/*=========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * */ #ifndef _hpp_ngs_read_collection_ #define _hpp_ngs_read_collection_ #ifndef _hpp_ngs_read_group_iterator_ #include #endif #ifndef _hpp_ngs_reference_iterator_ #include #endif #ifndef _hpp_ngs_alignment_iterator_ #include #endif namespace ngs { /*---------------------------------------------------------------------- * forwards and typedefs */ typedef class ReadCollectionItf * ReadCollectionRef; /*====================================================================== * ReadCollection * represents an NGS-capable object with a collection of Reads */ class ReadCollection { public: /* getName * returns the simple name of the read collection * this name is generally extracted from the "spec" * used to create the object, but may also be mapped * to a canonical name if one may be determined and * differs from that given in the spec. * * if the name is extracted from "spec" and contains * well-known file extensions that do not form part of * a canonical name (e.g. ".sra"), they will be removed. */ String getName () const throw ( ErrorMsg ); /*------------------------------------------------------------------ * READ GROUPS */ /* getReadGroups * returns an iterator of all ReadGroups used */ ReadGroupIterator getReadGroups () const throw ( ErrorMsg ); /* hasReadGroup * returns true if a call to "getReadGroup()" should succeed */ bool hasReadGroup ( const String & spec ) const throw (); /* getReadGroup */ ReadGroup getReadGroup ( const String & spec ) const throw ( ErrorMsg ); /*------------------------------------------------------------------ * REFERENCES */ /* getReferences * returns an iterator of all References used * iterator will be empty if no Reads are aligned */ ReferenceIterator getReferences () const throw ( ErrorMsg ); /* hasReference * returns true if a call to "getReference()" should succeed */ bool hasReference ( const String & spec ) const throw (); /* getReference */ Reference getReference ( const String & spec ) const throw ( ErrorMsg ); /*------------------------------------------------------------------ * ALIGNMENTS */ /* getAlignment * returns an individual Alignment * throws ErrorMsg if Alignment does not exist */ Alignment getAlignment ( const String & alignmentId ) const throw ( ErrorMsg ); /* getAlignments * returns an iterator of all Alignments from specified categories */ AlignmentIterator getAlignments ( Alignment :: AlignmentCategory categories ) const throw ( ErrorMsg ); /* getAlignmentCount * returns count of all alignments * "categories" provides a means of filtering by AlignmentCategory */ uint64_t getAlignmentCount () const throw ( ErrorMsg ); uint64_t getAlignmentCount ( Alignment :: AlignmentCategory categories ) const throw ( ErrorMsg ); /* getAlignmentRange * returns an iterator across a range of Alignments * "first" is an ordinal into set * "categories" provides a means of filtering by AlignmentCategory */ AlignmentIterator getAlignmentRange ( uint64_t first, uint64_t count ) const throw ( ErrorMsg ); AlignmentIterator getAlignmentRange ( uint64_t first, uint64_t count, Alignment :: AlignmentCategory categories ) const throw ( ErrorMsg ); /*------------------------------------------------------------------ * READS */ /* getRead * returns an individual Read * throws ErrorMsg if Read does not exist */ Read getRead ( const String & readId ) const throw ( ErrorMsg ); /* getReads * returns an iterator of all contained machine Reads * "categories" provides a means of filtering by ReadCategory */ ReadIterator getReads ( Read :: ReadCategory categories ) const throw ( ErrorMsg ); /* getReadCount * returns the number of reads in the collection * "categories" provides an optional means of filtering by ReadCategory */ uint64_t getReadCount () const throw ( ErrorMsg ); uint64_t getReadCount ( Read :: ReadCategory categories ) const throw ( ErrorMsg ); /* getReadRange * returns an iterator across a range of Reads * "first" is an ordinal into set * "categories" provides an optional means of filtering by ReadCategory */ ReadIterator getReadRange ( uint64_t first, uint64_t count ) const throw ( ErrorMsg ); ReadIterator getReadRange ( uint64_t first, uint64_t count, Read :: ReadCategory categories ) const throw ( ErrorMsg ); public: // C++ support ReadCollection & operator = ( ReadCollectionRef ref ) throw (); ReadCollection ( ReadCollectionRef ref ) throw (); ReadCollection & operator = ( const ReadCollection & obj ) throw (); ReadCollection ( const ReadCollection & obj ) throw (); ~ ReadCollection () throw (); protected: ReadCollectionRef self; }; } // namespace ngs #ifndef _inl_ngs_read_collection_ #include #endif #endif // _hpp_ngs_read_collection_