/*
   Copyright 2015 University of Washington

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

   http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.
*/

// CometWrapper.h

#pragma once

#include "CometData.h"
#include <msclr/marshal.h>
#include <msclr/marshal_cppstd.h>

using namespace System;
using namespace msclr::interop;
using namespace System::Runtime::InteropServices;

namespace CometWrapper {

    public enum class InputType
    {
        Unknown = -1,
        MS2 = 0,
        MZXML,
        MZML,
        CMS2
    };

    public enum class AnalysisType
    {
        Unknown = 0,
        DTA,
        SpecificScan,
        SpecificScanRange,
        EntireFile
    };

    public ref class IntRangeWrapper
    {
    public:
        IntRangeWrapper() { _pIntRange = new IntRange(); }
        IntRangeWrapper(IntRange &intRangeParam) { _pIntRange = new IntRange(intRangeParam); }
        IntRangeWrapper(int iStart, int iEnd) { _pIntRange = new IntRange(iStart, iEnd); }
        virtual ~IntRangeWrapper() 
        { 
            if (NULL != _pIntRange)
            {
                delete _pIntRange;
                _pIntRange = NULL;
            }
        }
        
        int get_iStart() {return _pIntRange->iStart;}
        void set_iStart(int iStart) {_pIntRange->iStart = iStart;}

        int get_iEnd() {return _pIntRange->iEnd;}
        void set_iEnd(int iEnd) {_pIntRange->iEnd = iEnd;}

        IntRange* get_IntRangePtr() {return _pIntRange;}

    private:
        IntRange* _pIntRange;
    };

    public ref class DoubleRangeWrapper
    {
    public:
        DoubleRangeWrapper() { _pDoubleRange = new DoubleRange(); }
        DoubleRangeWrapper(DoubleRange &doubleRangeParam) { _pDoubleRange = new DoubleRange(doubleRangeParam); }
        DoubleRangeWrapper(double dStart, double dEnd) { _pDoubleRange = new DoubleRange(dStart, dEnd); }
        virtual ~DoubleRangeWrapper() 
        { 
            if (NULL != _pDoubleRange)
            {
                delete _pDoubleRange;
                _pDoubleRange = NULL;
            }
        }
        
        int get_dStart() {return _pDoubleRange->dStart;}
        void set_dStart(double dStart) {_pDoubleRange->dStart = dStart;}

        int get_dEnd() {return _pDoubleRange->dEnd;}
        void set_dEnd(double dEnd) {_pDoubleRange->dEnd = dEnd;}

        DoubleRange* get_DoubleRangePtr() {return _pDoubleRange;}

    private:
        DoubleRange* _pDoubleRange;
    };

    public ref class VarModsWrapper
    {
    public:
        VarModsWrapper() { _pVarMods = new VarMods(); }
        VarModsWrapper(VarMods &varMods) { _pVarMods = new VarMods(varMods);}
        virtual ~VarModsWrapper() 
        { 
            if (NULL != _pVarMods)
            {
                delete _pVarMods;
                _pVarMods = NULL;
            }
        }

        int get_BinaryMod() {return _pVarMods->iBinaryMod;}
        void set_BinaryMod(int iBinaryMod) {_pVarMods->iBinaryMod = iBinaryMod;}

        int get_RequireThisMod() {return _pVarMods->bRequireThisMod;}
        void set_RequireThisMod(int bRequireThisMod) {_pVarMods->bRequireThisMod = bRequireThisMod;}

        int get_MaxNumVarModAAPerMod() {return _pVarMods->iMaxNumVarModAAPerMod;}
        void set_MaxNumVarModAAPerMod(int iMaxNumVarModAAPerMod) {_pVarMods->iMaxNumVarModAAPerMod = iMaxNumVarModAAPerMod;}

        int get_VarModTermDistance() {return _pVarMods->iVarModTermDistance;}
        void set_VarModTermDistance(int iVarModTermDistance) {_pVarMods->iVarModTermDistance = iVarModTermDistance;}

        int get_WhichTerm() {return _pVarMods->iWhichTerm;}
        void set_WhichTerm(int iWhichTerm) {_pVarMods->iWhichTerm = iWhichTerm;}

        int get_VarModMass() {return _pVarMods->dVarModMass;}
        void set_VarModMass(double dVarModMass) {_pVarMods->dVarModMass = dVarModMass;}

