NCBI C++ Toolkit Cross Reference

  C++/include/gui/widgets/aln_multiple/trace_data.hpp


#ifndef __GUI_WIDGETS_ALNMULTI___TRACE_DATA__HPP #define __GUI_WIDGETS_ALNMULTI___TRACE_DATA__HPP /* $Id: trace_data.hpp 14562 2007-05-18 11:48:21Z dicuccio $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Authors: Andrey Yazhuk * * File Description: * */ #include <corelib/ncbistl.hpp> #include <gui/gui_export.h> #include <objmgr/bioseq_handle.hpp> BEGIN_NCBI_SCOPE class CTraceData; //////////////////////////////////////////////////////////////////////////////// /// CTraceDataProxy - an object controlling availability and creation of /// CTraceData instance. class NCBI_GUIWIDGETS_ALNMULTIPLE_EXPORT CTraceDataProxy { public: typedef map<string, int> TTitleToType; CTraceDataProxy(const objects::CBioseq_Handle& handle, bool b_neg_strand); bool HasData() const; CTraceData* LoadData(); private: enum EStatus { eUnknown, eNoData, eHasData }; const objects::CBioseq_Handle& m_Handle; /// handle to Bioseq with traces bool m_bNegativeStrand; mutable EStatus m_Status; TTitleToType m_TitleToType; }; //////////////////////////////////////////////////////////////////////////////// /// CTraceData class CTraceData { public: typedef float TConfidence; typedef double TFloatSeqPos; typedef float TSignalValue; typedef vector<TFloatSeqPos> TPositions; typedef vector<TSignalValue> TValues; enum EChannel { eA, eC, eT, eG }; public: CTraceData() : m_From(0), m_To(-1) { } void Init(TSignedSeqPos from, TSignedSeqPos to, int samples, bool negative); /// Sequence related information inline TSignedSeqPos GetSeqFrom() const; inline TSignedSeqPos GetSeqTo() const; inline TSignedSeqPos GetSeqLength() const; inline bool IsNegative() const; inline TConfidence GetConfidence(TSignedSeqPos pos) const; inline void SetConfidence(TSignedSeqPos pos, TConfidence conf); // signal related information inline int GetSamplesCount() const; inline TPositions& GetPositions(); inline TValues& GetA(); inline TValues& GetC(); inline TValues& GetT(); inline TValues& GetG(); TValues& GetValues(EChannel signal); inline const TPositions& GetPositions() const; inline const TValues& GetA() const; inline const TValues& GetC() const; inline const TValues& GetT() const; inline const TValues& GetG() const; const TValues& GetValues(EChannel signal) const; void CalculateMax(); TConfidence GetMaxConfidence() const; TSignalValue GetMax(EChannel signal) const; protected: TSignedSeqPos m_From; TSignedSeqPos m_To; bool m_bNegative; vector<TConfidence> m_Confs; TPositions m_Positions; TValues m_ASig; TValues m_CSig; TValues m_TSig; TValues m_GSig; TConfidence m_MaxConfidence; TSignalValue m_MaxA; TSignalValue m_MaxC; TSignalValue m_MaxT; TSignalValue m_MaxG; }; /// Sequence related information TSignedSeqPos CTraceData::GetSeqFrom() const { return m_From; } TSignedSeqPos CTraceData::GetSeqTo() const { return m_To; } TSignedSeqPos CTraceData::GetSeqLength() const { return m_To - m_From + 1; } inline bool CTraceData::IsNegative() const { return m_bNegative; } CTraceData::TConfidence CTraceData::GetConfidence(TSignedSeqPos pos) const { return m_Confs[pos - m_From]; } void CTraceData::SetConfidence(TSignedSeqPos pos, TConfidence conf) { m_Confs[pos - m_From] = conf; } // signal related information int CTraceData::GetSamplesCount() const { return (int) m_Positions.size(); } CTraceData::TPositions& CTraceData::GetPositions() { return m_Positions; } CTraceData::TValues& CTraceData::GetA() { return m_ASig; } CTraceData::TValues& CTraceData::GetC() { return m_CSig; } CTraceData::TValues& CTraceData::GetT() { return m_TSig; } CTraceData::TValues& CTraceData::GetG() { return m_GSig; } const CTraceData::TPositions& CTraceData::GetPositions() const { return m_Positions; } const CTraceData::TValues& CTraceData::GetA() const { return m_ASig; } const CTraceData::TValues& CTraceData::GetC() const { return m_CSig; } const CTraceData::TValues& CTraceData::GetT() const { return m_TSig; } const CTraceData::TValues& CTraceData::GetG() const { return m_GSig; } END_NCBI_SCOPE #endif // __GUI_WIDGETS_ALNMULTI___TRACE_DATA__HPP

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