gnFragmentSpec.h Source File

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# gnFragmentSpec.h

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    00001 /////////////////////////////////////////////////////////////////////////////
    00002 // File:            gnFragmentSpec.h
    00003 // Purpose:         abstract Spec class
    00004 // Description:     Genome level spec class
    00005 // Changes:
    00006 // Version:         libGenome 0.5.1
    00007 // Author:          Aaron Darling
    00008 // Modified by:
    00009 // Copyright:       (c) Aaron Darling
    00010 // Licenses:        See COPYING file for details
    00011 /////////////////////////////////////////////////////////////////////////////
    00012 #ifndef _gnFragmentSpec_h_
    00013 #define _gnFragmentSpec_h_
    00014
    00015 #include "gn/gnDefs.h"
    00016
    00017 #include <vector>
    00018 #include <string>
    00019
    00020 #include "gn/gnClone.h"
    00021 #include "gn/gnBaseFeature.h"
    00022 #include "gn/gnBaseHeader.h"
    00023 #include "gn/gnContigSpec.h"
    00024 #include "gn/gnMultiSpec.h"
    00025 #include "gn/gnException.h"
    00026
    00027 /**
    00028  * gnFragmentSpec contains a list of specs which make up a sequence
    00029  * fragment.  It also contains a list of features which relate to
    00030  * the sequence fragment.  Finally it contains a list of sequence
    00031  * related header data.  This class is usually created and filled by
    00032  * a file reader class like gnGBKSource.
    00033  */
    00034 class GNDLLEXPORT gnFragmentSpec : public gnMultiSpec
    00035 {
    00036 public:
    00037         gnFragmentSpec();
    00038         /**
    00039          * Destructor, frees memory.
    00040          */
    00041         virtual ~gnFragmentSpec();
    00042         /**
    00043          * Copy constructor.
    00044          * @param s the gnGenomeSpec to copy.
    00045          */
    00046         gnFragmentSpec( const gnFragmentSpec& s);
    00047         virtual gnFragmentSpec* Clone() const;
    00048         virtual void Clear();
    00049 // Base Spec stuff
    00050         virtual void SetReverseComplement( const boolean value );
    00051
    00052 //Multispec stuff
    00053         virtual uint32 GetSpecListLength() const;
    00054         virtual gnContigSpec* GetSpec( const uint32 i ) const;
    00055         virtual gnContigSpec* GetSpecByBase( const gnSeqI baseI ) const;
    00056         virtual void AddSpec( gnBaseSpec* spec, const uint32 i = UINT32_MAX );
    00057         virtual void RemoveSpec( uint32 i );
    00058
    00059         virtual void CropStart( gnSeqI cropLen );
    00060         virtual void CropEnd( gnSeqI cropLen );
    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 );
    00068
    00069         /**
    00070          * Copies a specified range of bases and returns a pointer to
    00071          * the resulting gnFragmentSpec.  You must delete the copy when you
    00072          * are finished with it.
    00073          * @param startI The first base pair to copy
    00074          * @param len The length of the piece to copy
    00075          * @return A copy of the gnFragmentSpec containing only the specified bases
    00076          */
    00077         virtual gnFragmentSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const;
    00078
    00079 protected:
    00080         vector <gnContigSpec*> m_SpecList;
    00081         //Feature stuff...
    00082         vector <gnBaseFeature*> m_featureList;
    00083
    00084 }; // class gnFragmentSpec
    00085
    00086 inline
    00087 gnFragmentSpec* gnFragmentSpec::Clone() const{
    00088         return new gnFragmentSpec(*this);
    00089 }
    00090
    00091 inline
    00092 uint32 gnFragmentSpec::GetSpecListLength() const{
    00093         return m_SpecList.size();
    00094 }
    00095
    00096 inline
    00097 gnContigSpec *gnFragmentSpec::GetSpec( const uint32 i ) const{
    00098         if(i < m_SpecList.size())
    00099                 return m_SpecList[i];
    00100         Throw_gnEx(ContigIndexOutOfBounds());
    00101 }
    00102
    00103 inline
    00104 gnContigSpec* gnFragmentSpec::GetSpecByBase( const gnSeqI baseI ) const{
    00105         return m_SpecList[GetSpecIndexByBase(baseI)];
    00106 }
    00107
    00108 inline
    00109 void gnFragmentSpec::AddSpec( gnBaseSpec* spec, const uint32 i ){
    00110         uint32 index = i == UINT32_MAX ? m_SpecList.size() : i;
    00111         if(index <= m_SpecList.size()){
    00112                 m_SpecList.insert(m_SpecList.begin() + index, (gnContigSpec*)spec);
    00113         }
    00114 }
    00115
    00116 inline
    00117 void gnFragmentSpec::RemoveSpec( uint32 i ){
    00118         if(i < GetSpecListLength()){
    00119                 m_SpecList.erase(m_SpecList.begin() + i);
    00120         }else
    00121                 Throw_gnEx(ContigIndexOutOfBounds());
    00122 }
    00123
    00124 inline
    00125 uint32 gnFragmentSpec::AddFeature( gnBaseFeature* feat )
    00126 {
    00127         m_featureList.push_back(feat);
    00128         feat->SetSpec(this);
    00129         return m_featureList.size()-1;
    00130 }
    00131 inline
    00132 uint32 gnFragmentSpec::GetFeatureListLength() const
    00133 {
    00134         return m_featureList.size();
    00135 }
    00136 inline
    00137 gnBaseFeature* gnFragmentSpec::GetFeature(const uint32 i) const
    00138 {
    00139         return m_featureList[i]->Clone();
    00140 }
    00141 inline
    00142 void gnFragmentSpec::RemoveFeature( const uint32 i)
    00143 {
    00144         if(i >= m_featureList.size())
    00145                 Throw_gnEx(FeatureIndexOutOfBounds());
    00146         delete m_featureList[i];
    00147         m_featureList.erase(m_featureList.begin() + i);
    00148 }
    00149
    00150 #endif
    00151         // _gnFragmentSpec_h_