Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 1234]

▼Nalgo	PLAST algorithm concepts
►Ncore	Concept for configuring and running PLAST
►Nimpl	Implementation of concepts for configuring and running PLAST
CAbstractAlgorithm	Default implementation of IAlgorithm
CAlgorithmPlastn	Implementation of the plastn algorithm (ADN/ADN)
CAlgorithmPlastp	Implementation of the plastp algorithm (protein/protein)
CAlgorithmPlastx	Implementation of the plastx algorithm (protein/ADN)
CAlgorithmTplastn	Implementation of the tplastn algorithm (ADN/protein)
CAlgorithmTplastx	Implementation of the tplastx algorithm (ADN/ADN)
CBasicIndexator	Default implementation of the IIndexator interface
CBasicSortedIndexator	Default implementation of the IIndexator interface with sorted seeds
CDatabasesProvider	Provides means for getting the subject and query databases
CDefaultConfiguration	Default implementation of the IConfiguration interface
CDefaultEnvironment	Default implementation of the IEnvironment interface
CHitIterationCommand
CIndexatorNucleotide	Default implementation of the IIndexator interface
CPlastnConfiguration	Plastn implementation of the IConfiguration interface
CScoreMatrix	Implementation of IScoreMatrix interface
CScoreMatrixManager	Factory that creates IScoreMatrix instances
CAlgoEventWithStatus	Provides iteration status
CAlgorithmConfigurationEvent	Provides algorithm progression information
CAlgorithmReadingFrameEvent	Provides information about Open Reading Frames (ORF)
CAlgorithmReportEvent	Provides information about the algorithm
CAlignmentProgressionEvent	Provides information about the ungap/gap alignments list
CAlignmentsContainerEvent	Provides information about the gap alignments list
CCancelRequestedEvent	Notification that a cancel is requested
CDatabasesInformationEvent	Provides information about the two compared databases
CIAlgorithm	Interface that defines an algorithm
CIConfiguration	Factory that creates many kind of objects
CIDatabasesProvider	Provides means for getting the subject and query databases
CIEnvironment	High level interface for configuring/launching the plast algorithm
CIIndexator	Interface providing the source IHitIterator instance
CIParameters	Define several piece of information used for parameterizing the algorithm
CIScoreMatrix	Definition of a score matrix
CIScoreMatrixManager	Factory for score matrix
CScoreMatrixFailure	Exception for score matrix management
CTimeInfoEvent	Notification that provides time information
►Nhits	Concept for hits iteration
►Ncommon	Abstract implementations for IHitIterator interface
CAbstractHitIterator	Abstract implementation of IHitIterator interface
CAbstractPipeHitIterator	Abstract implementation of IHitIterator interface for linking hits iterators
►Ngapped	Implementation of IHitIterator interface for small gap alignments
CCompositionHitIterator	Implementation of IHitIterator for full gap alignments
CCompositionHitIteratorNull	Null implementation of IHitIterator for full gap alignments
CFullGapHitIterator	Implementation of IHitIterator for full gap alignments
CFullGapHitIteratorNull	Null implementation of IHitIterator for full gap alignments
CSmallGapHitIterator	Implementation of IHitIterator for small gap alignments
CSmallGapHitIteratorNull	Null implementation of IHitIterator for small gap alignments
CSmallGapHitIteratorSSE8	Implementation of IHitIterator for small gap alignments with SIMD usage
►Nseed	Implementations for IHitIterator interface from databases indexations
CSeedHitIterator	Hits iterator from two database indexes
CSeedHitIteratorCached	Hits iterator from two database indexes with a memory cache
CSeedHitIteratorCachedWithSortedSeeds	Hits iterator from two database indexes with optimized seeds order
►Nungapped	Implementation of IHitIterator interface for ungap alignments
CUngapExtendHitIterator	IHitIterator for ungap alignments
CUngapHitIterator	IHitIterator for ungap alignments
CUngapHitIteratorNull	Null implementation of IHitIterator for ungap alignments
CUngapHitIteratorSSE16	IHitIterator for ungap alignments with SIMD usage
CUngapHitIteratorSSE8	IHitIterator for ungap alignments with SIMD usage
CHit	Define a match in two databases for a given seed
CIHitIterator	Iteration over all seed matches in both subject and query databases
▼Nalignment
►Ncore
►Nimpl
CAbstractAlignmentContainer	Abstract implementation of IAlignmentResult interface
