// -*- mode: c++; indent-tabs-mode: nil; -*-
//
// Copyright 2009 Illumina, Inc.
//
// This software is covered by the "Illumina Genome Analyzer Software
// License Agreement" and the "Illumina Source Code License Agreement",
// and certain third party copyright/licenses, and any user of this
// source file is bound by the terms therein (see accompanying files
// Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
// Illumina_Source_Code_License_Agreement.pdf and third party
// copyright/license notices).
//
//

/// \file

#ifndef EXPORT_H
#define EXPORT_H

#include <vector>
#include <string>

// Read type definitions
const unsigned int RT_UNKOWN_ALN = 0;
const unsigned int RT_SHADOW_ALN = 1;
const unsigned int RT_GAPPED_ALN = 2;
const unsigned int RT_POORLY_ALN = 3;

// Define export field formats, hopefully this
//  won't change, but if it does, change it here
const unsigned int EXP_MACHINE_NAME_IDX   = 0;
const unsigned int EXP_RUN_NUM_IDX        = 1;
const unsigned int EXP_LANE_NUM_IDX       = 2;
const unsigned int EXP_TILE_IDX           = 3;
const unsigned int EXP_XCORD_IDX          = 4;
const unsigned int EXP_YCORD_IDX          = 5;
const unsigned int EXP_INDEX_STR_IDX      = 6;
const unsigned int EXP_READ_NUM_IDX       = 7;
const unsigned int EXP_READ_IDX           = 8;
const unsigned int EXP_QUAL_STR_IDX       = 9;
const unsigned int EXP_MATCH_CHR_IDX      = 10;
const unsigned int EXP_MATCH_CONTIG_IDX   = 11;
const unsigned int EXP_MATCH_POS_IDX      = 12;
const unsigned int EXP_MATCH_STRAND_IDX   = 13;
const unsigned int EXP_MATCH_DESC_IDX     = 14;
const unsigned int EXP_SINGLE_ALN_IDX     = 15;
const unsigned int EXP_PAIRED_ALN_IDX     = 16;
const unsigned int EXP_PARTNER_CHR_IDX    = 17;
const unsigned int EXP_PARTNER_CONTIG_IDX = 18;
const unsigned int EXP_PARTNER_OFFSET_IDX = 19;
const unsigned int EXP_PARTNER_STRAND_IDX = 20;
const unsigned int EXP_FILTER_IDX         = 21;
const unsigned int EXP_RANGE_START_IDX    = 22;
const unsigned int EXP_RANGE_END_IDX      = 23;
const unsigned int EXP_READ_TYPE_IDX      = 24;

// This is exactly what I was talking about
//  above regarding export file format changing
// This format is for indel finding and is 
//  prefix with range start and stop and then
//  follows with normal export format. There
//  is a different contstructor for this format
//  with a flag to tell the constructor its this
//  format
const unsigned int EXP2_RANGE_START_IDX    = 0;
const unsigned int EXP2_RANGE_END_IDX      = 1;
const unsigned int EXP2_MACHINE_NAME_IDX   = 2;
const unsigned int EXP2_RUN_NUM_IDX        = 3;
const unsigned int EXP2_LANE_NUM_IDX       = 4;
const unsigned int EXP2_TILE_IDX           = 5;
const unsigned int EXP2_XCORD_IDX          = 6;
const unsigned int EXP2_YCORD_IDX          = 7;
const unsigned int EXP2_INDEX_STR_IDX      = 8;
const unsigned int EXP2_READ_NUM_IDX       = 9;
const unsigned int EXP2_READ_IDX           = 10;
const unsigned int EXP2_QUAL_STR_IDX       = 11;
const unsigned int EXP2_MATCH_CHR_IDX      = 12;
const unsigned int EXP2_MATCH_CONTIG_IDX   = 13;
const unsigned int EXP2_MATCH_POS_IDX      = 14;
const unsigned int EXP2_MATCH_STRAND_IDX   = 15;
const unsigned int EXP2_MATCH_DESC_IDX     = 16;
const unsigned int EXP2_SINGLE_ALN_IDX     = 17;
const unsigned int EXP2_PAIRED_ALN_IDX     = 18;
const unsigned int EXP2_PARTNER_CHR_IDX    = 19;
const unsigned int EXP2_PARTNER_CONTIG_IDX = 20;
const unsigned int EXP2_PARTNER_OFFSET_IDX = 21;
const unsigned int EXP2_PARTNER_STRAND_IDX = 22;
const unsigned int EXP2_FILTER_IDX         = 23;
const unsigned int EXP2_READ_TYPE_IDX      = 24;

