gnSourceSpec.h Source File

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# gnSourceSpec.h

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    00001
    00002 // File:            gnSourceSpec.h
    00003 // Purpose:         implements gnBaseSpec for source specs
    00004 // Description:
    00005 // Changes:
    00006 // Version:         libGenome 0.1.0
    00007 // Author:          Aaron Darling
    00008 // Last Edited:     April 15, 2001, 10:34:50pm
    00009 // Modified by:
    00010 // Copyright:       (c) Aaron Darling
    00011 // Licenses:        Proprietary
    00013 #ifndef _gnSourceSpec_h_
    00014 #define _gnSourceSpec_h_
    00015
    00016 #include "gn/gnDefs.h"
    00017
    00018 #include <string>
    00019 #include "gn/gnContigSpec.h"
    00020 #include "gn/gnBaseSource.h"
    00021
    00027 class GNDLLEXPORT gnSourceSpec : public gnContigSpec
    00028 {
    00029 public:
    00033         gnSourceSpec();
    00043         gnSourceSpec( gnBaseSource* m_pSource, const uint32 m_ContigIndex=ALL_CONTIGS, const gnSeqI start=0, const gnSeqI endI=GNSEQI_END, const boolean revComp = false);
    00048         gnSourceSpec( const gnSourceSpec& s );
    00049         ~gnSourceSpec();
    00050
    00051         gnSourceSpec* Clone() const;
    00052 // Source Spec Specific functions
    00053         virtual void Clear();
    00054         virtual gnSeqI GetSourceLength() const;
    00055         virtual gnBaseSource *GetSource() const;
    00056
    00065         virtual gnSourceSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const;
    00066
    00067 protected:
    00068         virtual boolean Read(const gnSeqI start, gnSeqC* buf, uint32& bufLen ) const;
    00069         gnBaseSource* m_pSource;
    00070
    00071 }; // class gnSourceSpec
    00072
    00073 inline
    00074 gnSourceSpec* gnSourceSpec::Clone() const
    00075 {
    00076         return new gnSourceSpec( *this );
    00077 }
    00078 inline
    00079 gnSeqI gnSourceSpec::GetSourceLength() const{
    00080         return m_pSource->GetContigSeqLength(m_SourceContigIndex);
    00081 }
    00082 inline
    00083 gnBaseSource* gnSourceSpec::GetSource() const
    00084 {
    00085         return m_pSource;
    00086 }
    00087
    00088 inline
    00089 boolean gnSourceSpec::Read(const gnSeqI start, gnSeqC* buf, uint32& bufLen) const{
    00090         return m_pSource->SeqRead(start, buf, bufLen, m_SourceContigIndex);
    00091 }
    00092
    00093 #endif
    00094         // _gnSourceSpec_h_