gnMultiSpec.h Source File

00001 
00002 // File:            gnMultiSpec.h
00003 // Purpose:         abstract multiple spec class
00004 // Description:     For specs which can contain multiple data sources
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 _gnMultiSpec_h_
00014 #define _gnMultiSpec_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 #include "gn/gnBaseSpec.h"
00025 
00030 class GNDLLEXPORT gnMultiSpec : public gnBaseSpec
00031 {
00032 public:
00033         gnMultiSpec(){}
00037         virtual ~gnMultiSpec(){}
00038         virtual gnMultiSpec* Clone() const = 0;
00039 
00040 // Base Spec stuff
00041         virtual gnSeqI GetLength() const;
00042         virtual void CropStart( gnSeqI cropLen );
00043         virtual void CropEnd( gnSeqI cropLen );
00044 
00045         virtual string GetSourceName() const;
00046         virtual void SetSourceName(const string& sourceName);
00047         virtual void Clear();
00048 
00049         virtual boolean SeqRead(const gnSeqI start, gnSeqC* buf, uint32& bufLen, const uint32 contigI ) const;
00050 
00051 //Multispec stuff
00056         virtual uint32 GetSpecListLength() const = 0;
00062         virtual gnBaseSpec* GetSpec( const uint32 i ) const = 0;
00068         virtual gnBaseSpec* GetSpecByBase( const gnSeqI baseI ) const = 0;
00074         virtual uint32 GetSpecIndexByBase( const gnSeqI baseI ) const;
00080         virtual uint32 GetSpecIndexByName( const string& name ) const;
00086         virtual gnSeqI GetSpecStartBase( const uint32 specI ) const;
00092         virtual gnSeqI GetSpecEndBase( const uint32 specI ) const;
00100         virtual void AddSpec( gnBaseSpec* spec, const uint32 i = UINT32_MAX ) = 0;
00105         virtual void RemoveSpec( uint32 i ) = 0;
00106 
00111         virtual uint32 GetHeaderListLength() const;
00118         virtual void AddHeader( gnBaseHeader *head, const uint32 i = UINT32_MAX);
00125         virtual gnBaseHeader* GetHeader( const uint32 i ) const;
00132         virtual gnBaseHeader* GetHeader( const string& name, uint32& i) const;
00138         virtual void RemoveHeader( uint32 i );
00139 
00146         uint32 AddFeature( gnBaseFeature* feat );
00151         virtual uint32 GetFeatureListLength() const = 0;
00157         virtual gnBaseFeature* GetFeature( const uint32 i ) const = 0;
00164         virtual void GetContainedFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector, vector<uint32>& index_vector) const = 0;
00171         virtual void GetIntersectingFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector, vector<uint32>& index_vector) const = 0;
00177         virtual void GetBrokenFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector) const = 0;
00183         virtual void RemoveFeature( const uint32 i ) = 0;
00184         
00185 protected:
00186         string m_sourceName;
00187         
00188         vector <gnBaseHeader*> m_headerList;
00189 private:
00190 
00191 }; // class gnMultiSpec
00192 
00193 inline
00194 uint32 gnMultiSpec::GetHeaderListLength() const
00195 {
00196         return m_headerList.size();
00197 }
00198 inline
00199 gnBaseHeader* gnMultiSpec::GetHeader(const uint32 i) const
00200 {
00201         if(i < m_headerList.size()){
00202                 return m_headerList[i];
00203         }
00204         return 0;
00205 }
00206 
00207 inline
00208 string gnMultiSpec::GetSourceName() const{
00209         return m_sourceName;
00210 }
00211 
00212 inline
00213 void gnMultiSpec::SetSourceName(const string& sourceName){
00214         m_sourceName = sourceName;
00215 }
00216 
00217 #endif
00218         // _gnMultiSpec_h_