        System::String^% get_VarModChar() { return gcnew String(Marshal::PtrToStringAnsi(static_cast<IntPtr>(const_cast<char *>(_pVarMods->szVarModChar))));}
        void set_VarModChar(System::String^ varModChar) 
        {
            std::string stdVarModChar = marshal_as<std::string>(varModChar);    
            strcpy(_pVarMods->szVarModChar, stdVarModChar.c_str());
        }

        VarMods* get_VarModsPtr() {return _pVarMods;}

    private:
        VarMods *_pVarMods;
    };

    public ref class EnzymeInfoWrapper
    {
    public:
        EnzymeInfoWrapper() { _pEnzymeInfo = new EnzymeInfo(); }
        EnzymeInfoWrapper(EnzymeInfo &enzymeInfo) { _pEnzymeInfo = new EnzymeInfo(enzymeInfo);}
        virtual ~EnzymeInfoWrapper() 
        { 
            if (NULL != _pEnzymeInfo)
            {
                delete _pEnzymeInfo;
                _pEnzymeInfo = NULL;
            }
        }
        
        EnzymeInfo* get_EnzymeInfoPtr() {return _pEnzymeInfo;}

        int get_AllowedMissedCleavge() {return _pEnzymeInfo->iAllowedMissedCleavage;}
        void set_AllowedMissedCleavge(int iAllowedMissedCleavage) {_pEnzymeInfo->iAllowedMissedCleavage = iAllowedMissedCleavage;}

        int get_SearchEnzymeOffSet() {return _pEnzymeInfo->iSearchEnzymeOffSet;}
        void set_SearchEnzymeOffSet(int iSearchEnzymeOffSet) {_pEnzymeInfo->iSearchEnzymeOffSet = iSearchEnzymeOffSet;}

        int get_SampleEnzymeOffSet() {return _pEnzymeInfo->iSampleEnzymeOffSet;}
        void set_SampleEnzymeOffSet(int iSampleEnzymeOffSet) {_pEnzymeInfo->iSampleEnzymeOffSet = iSampleEnzymeOffSet;}

        System::String^% get_SearchEnzymeName() { return gcnew String(Marshal::PtrToStringAnsi(static_cast<IntPtr>(const_cast<char *>(_pEnzymeInfo->szSearchEnzymeName))));}
        void set_SearchEnzymeName(System::String^ searchEnzymeName) 
        {
            std::string stdSearchEnzymeName = marshal_as<std::string>(searchEnzymeName);    
            strcpy(_pEnzymeInfo->szSearchEnzymeName, stdSearchEnzymeName.c_str());
        }

        System::String^% get_SearchEnzymeBreakAA() { return gcnew String(Marshal::PtrToStringAnsi(static_cast<IntPtr>(const_cast<char *>(_pEnzymeInfo->szSearchEnzymeBreakAA))));}
        void set_SearchEnzymeBreakAA(System::String^ searchEnzymeBreakAA) 
        {
            std::string stdSearchEnzymeBreakAA = marshal_as<std::string>(searchEnzymeBreakAA);    
            strcpy(_pEnzymeInfo->szSearchEnzymeBreakAA, stdSearchEnzymeBreakAA.c_str());
        }

        System::String^% get_SearchEnzymeNoBreakAA() { return gcnew String(Marshal::PtrToStringAnsi(static_cast<IntPtr>(const_cast<char *>(_pEnzymeInfo->szSearchEnzymeNoBreakAA))));}
        void set_SearchEnzymeNoBreakAA(System::String^ searchEnzymeNoBreakAA) 
        {
            std::string stdSearchEnzymeNoBreakAA = marshal_as<std::string>(searchEnzymeNoBreakAA);    
            strcpy(_pEnzymeInfo->szSearchEnzymeNoBreakAA, stdSearchEnzymeNoBreakAA.c_str());
        }

