gnBaseSpec.h Source File

00001 
00002 // File:            gnBaseSpec.h
00003 // Purpose:         abstract Spec class
00004 // Description:     Defines a basic interface for all 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 _gnBaseSpec_h_
00014 #define _gnBaseSpec_h_
00015 
00016 #include "gn/gnDefs.h"
00017 
00018 #include <vector>
00019 #include <string>
00020 
00021 #include "gn/gnClone.h"
00022 #include "gn/gnBaseFeature.h"
00023 #include "gn/gnBaseHeader.h"
00024 
00028 class GNDLLEXPORT gnBaseSpec : public gnClone
00029 {
00030 public:
00031         gnBaseSpec(){}
00035         virtual ~gnBaseSpec(){}
00036         virtual gnBaseSpec* Clone() const = 0;
00037         virtual gnBaseSpec* CloneRange( const uint32 startI, const uint32 len ) const = 0;
00042         virtual string GetName() const;
00048         virtual void SetName( const string& name );
00053         virtual gnSeqI GetLength() const = 0;
00058         virtual boolean IsReverseComplement() const;
00063         virtual boolean IsCircular() const;
00068         virtual void SetReverseComplement( const boolean value ) = 0;
00075         virtual void SetCircular( const boolean value );
00081         virtual void CropStart( gnSeqI cropLen ) = 0;
00087         virtual void CropEnd( gnSeqI cropLen ) = 0;
00088 
00102         virtual boolean SeqRead(const gnSeqI start, gnSeqC* buf, uint32& bufLen, const uint32 contigI ) const = 0;
00106         virtual void Clear();
00107 protected:
00108         boolean m_reverseComplement;
00109         boolean m_circular;
00110         
00111         string m_name;
00112         string m_sourceName;
00113         
00114 }; // class gnBaseSpec
00115 
00116 inline
00117 string gnBaseSpec::GetName() const{
00118         return m_name;
00119 }
00120 inline
00121 void gnBaseSpec::SetName( const string& name ){
00122         m_name = name;
00123 }
00124 inline
00125 boolean gnBaseSpec::IsReverseComplement() const{
00126         return m_reverseComplement;
00127 }
00128 inline
00129 boolean gnBaseSpec::IsCircular() const{
00130         return m_circular;
00131 }
00132 inline
00133 void gnBaseSpec::SetCircular( const boolean value ){
00134         m_circular = value;
00135 }
00136 inline
00137 void gnBaseSpec::Clear(){
00138         m_sourceName = "";
00139         m_name = "";
00140         m_reverseComplement = false;
00141         m_circular = false;
00142 }
00143 
00144 #endif
00145         // _gnBaseSpec_h_