CAlignmentContainerFactory	Implementation of the IAlignmentContainerFactory interface
CBasicAlignmentContainer	Default implementation of IAlignmentContainer interface for gap alignments
CBasicAlignmentContainerBis	Default implementation of IAlignmentContainer interface for gap alignments
CNullAlignmentResult	Null implementation of IAlignmentResult interface
CReaderAlignmentContainer	Default implementation of IAlignmentResult interface for gap alignments
CSortAlignmentsFunctor
CSortHitsFunctor
CUngapAlignmentResult	Implementation of IAlignmentResult for ungap alignments
►CAlignment	Definition of an alignment between two databases
CAlignExtraInfo
CAlignSequenceInfo
CIAlignmentContainer	Interface for managing Alignment instances
CIAlignmentContainerFactory	Factory that builds IAlignmentContainer instances
CIAlignmentContainerVisitor	Visitor Design Pattern that can visit IAlignmentContainer instances
►CIHspContainer	Interface of what an HSP container can be
CHSP
CIQueryLevel	Define an iterator that iterates subject information
CIRootLevel	Define an iterator that iterates query information
CISubjectLevel	Define an iterator that iterates alignments information
►Nfilter
►Nimpl
CAbstractAlignmentFilter
CAbstractAlignmentFilterFactory	Definition of an alignment filtering manager
CAlignmentFilterAnd	Definition of an alignment filtering
CAlignmentFilterBinaryOperator	Definition of an alignment filtering
CAlignmentFilterFactory	Definition of an alignment filtering manager
CAlignmentFilterFactoryXML	Definition of an alignment filtering manager
CAlignmentFilterOr	Definition of an alignment filtering
CAlignmentFilterUnaryOperator
CIAlignmentFilter	Definition of an alignment filtering
CIAlignmentFilterFactory	Definition of an alignment filtering manager
►Ntools
►Nimpl
CAbstractAlignmentOverlapCmd	Definition of an alignment filtering
CAlignmentContainerShrinkCmd	Definition of an alignment filtering
CAlignmentOverlapCmd	Definition of an alignment filtering
CAlignmentSplitter	Implementation of IAlignmentResult for splitting a gap alignment into ungap alignments
CAlignmentSplitterBanded	Implementation of IAlignmentResult for splitting a gap alignment into ungap alignments
CSemiGapAlign	To be completed
CSemiGapAlignTraceback	To be completed
►CIAlignmentSplitter	Interface providing means for splitting a gap alignment into ungap alignments
CSplitOutput
CISemiGapAlign	To be completed
►Nvisitors
►Nimpl
CAdapterAlignmentResultVisitor	Stub all methods
CAlignmentsProxyVisitor	Visitor proxy
CCompareContainerVisitor	Visitor that fills a list holding all Alignment instances
CCompareResultQryVisitor	Visitor that fills a list holding all Alignment instances
CCompareResultVisitor	Visitor that fills a list holding all Alignment instances
CFileVisitor	Abstract implementation of IAlignmentContainerVisitor with output stream management
CFilterContainerVisitor	Visitor that fills a list holding all Alignment instances
CHierarchyAlignmentResultVisitor	TO DO
CMaxHitsPerQueryVisitor	Visitor that limits the number of visited alignments
CModifierContainerVisitor	Visitor that fills a list holding all Alignment instances
CNucleotidConversionVisitor	Visitor that fills a list holding all Alignment instances
COstreamVisitor	Abstract implementation of IAlignmentContainerVisitor with output stream management
CRawOutputVisitor	Alignments file dump in raw format
CReverseStrandVisitor	Visitor that fills a list holding all Alignment instances
CShrinkContainerVisitor	Visitor that fills a list holding all Alignment instances
CSortContainerVisitor	Visitor that sort alignments
CTabulatedOutputExtendedVisitor	Alignments file dump in tabulated format Extends the AlignmentResultOutputTabulatedVisitor implementation by adding two columns:
CTabulatedOutputVisitor	Alignments file dump in tabulated format
CXmlOutputVisitor	Alignments file dump in XML format
▼Ndatabase	Definition of concepts related to genomic databases
►Nimpl	Implementation of concepts related to genomic databases
CAbstractSequenceIterator	Implementation of a part of ISequenceIterator interface
CAminoAcidDatabaseQuickReader	Implementation of IDatabaseQuickReader for amino acid database
CBasicSequenceBuilder	Basic implementation of the ISequenceBuilder interface
CBlastdbAsn1HeaderDecoder	Implementation of an interface to decode the comment of the the blast header
CBlastdbDatabaseQuickReader	Implementation of IDatabaseQuickReader interface for Blast db format
