gnABISource.h Source File

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# gnABISource.h

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    00001 /////////////////////////////////////////////////////////////////////////////
    00002 // File:            gnABISource.h
    00003 // Purpose:         Implements gnBaseSource for ABI files
    00004 // Description:
    00005 // Changes:
    00006 // Version:         libGenome 0.5.1
    00007 // Author:          Aaron Darling
    00008 // Modified by:
    00009 // Copyright:       (c) Aaron Darling
    00010 // Licenses:        See COPYING file for details
    00011 /////////////////////////////////////////////////////////////////////////////
    00012 #ifndef _gnABISource_h_
    00013 #define _gnABISource_h_
    00014
    00015 #include "gn/gnDefs.h"
    00016
    00017 #include <string>
    00018 #include "gn/gnFileSource.h"
    00019 #include "gn/gnFileContig.h"
    00020 #include "gn/gnSourceSpec.h"
    00021 #include "gn/gnFilter.h"
    00022
    00023 /**
    00024  * gnABISource is not implemented.
    00025  */
    00026 class GNDLLEXPORT gnABISource : public gnFileSource
    00027 {
    00028 public:
    00029         gnABISource();
    00030         /**
    00031          * Clone Constructor copies the specified gnSEQSource.
    00032          * @param s The gnABISource to copy.
    00033          */
    00034         gnABISource( const gnABISource& s );
    00035         ~gnABISource();
    00036         gnABISource* Clone() const;
    00037
    00038         uint32 GetContigListLength() const;
    00039         boolean HasContig( const string& name ) const;
    00040         uint32 GetContigID( const string& name ) const;
    00041         string GetContigName( uint32 i ) const;
    00042         gnSeqI GetContigSeqLength( uint32 i ) const;
    00043         gnFileContig* GetContig( const uint32 i ) const;
    00044
    00045         boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS );
    00046
    00047         /**
    00048          * Writes the specified gnSequence to an ABI file named "filename".
    00049          * @param sequence The gnSequence to write out.
    00050          * @param filename The name of the file to write.
    00051          * @return True if successful, false otherwise.
    00052          */
    00053         static boolean Write(gnSequence& sequence, const string& filename);
    00054         gnGenomeSpec *GetSpec() const;
    00055
    00056         gnFileContig* GetFileContig( const uint32 contigI ) const;
    00057 private:
    00058         boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes );
    00059         boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes );
    00060         boolean ParseStream( istream& fin );
    00061
    00062         gnGenomeSpec *m_spec;
    00063         vector< gnFileContig* > m_contigList;
    00064
    00065 };// class gnABISource
    00066
    00067 inline
    00068 gnABISource* gnABISource::Clone() const
    00069 {
    00070         return new gnABISource( *this );
    00071 }
    00072 inline
    00073 uint32 gnABISource::GetContigListLength() const
    00074 {
    00075         return m_contigList.size();
    00076 }
    00077 inline
    00078 gnGenomeSpec *gnABISource::GetSpec() const
    00079 {
    00080         return m_spec->Clone();
    00081 }
    00082
    00083 #endif
    00084         // _gnABISource_h_