gnContigSpec.h Source File

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_