// Define export file types for the silly issue above
const unsigned int EXPORT_TYPE_NORMAL      = 0;
const unsigned int EXPORT_TYPE_INDELFINDER = 1;

// Exit codes
const unsigned int EXIT_CODE_SUCCESS = 0;
const unsigned int EXIT_CODE_FAILURE = 1;
const unsigned int EXIT_CODE_INPUT   = 2;
const unsigned int EXIT_CODE_DESC    = 3;

class Export
{
 public:
  // Standard export file constructor
    Export(const std::string& line, unsigned int expType = EXPORT_TYPE_NORMAL);
  // Special indel finder export2 constructor
  //Export(string line);
  ~Export() {}

  //
  // Access functions
  //
  const std::string& getMachineName() const {
    return(machineName);
  }
  unsigned getRunNum() const {
    return(runNum);
  }
  unsigned getLane() const {
    return(lane);
  }
  unsigned getTile() const {
    return(tile);
  }
  unsigned getXCord() const {
    return(xCord);
  }
  unsigned getYCord() const {
    return(yCord);
  }
  const std::string& getIndexStr() const {
    return(indexStr);
  }
  const std::string& getRead() const {
    return(read);
  }
  const std::string& getQualString() const {
    return(qualStr);
  }
  const std::string& getMatchChr() const {
    return(matchChr);
  }
  const std::string& getMatchContig() const {
    return(matchContig);
  }
  int getMatchStart() const {
    return(matchStart);
  }
  char getMatchStrand() const {
    return(matchStrand);
  }
  const std::string& getMatchDesc() const {
    return(matchDesc);
  }
  double getSingleAlnScore() const {
    return(singleAlnScore);
  }
  double getPairedAlnScore() const {
    return(pairedAlnScore);
  }
  const std::string& getPartnerChr() const {
    return(partnerChr);
  }
  const std::string& getPartnerContig() const {
    return(partnerContig);
  }
  int getPartnerOffset() const {
    return(partnerOffset);
  }
  const std::string& getPartnerStrand() const {
    return(partnerStrand);
  }
  char getFilterStatus() const {
    return(filterStatus);
  }
  unsigned getReadType() const {
    return(readType);
  }

  bool isPoorlyAligned() const {
    return (readType == RT_POORLY_ALN);
  }
  bool isShadow() const {
    return (readType == RT_SHADOW_ALN);
  }
  bool isGapped() const {
    return (readType == RT_GAPPED_ALN);
  }
  bool isUnkType() const {
    return (readType == RT_UNKOWN_ALN);
  }
  int getRangeStart() const {
    return(rangeStart);
  }
  int getRangeEnd() const {
    return(rangeEnd);
  }

  std::string toString();

  //
  // Manipuation fucntions
  //
  void setMatchStart(unsigned int s) {
    // Update partner offset
    int delta = s - matchStart;
    partnerOffset -= delta;
    matchStart = s;
  }
  void setMatchDesc(const std::string& desc) {
    matchDesc = desc;
  }
  void setRangeStart(const int s) {
    rangeStart = s;
  }
  void setRangeEnd(const int e) {
    rangeEnd = e;
  }
  void setSingleAlnScore(const double s) {
    singleAlnScore = s;
  }
  void setPartnerOffset(const int o) {
    partnerOffset = o;
  }

  //
  // Auxillary functions (static)
  //
  static void   forceOnlyACTGN(std::string& seq);
  static void   stringToUpper(std::string& seq);
  static std::string complement(const std::string& seq);
  static std::string reverse(const std::string& seq);
  static void   tsvToArray(const std::string& line, std::vector<std::string>& data, char sep);

 private:
  std::string       machineName;
  unsigned int runNum;
  unsigned int lane;
  unsigned int tile;
  unsigned int xCord;
  unsigned int yCord;
  std::string       indexStr;
  unsigned int readNum;
  std::string       read;
  std::string       qualStr;
  std::string       matchChr;
  std::string       matchContig;
  int matchStart;
  char         matchStrand;
  std::string       matchDesc;
  double       singleAlnScore;
  double       pairedAlnScore;
  std::string       partnerChr;
  std::string       partnerContig;
  int          partnerOffset;
  std::string       partnerStrand;
  char         filterStatus;

  int rangeStart;
  int rangeEnd;

  unsigned readType;

  // This defines the export format type
  // 0  = Normal format
  // 1  = Indel file format (prefix with range start and stop)
  unsigned int EXP_FORMAT_TYPE;
};

#endif

// END OF FILE