CBlastdbFileIndexReader	Implementation of an interface to read the file index for Blast db format
CBlastdbSequenceIterator	Sequence iterator that parses BLAST Database files
CBlastdbSequenceIteratorFactory	Implementation of ISequenceIteratorFactory interface
CBufferedCachedSequenceDatabase	ISequenceDatabase implementation with all data kept in memory
CBufferedSegmentSequenceBuilder	Sequence building with sequence filtering out
CBufferedSequenceBuilder	SequenceBuilder that builds memory cache
►CBufferedSequenceDatabase	ISequenceDatabase implementation with memory cache
CBufferedSequenceIterator	Sequence iterator that uses information of cache
CCompositeSequenceDatabase	Composite database made of children ISequenceDatabase instances
CCompositeSequenceIterator	Sequence iterator for a list of ISequenceIterator instances
CDatabaseLookupType	Implementation of function to find the database type
CFastaDatabaseQuickReader	Implementation of IDatabaseQuickReader interface for FASTA format
CFastaSequenceIterator	Sequence iterator that parses FASTA files
CFastaSequenceIteratorFactory	Implementation of ISequenceIteratorFactory interface
CFastaSequenceOutput	Dump sequences into a FASTA file
CReadingFrameSequenceCommand	Define a command for building ReadingFrameSequenceDatabase instances
CReadingFrameSequenceDatabase	Interpret a nucleotide database as an amino acid database
CReadingFrameSequenceIterator	ISequenceIterator on amino acid sequences from an iterator on nucleotides
CReverseStrandSequenceIterator	ISequenceIterator on reverse strand of nucleotides sequences
CReverseStrandSequenceIteratorFactory	Implementation that returns instances of ReverseStrandSequenceIterator
CSequenceTokenizer	Tokenizer that splits a sequence in valid sub sequences (with valid letters)
CStringSequenceIterator	Sequence iterator parsing a simple string
CTruncatedSequenceIterator	Sequence iterator that controls the number of iterated items
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...)
CCartesianIterator	Iterator over several iterators of same type
CConfigFileProperties
CDefaultCommandInvoker	Default command invoker that uses an OS thread factory for creating threads
CDirectoryIterator	Iterator that loops over the files of a directory
CEventCatch	Tool for catching specific notification information
CFileLineIterator	Iterator that loops over the lines of a file
CIteratorCommand	ICommand that iterates items from an IteratorGet instance
CIteratorGet	Iterate items through a single method
CListIterator	Iterator that loops over std::list
CParallelCommandDispatcher	Launches commands in different threads
CProductIterator	Iterator over two iterators
CProperties	Implementation of IProperties interface
CRangeIterator	Iterator that splits a range in several range of given size
CRawDumpPropertiesVisitor	Raw dump of a IProperties instance
CSerialCommandDispatcher	Launches commands in current thread
CSubject	Class that notifies potential observers
CSystemCommand	ICommand implementation for launching system commands (ie through 'system' calls)
CTokenizerIterator	String tokenizer as an Iterator
CVectorIterator	Iterator that loops over std::vector
CWrapperIterator	String wrapper as an Iterator
CXmlDumpPropertiesVisitor	XML serialization of a IProperties instance
CXmlEvent
CXmlReader	Simple implementation of an XML (SAX) parser
CXmlTagAttributeEvent
CXmlTagCloseEvent
CXmlTagOpenEvent
CXmlTagTextEvent
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
CAbstractDatabaseIndex	Partial implementation of IDatabaseIndex interface
►CDatabaseIndex	Simple implementation of the IDatabaseIndex interface
CDatabaseOccurrenceBlockIterator	IOccurrenceIterator implementation used by DatabaseIndex::createOccurrenceBlockIterator class
CDatabaseOccurrenceIterator	IOccurrenceIterator implementation used by DatabaseIndex::createOccurrenceIterator class
CDatabaseIndexCodonStopOptim	Simple implementation of the IDatabaseIndex interface
CDatabaseIndexCodonStopOptimFactory	Factory that creates DatabaseIndexCodonStopOptim instances
CDatabaseIndexFactory	Factory that creates DatabaseIndexCodonStopOptim instances
CDatabaseIndexHash	Implementation of IDatabaseIndex by means of perfect hash tables. DON'T USE IT, NEEDS IMPROVEMENTS
►CDatabaseNucleotidIndex	Nucleotide implementation of the IDatabaseIndex interface
CCountSeedsCmd
CFillSeedsCmd
CDatabaseNucleotidIndexFactory	Factory that creates DatabaseIndexCodonStopOptim instances
