene                               X           Z
ServerPreferences                   /           Z
                        --------KERNEL-------
Client                              E           Z
ClientScene                         EI          Z
ColorExtension                      E           Z
ColorExtension2                     E           Z
ColorExtension3                     E           Z
ColorExtension4                     E           Z
ColorExtension5                     E           Z
ConnectionObject                    E           Z
GeometricObject                     /           Z
LogView                             E           Z
Message                             E           Z
  CompositeMessage
  NewCompositeMessage
  RemovedCompositeMessage
  ChangedCompositeMessage
  DisplayMessage
  SceneMessage
  WindowMessage
  SelectionMessage
  GeometricObjectSelectionMessage
NormalVector                        E           Z
QTTimer                             /           Z
Radius                              /           Z
Vertex1                             E           Z
Vertex2                             E           Z
                        --------PRIMITIV-------
BaseTube                            (I)         Z
Label                               (I)         Z
Line                                (I)         Z
Point                               (I)         Z
Mesh                                (I)         Z
SimpleBox                           (I)         Z
Sphere                              (I)         Z
Tube                                (I)         Z
