PlastLibrary
database::impl Namespace Reference

Implementation of concepts related to genomic databases. More...

Classes

class  AbstractSequenceIterator
 Implementation of a part of ISequenceIterator interface. More...
 
class  AminoAcidDatabaseQuickReader
 Implementation of IDatabaseQuickReader for amino acid database. More...
 
class  BasicSequenceBuilder
 Basic implementation of the ISequenceBuilder interface. More...
 
class  BlastdbAsn1HeaderDecoder
 Implementation of an interface to decode the comment of the the blast header. More...
 
class  BlastdbDatabaseQuickReader
 Implementation of IDatabaseQuickReader interface for Blast db format. More...
 
class  BlastdbFileIndexReader
 Implementation of an interface to read the file index for Blast db format. More...
 
class  BlastdbSequenceIterator
 Sequence iterator that parses BLAST Database files. More...
 
class  BlastdbSequenceIteratorFactory
 Implementation of ISequenceIteratorFactory interface. More...
 
class  BufferedCachedSequenceDatabase
 ISequenceDatabase implementation with all data kept in memory. More...
 
class  BufferedSegmentSequenceBuilder
 Sequence building with sequence filtering out. More...
 
class  BufferedSequenceBuilder
 SequenceBuilder that builds memory cache. More...
 
class  BufferedSequenceDatabase
 ISequenceDatabase implementation with memory cache. More...
 
class  CompositeSequenceDatabase
 Composite database made of children ISequenceDatabase instances. More...
 
class  CompositeSequenceIterator
 Sequence iterator for a list of ISequenceIterator instances. More...
 
class  DatabaseLookupType
 Implementation of function to find the database type. More...
 
class  FastaDatabaseQuickReader
 Implementation of IDatabaseQuickReader interface for FASTA format. More...
 
class  FastaSequenceIterator
 Sequence iterator that parses FASTA files. More...
 
class  FastaSequenceIteratorFactory
 Implementation of ISequenceIteratorFactory interface. More...
 
class  FastaSequenceOutput
 Dump sequences into a FASTA file. More...
 
class  ReadingFrameSequenceCommand
 Define a command for building ReadingFrameSequenceDatabase instances. More...
 
class  ReadingFrameSequenceDatabase
 Interpret a nucleotide database as an amino acid database. More...
 
class  ReadingFrameSequenceIterator
 ISequenceIterator on amino acid sequences from an iterator on nucleotides. More...
 
class  ReverseStrandSequenceIterator
 ISequenceIterator on reverse strand of nucleotides sequences. More...
 
class  ReverseStrandSequenceIteratorFactory
 Implementation that returns instances of ReverseStrandSequenceIterator. More...
 
class  SequenceTokenizer
 Tokenizer that splits a sequence in valid sub sequences (with valid letters) More...
 
class  StringSequenceIterator
 Sequence iterator parsing a simple string. More...
 
class  TruncatedSequenceIterator
 Sequence iterator that controls the number of iterated items. More...
 

Detailed Description

Implementation of concepts related to genomic databases.