        System::String^% get_SampleEnzymeName() { return gcnew String(Marshal::PtrToStringAnsi(static_cast<IntPtr>(const_cast<char *>(_pEnzymeInfo->szSampleEnzymeName))));}
        void set_SampleEnzymeName(System::String^ sampleEnzymeName) 
        {
            std::string stdSampleEnzymeName = marshal_as<std::string>(sampleEnzymeName);    
            strcpy(_pEnzymeInfo->szSampleEnzymeName, stdSampleEnzymeName.c_str());
        }

        System::String^% get_SampleEnzymeBreakAA() { return gcnew String(Marshal::PtrToStringAnsi(static_cast<IntPtr>(const_cast<char *>(_pEnzymeInfo->szSampleEnzymeBreakAA))));}
        void set_SampleEnzymeBreakAA(System::String^ sampleEnzymeBreakAA) 
        {
            std::string stdSampleEnzymeBreakAA = marshal_as<std::string>(sampleEnzymeBreakAA);    
            strcpy(_pEnzymeInfo->szSampleEnzymeBreakAA, stdSampleEnzymeBreakAA.c_str());
        }

        System::String^% get_SampleEnzymeNoBreakAA() { return gcnew String(Marshal::PtrToStringAnsi(static_cast<IntPtr>(const_cast<char *>(_pEnzymeInfo->szSampleEnzymeNoBreakAA))));}
        void set_SampleEnzymeNoBreakAA(System::String^ sampleEnzymeNoBreakAA) 
        {
            std::string stdSampleEnzymeNoBreakAA = marshal_as<std::string>(sampleEnzymeNoBreakAA);    
            strcpy(_pEnzymeInfo->szSampleEnzymeNoBreakAA, stdSampleEnzymeNoBreakAA.c_str());
        }

    private:
        EnzymeInfo *_pEnzymeInfo;
    };

    public ref class InputFileInfoWrapper
    {
    public:
        InputFileInfoWrapper() { _pInputFileInfo = new InputFileInfo(); }
        InputFileInfoWrapper(InputFileInfo &inputFileInfo) { _pInputFileInfo = new InputFileInfo(inputFileInfo);}
        virtual ~InputFileInfoWrapper() 
        { 
            if (NULL != _pInputFileInfo)
            {
                delete _pInputFileInfo;
                _pInputFileInfo = NULL;
            }
        }
        
        InputFileInfo* get_InputFileInfoPtr() {return _pInputFileInfo;}

        InputType get_InputType() {return static_cast<InputType>(_pInputFileInfo->iInputType);}
        void set_InputType(InputType inputType) {_pInputFileInfo->iInputType = static_cast<int>(inputType);}

        AnalysisType get_AnalysisType() {return static_cast<AnalysisType>(_pInputFileInfo->iAnalysisType);}
        void set_AnalysisType(AnalysisType analysisType) {_pInputFileInfo->iAnalysisType = static_cast<int>(analysisType);}

        int get_FirstScan() {return _pInputFileInfo->iFirstScan;}
        void set_FirstScan(int iFirstScan) {_pInputFileInfo->iFirstScan = iFirstScan;}

        int get_LastScan() {return _pInputFileInfo->iLastScan;}
        void set_LastScan(int iLastScan) {_pInputFileInfo->iLastScan = iLastScan;}

        System::String^% get_FileName() { return gcnew String(Marshal::PtrToStringAnsi(static_cast<IntPtr>(const_cast<char *>(_pInputFileInfo->szFileName))));}
        void set_FileName(System::String^ fileName) 
        {
            std::string stdFileName = marshal_as<std::string>(fileName);    
            strcpy(_pInputFileInfo->szFileName, stdFileName.c_str());
        }

        System::String^% get_BaseName() { return gcnew String(Marshal::PtrToStringAnsi(static_cast<IntPtr>(const_cast<char *>(_pInputFileInfo->szBaseName))));}
        void set_BaseName(System::String^ baseName) 
        {
            std::string stdBaseName = marshal_as<std::string>(baseName);
            strcpy(_pInputFileInfo->szBaseName, stdBaseName.c_str());
        }

    private:
        InputFileInfo *_pInputFileInfo;
    };
}