PlastLibrary
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▼Nalgo | PLAST algorithm concepts |
►Ncore | Concept for configuring and running PLAST |
►Nhits | Concept for hits iteration |
▼Nalignment | |
►Ncore | |
►Nfilter | |
►Ntools | |
►Nvisitors | |
▼Ndatabase | Definition of concepts related to genomic databases |
►Nimpl | Implementation of concepts related to genomic databases |
CDatabaseVisitor | Define a database visitor instance |
CEncodingManager | Management of alphabet encoding |
CIAlphabet | Definition of IAlphabet concept |
CIDatabaseQuickReader | Extract information about genomic database |
CISequence | Genomic sequence definition |
CISequenceBuilder | Interface that can modify a ISequence instance internals |
CISequenceCache | Provides a data structure for caching a database content into memory |
CISequenceDatabase | Define a database as a container of ISequence instances |
CISequenceIterator | Iteration of ISequence objects |
CISequenceIteratorFactory | Interface of a Factory that builds ISequenceIterator instances |
CIWord | Definition of a word |
▼Ndp | Design Pattern tools (Observer, SmartPointer, Command...) |
►Nimpl | Implementation of Design Pattern tools (Observer, SmartPointer, Command...) |
CEventInfo | Piece of information linked to a notification |
CICommand | Interface of what a command is |
CICommandDispatcher | Dispatching of commands |
CICommandFactory | Interface for ICommand factories |
CICommandInvoker | Execution of ICommand instances |
CIObserver | Interface of the Observer Design Pattern |
CIProperties | Container of IProperty instances with DP Visitor capability |
CIPropertiesVisitor | Visitor for a IProperty instance |
CIProperty | Definition of a property as a [key,value] entry with a given depth |
CISubject | Interface of the Subject in the Observer Design Pattern |
CIterationStatusEvent | Notification class specific to iteration |
CIterator | Definition of the Design Pattern Iterator interface |
CLocalObject | Local usage of SmartPointer instance |
CNullIterator | Null implementation of the Iterator interface |
CSmartIterator | Iterators that can return the number of items it can iterate |
CSmartPointer | Tool for managing instances life cycle |
▼Nindexation | Genomic database indexation concepts |
►Nimpl | Implementation of genomic database indexation concepts |
►CIDatabaseIndex | Interface of an index for a database |
CIDatabaseIndexFactory | Interface of a factory for creating IDatabaseIndex instances |
CIOccurrenceBlockIterator | Iterates over seed occurrences for a given seed in a given sequence |
CIOccurrenceIterator | Iterates over seed occurrences for a given seed in a given sequence |
CISeedOccurrence | Occurrence of a seed in a genomic sequence |
▼Nlauncher | PLAST command line |
►Ncore | Tools (command line options management) |
►Nobservers | Observers definitions |
▼Nmisc | Miscellanous definitions |
►Nimpl | Tools (command line options management) |
CCompleteSubjectDatabaseStats | Define statistics of the complete subject database |
CProgressInfo | |
CRange | Definition of an interval (inspired by std::pair). It is possible to define 'reversed' range, ie. with a beginning greater than the end |
CStringRepository | |
CVector | Std::vector-like class |
▼Nos | Operating System abstraction layer |
►Nimpl | Implementation of Operating System abstraction layer |
CIFactory | Interface providing factories for managing operating system resources |
CIFile | Abstraction of what we need about file system |
CIFileFactory | Factory that creates IFile instance |
CIMemoryAllocator | Interface providing methods for dynamic allocation |
CIMemoryFile | Abstraction of what we need about memory file system |
CIMemoryFileFactory | Factory that creates IMemoryFile instance |
CIResource | Abstraction of what an operating resource is |
CISynchronizer | Define a synchronization abstraction |
CIThread | Define what a thread is |
CIThreadFactory | Factory that creates IThread instances |
CITime | Interface that provides methods returning time |
CLocalSynchronizer | Tool for locally managing synchronization |
CMemoryFailure | Exception class for memory failure |
▼Nseed | Seed based concepts |
►Nimpl | Implementation of seed based concepts |
CISeed | Definition of a seed |
CISeedIterator | Iteration on seeds |
CISeedModel | Definition of a seed model |
▼Nstatistics | Statistics concepts |
►Nimpl | Implementation of statistics concepts |
CGlobalParametersFailure | Exception class for bad statistical parameters |
CIGlobalParameters | Interface that provides global statistical information |
►CIQueryInformation | Interface that provides statistical information for query sequences |