gnContigSpec.h Source File

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# gnContigSpec.h

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    00001
    00002 // File:            gnContigSpec.h
    00003 // Purpose:         Abstract Contig Spec class
    00004 // Description:     Defines an interface for contig specs
    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 _gnContigSpec_h_
    00014 #define _gnContigSpec_h_
    00015
    00016 #include "gn/gnDefs.h"
    00017
    00018 #include <vector>
    00019 #include <string>
    00020
    00021 #include "gn/gnBaseSpec.h"
    00022 #include "gn/gnBaseFeature.h"
    00023 #include "gn/gnDebug.h"
    00028 class GNDLLEXPORT gnContigSpec : public gnBaseSpec
    00029 {
    00030 public:
    00031         gnContigSpec(){}
    00035         virtual ~gnContigSpec(){}
    00036         virtual gnContigSpec* Clone() const = 0;
    00037         virtual gnContigSpec* CloneRange( const uint32 startI, const uint32 len ) const = 0;
    00042         virtual string GetSourceName() const;
    00047         virtual gnSeqI GetStart() const;
    00052         virtual gnSeqI GetLength() const;
    00057         virtual gnSeqI GetSourceLength() const = 0;
    00062         virtual uint32 GetSourceContigIndex() const;
    00068         virtual void SetSourceName( const string& sourceName );
    00076         virtual void SetStart( const gnSeqI start );
    00084         virtual void SetLength( const gnSeqI len );
    00089         virtual void SetSourceContigIndex( const uint32 contigI );
    00096         virtual void SetReverseComplement( const boolean value );
    00097
    00098         virtual void CropStart( gnSeqI cropLen );
    00099         virtual void CropEnd( gnSeqI cropLen );
    00100
    00101         virtual boolean SeqRead(const gnSeqI start, gnSeqC* buf, uint32& bufLen, const uint32 contigI ) const;
    00102         virtual void Clear();
    00103 protected:
    00104         gnSeqI m_start;  //start within the genome.
    00105         gnSeqI m_length;
    00106         uint32 m_SourceContigIndex;
    00107
    00112         virtual boolean Read(const gnSeqI start, gnSeqC* buf, uint32& bufLen ) const = 0;
    00113
    00114 private:
    00115
    00116 }; // class gnContigSpec
    00117
    00118
    00119 inline
    00120 string gnContigSpec::GetSourceName() const{
    00121         return m_sourceName;
    00122 }
    00123 inline
    00124 void gnContigSpec::SetSourceName(const string& sourceName){
    00125         m_sourceName = sourceName;
    00126 }
    00127
    00128 inline
    00129 gnSeqI gnContigSpec::GetStart() const
    00130 {
    00131         return m_start;
    00132 }
    00133 inline
    00134 gnSeqI gnContigSpec::GetLength() const
    00135 {
    00136         return m_length;
    00137 }
    00138 // SET
    00139 inline
    00140 void gnContigSpec::SetStart( const gnSeqI start )
    00141 {
    00142         m_start = start;
    00143 }
    00144 inline
    00145 void gnContigSpec::SetLength( const gnSeqI len )
    00146 {
    00147         m_length = len;
    00148 }
    00149 inline
    00150 uint32 gnContigSpec::GetSourceContigIndex() const{
    00151         return m_SourceContigIndex;
    00152 }
    00153 inline
    00154 void gnContigSpec::SetSourceContigIndex( const uint32 contigI ){
    00155         m_SourceContigIndex = contigI;
    00156 }
    00157
    00158 #endif
    00159         // _gnContigSpec_h_