gnFragmentSpec.h Source File

00001 
00002 // File:            gnFragmentSpec.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 _gnFragmentSpec_h_
00014 #define _gnFragmentSpec_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/gnContigSpec.h"
00025 #include "gn/gnMultiSpec.h"
00026 #include "gn/gnException.h"
00027 
00035 class GNDLLEXPORT gnFragmentSpec : public gnMultiSpec
00036 {
00037 public:
00038         gnFragmentSpec();
00042         virtual ~gnFragmentSpec();
00047         gnFragmentSpec( const gnFragmentSpec& s);
00048         virtual gnFragmentSpec* 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 gnContigSpec* GetSpec( const uint32 i ) const;
00056         virtual gnContigSpec* GetSpecByBase( const gnSeqI baseI ) const;
00057         virtual void AddSpec( gnBaseSpec* spec, const uint32 i = UINT32_MAX );
00058         virtual void RemoveSpec( uint32 i );
00059 
00060         virtual void CropStart( gnSeqI cropLen );
00061         virtual void CropEnd( gnSeqI cropLen );
00062         virtual uint32 AddFeature( gnBaseFeature* feat );
00063         virtual uint32 GetFeatureListLength() const;
00064         virtual gnBaseFeature* GetFeature( const uint32 i ) const;
00065         virtual void GetContainedFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector, vector<uint32>& index_vector) const;
00066         virtual void GetIntersectingFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector, vector<uint32>& index_vector) const;
00067         virtual void GetBrokenFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector) const;
00068         virtual void RemoveFeature( const uint32 i );
00069 
00078         virtual gnFragmentSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const;
00079         
00080 protected:
00081         vector <gnContigSpec*> m_SpecList;
00082         //Feature stuff...
00083         vector <gnBaseFeature*> m_featureList;
00084         
00085 }; // class gnFragmentSpec
00086 
00087 inline
00088 gnFragmentSpec* gnFragmentSpec::Clone() const{
00089         return new gnFragmentSpec(*this);
00090 }
00091 
00092 inline
00093 uint32 gnFragmentSpec::GetSpecListLength() const{
00094         return m_SpecList.size();
00095 }
00096 
00097 inline
00098 gnContigSpec *gnFragmentSpec::GetSpec( const uint32 i ) const{
00099         if(i < m_SpecList.size())
00100                 return m_SpecList[i];
00101         Throw_gnEx(ContigIndexOutOfBounds());
00102 }
00103 
00104 inline
00105 gnContigSpec* gnFragmentSpec::GetSpecByBase( const gnSeqI baseI ) const{
00106         return m_SpecList[GetSpecIndexByBase(baseI)];
00107 }
00108 
00109 inline
00110 void gnFragmentSpec::AddSpec( gnBaseSpec* spec, const uint32 i ){
00111         uint32 index = i == UINT32_MAX ? m_SpecList.size() : i;
00112         if(index <= m_SpecList.size()){
00113                 m_SpecList.insert(m_SpecList.begin() + index, (gnContigSpec*)spec);
00114         }
00115 }
00116 
00117 inline
00118 void gnFragmentSpec::RemoveSpec( uint32 i ){
00119         if(i < GetSpecListLength()){
00120                 m_SpecList.erase(m_SpecList.begin() + i);
00121         }else
00122                 Throw_gnEx(ContigIndexOutOfBounds());
00123 }
00124 
00125 inline
00126 uint32 gnFragmentSpec::AddFeature( gnBaseFeature* feat ) 
00127 {
00128         m_featureList.push_back(feat);
00129         feat->SetSpec(this);
00130         return m_featureList.size()-1;
00131 }
00132 inline
00133 uint32 gnFragmentSpec::GetFeatureListLength() const
00134 {
00135         return m_featureList.size();
00136 }
00137 inline
00138 gnBaseFeature* gnFragmentSpec::GetFeature(const uint32 i) const
00139 {
00140         return m_featureList[i]->Clone();
00141 }
00142 inline
00143 void gnFragmentSpec::RemoveFeature( const uint32 i) 
00144 {
00145         if(i >= m_featureList.size())
00146                 Throw_gnEx(FeatureIndexOutOfBounds());
00147         delete m_featureList[i];
00148         m_featureList.erase(m_featureList.begin() + i);
00149 }
00150 
00151 #endif
00152         // _gnFragmentSpec_h_