gnGenomeSpec.h Source File

00001 
00002 // File:            gnGenomeSpec.h
00003 // Purpose:         abstract Spec class
00004 // Description:     Genome level spec class
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 _gnGenomeSpec_h_
00014 #define _gnGenomeSpec_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/gnMultiSpec.h"
00025 #include "gn/gnFragmentSpec.h"
00026 #include "gn/gnException.h"
00027 
00034 class GNDLLEXPORT gnGenomeSpec : public gnMultiSpec
00035 {
00036 public:
00037         gnGenomeSpec();
00042         gnGenomeSpec( const gnGenomeSpec& s);
00046         virtual ~gnGenomeSpec();
00047 // Clone
00048         virtual gnGenomeSpec* Clone() const;
00049         virtual void Clear();
00050 // Base Spec stuff
00051         virtual void SetReverseComplement( const boolean value );
00052 
00053 //Multispec stuff
00054         virtual uint32 GetSpecListLength() const;
00055         virtual gnFragmentSpec* GetSpec( const uint32 i ) const;
00056         virtual gnFragmentSpec* GetSpecByBase( const gnSeqI baseI ) const;
00057         virtual void AddSpec( gnBaseSpec* spec, const uint32 i = UINT32_MAX );
00058         virtual void RemoveSpec( uint32 i );
00059         virtual void MergeFragments( const uint32 startC, const uint32 endC);
00060 
00061         virtual uint32 AddFeature( gnBaseFeature* feat );
00062         virtual uint32 GetFeatureListLength() const;
00063         virtual gnBaseFeature* GetFeature( const uint32 i ) const;
00064         virtual void GetContainedFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector, vector<uint32>& index_vector) const;
00065         virtual void GetIntersectingFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector, vector<uint32>& index_vector) const;
00066         virtual void GetBrokenFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector) const;
00067         virtual void RemoveFeature( const uint32 i );
00076         virtual gnGenomeSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const;
00077 
00078 protected:
00079         vector <gnFragmentSpec*> m_SpecList;
00080         
00081 }; // class gnGenomeSpec
00082 
00083 inline
00084 gnGenomeSpec* gnGenomeSpec::Clone() const{
00085         return new gnGenomeSpec(*this);
00086 }
00087 
00088 inline
00089 uint32 gnGenomeSpec::GetSpecListLength() const{
00090         return m_SpecList.size();
00091 }
00092 
00093 inline
00094 gnFragmentSpec* gnGenomeSpec::GetSpec( const uint32 i ) const{
00095         if(i < m_SpecList.size())
00096                 return m_SpecList[i];
00097         Throw_gnEx(FragmentIndexOutOfBounds());
00098 }
00099 
00100 inline
00101 gnFragmentSpec* gnGenomeSpec::GetSpecByBase( const gnSeqI baseI ) const{
00102         return m_SpecList[GetSpecIndexByBase(baseI)];
00103 }
00104 
00105 inline
00106 void gnGenomeSpec::AddSpec( gnBaseSpec* spec, const uint32 i ){
00107         uint32 index = i == UINT32_MAX ? m_SpecList.size() : i;
00108         if(index <= m_SpecList.size()){
00109                 m_SpecList.insert(m_SpecList.begin() + index, (gnFragmentSpec*)spec);
00110         }
00111 }
00112 
00113 inline
00114 void gnGenomeSpec::RemoveSpec( uint32 i ){
00115         if(i < GetSpecListLength()){
00116                 m_SpecList.erase(m_SpecList.begin() + i);
00117         }
00118 }
00119 
00120 #endif
00121         // _gnGenomeSpec_h_