CDatabaseNucleotidIndexOptim	Nucleotide implementation of the IDatabaseIndex interface
CDatabaseNucleotidIndexOptimFactory	Factory that creates DatabaseIndexCodonStopOptim instances
►CIDatabaseIndex	Interface of an index for a database
CIndexEntry
CSeedOccurrence
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)
CPlastCmd	High level ICommand implementation for launching PLAST algorithm
CPlastOptionsParser	Specific parser for PLAST command line options
►Nobservers	Observers definitions
CAbstractObserver	Define common class for target observer implementations
CAbstractProgressionObserver	Abstract class for observer interested by PLAST algorithm progression
CAlgoHitsPropertiesObserver	Observer that dumps statistics about hits iterators
CAlgoPropertiesObserver	Observer that dumps algorithm properties
CAlgoVerboseObserver	Observer that displays some verbose messages during algorithm execution
CAlignmentProgressionObserver	Dump into a file information about HSP number, alignments number and execution time
CBargraphObserver	Observer that displays a progression bargraph
CFileProgressionObserver	Dump the progression percentage into a file
CResourcesObserver	Dump into a file information about algorithm observables and resources observables
▼Nmisc	Miscellanous definitions
►Nimpl	Tools (command line options management)
CObsfucatedString	Class that can encode/decode strings
COption	Interface for command line option
COptionFailure	Exception class to be used for option management error
COptionNoParam	Option that has no argument
COptionOneParam	Option that has one argument
COptionsParser	Parser that analyzes command line options
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
CCommonFile	Abstract implementation of IFile interface
CCommonMemory	Abstract implementation of IMemory interface
CDefaultFactory	Default implementation of OS abstraction layer
CLinuxFileFactory	Factory that creates IFile instance for Linux OS
CLinuxMemoryAllocator	Linux abstraction of memory management
CLinuxMemoryFileFactory	Factory that creates IMemoryFile instance for Linux OS
CLinuxThreadFactory	Factory that creates IThread instances
CLinuxTime	Linux implementation that provides methods returning time
CMacOsFileFactory	Factory that creates IFile instance for Mac OS
CMacOsMemoryFactory	MacOs abstraction of memory management
CMacOsMemoryFileFactory	Factory that creates IMemoryFile instance for MAC OS
CMacOsThreadFactory	Factory that creates IThread instances
CMacOsTime	MacOs implementation that provides methods returning time
CSerialThreadFactory	Factory that creates IThread instances in current context (ie. "null" thread)
CTimeInfo	Tool for time statistics
CWindowsFileFactory	Factory that creates IFile instance for Windows OS
CWindowsMemoryFactory	Linux abstraction of memory management
CWindowsMemoryFileFactory	Factory that creates IMemoryFile instance for Windows OS
CWindowsThreadFactory	Factory that creates IThread instances
CWindowsTime	Windows implementation that provides methods returning time
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
CAbstractSeedIterator	Define seed iterator with a seed model
CAbstractSeedModel	Abstract class factorizing common parts between the ISeedModel implementors
CBasicSeedModel	Basic implementation of ISeedModel interface
CNullSeedIterator	Null implementation of the ISeedIterator interface
►CSubSeedModel	Seed model that uses subseed set concept
CAllSeedsIterator	All seeds iteration for the sub seed model
CDataSeedIterator	Data seed iteration for the sub seed model
CDataSeedIteratorWithTokenizer	Data seed iteration for the sub seed model
CISeed	Definition of a seed
CISeedIterator	Iteration on seeds
CISeedModel	Definition of a seed model
▼Nstatistics	Statistics concepts
►Nimpl	Implementation of statistics concepts
►CAbstractGlobalParameters
CInfo
CGlobalParameters	Implementation of IGlobalParameters interface
CGlobalParametersPlastn	Implementation of IGlobalParameters interface
►CGlobalParametersSpouge	Implementation of IGlobalParametersSpouge interface
CInfo
CQueryInformation	Implementation of IQueryInformation interface
CGlobalParametersFailure	Exception class for bad statistical parameters
CIGlobalParameters	Interface that provides global statistical information
►CIQueryInformation	Interface that provides statistical information for query sequences
CSequenceInfo	Statistics for a sequence