SNPInfo{//helper class for calculations and constants used in the other classes
  const <baseSingle = #[\A, \C, \G, \T];
  const <basePair = #[\AA, \AC, \AG, \AT, \CC, \CG, \CT, \GG, \GT, \TT];
  const <unknownBasePair = #[\AA, \CC, \GG, \TT];
  const <emptyBasePair = #[\none, \none];
  const <emptyBase = #[\none];
//  const <chromosomesLength = #[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569];
  const <chromosomesLength = #[247199719, 242751149, 199446827, 191263063, 180837866, 170896993, 158821424, 146274826, 140442298, 135374737, 134452384, 132289534, 114127980, 106360585, 100338915, 88822254, 78654742, 76117153, 63806651, 62435965, 46944323, 49528953, 154913754, 57741652, 16569];
  const <chromosomesFactor = #[ 1, 1.0183256393155, 1.2394266818795, 1.2924592711349, 1.3669687907067, 1.4464837248482, 1.556463308124, 1.6899676161638, 1.7601514822835, 1.8260402529905, 1.8385670201281, 1.868626425126, 2.1659869823333, 2.324166597993, 2.4636475190109, 2.7830831561649, 3.142845716791, 3.2476217154365, 3.8741998698537, 3.9592519952242, 5.265806453317, 4.9910144274602, 1.5957247992325, 4.2811334701681, 14919.410887803 ];
//  const <chromosomesFactor = #[1, 1.0248818404643, 1.2586989312271, 1.3039238578163, 1.3777202708052, 1.4566257978907, 1.5662480524924, 1.7029500665129, 1.7650631334069, 1.8390163889117, 1.8462117858074, 1.8621374094106, 2.1641997484794, 2.3218601681945, 2.4309688587862, 2.7585778581012, 3.0697700147583, 3.1923592004677, 4.2153713518124, 3.9547570730079, 5.1787069346401, 4.85825415617, 1.6052664523139, 4.1980065842769, 15043.190355483];
  const <lengthAtOneMs = 69.236283611;//in hours
  const <sCompany = #["ftdna-illumina", "23andme", "23andme-exome-vcf", "decodeme"];
  const <a = #[1,0,0,0];
  const <c = #[0,1,0,0];
  const <g = #[0,0,1,0];
  const <t = #[0,0,0,1];
  const <e = #[0,0,0,0];
  const <colorA = "#80ff00";
  const <colorC = "#ff0000";
  const <colorG = "#8000ff";
  const <colorT = "#00ffff";
  classvar <workingSCompany = #[1];//the companies working with this software (so far)

  *calcPosition{//normalize all positions on chromosomes to the longest (the first) by chromosomesFactor of chromosomesFactor
    arg chromosome, position;
    var factor = 0.0, outPos = 0.0;
    switch(chromosome.asSymbol,
      \1,{factor = chromosomesFactor[0]},
      \2,{factor = chromosomesFactor[1]},
      \3,{factor = chromosomesFactor[2]},
      \4,{factor = chromosomesFactor[3]},
      \5,{factor = chromosomesFactor[4]},
      \6,{factor = chromosomesFactor[5]},
      \7,{factor = chromosomesFactor[6]},
      \8,{factor = chromosomesFactor[7]},
      \9,{factor = chromosomesFactor[8]},
      \10,{factor = chromosomesFactor[9]},
      \11,{factor = chromosomesFactor[10]},
      \12,{factor = chromosomesFactor[11]},
      \13,{factor = chromosomesFactor[12]},
      \14,{factor = chromosomesFactor[13]},
      \15,{factor = chromosomesFactor[14]},
      \16,{factor = chromosomesFactor[15]},
      \17,{factor = chromosomesFactor[16]},
      \18,{factor = chromosomesFactor[17]},
      \19,{factor = chromosomesFactor[18]},
      \20,{factor = chromosomesFactor[19]},
      \21,{factor = chromosomesFactor[20]},
      \22,{factor = chromosomesFactor[21]},
      \X,{factor = chromosomesFactor[22]},
      \Y,{factor = chromosomesFactor[23]},
      \MT,{factor = chromosomesFactor[24]}
    );
    ^outPos = round(position.asFloat*factor);//round to the next possible slot
  }

  *convertChromosome{//convert funky names of chromosomes to valid numbers
    arg chrom;
    switch(chrom,
      \X, {^23},
      \Y, {^24},
      \MT,{^25},
      "X", {^23},
      "Y", {^24},
      "MT",{^25},
      {^chrom.asInt}
    );
  }

  *baseToVec{//calculate unique vectors on basis of the base given
    arg base;
    var out = [[],[]];
    if(base.isArray, {//unwrap items in Array
      base.do({
        arg item, i;
        if(item.notNil, {
          out.put(i, this.baseToVec(item));
        });
      });
      ^out;
    },{
      if(this.isBasePair(base),{//if it's a base pair calc
        switch(base,
          \AA, {^a},
          \AC, {^(a-c)},
          \AG, {^(a-g)},
          \AT, {^(a-t)},
          \CC, {^c},
          \CG, {^(c-g)},
          \CT, {^(c-t)},
          \GG, {^g},
          \GT, {^(g-t)},
          \TT, {^t},
        );
      },{
        if(this.isBase(base),{//if it's a single base, return
          switch(base,
            \A, {^a},
            \C, {^c},
            \G, {^g},
            \T, {^t}
          );
        },{
          if(base == \none,{//if it's unknown, return empty
            ^e;
          });
        });
      });
    });
  }

  *createResolverForPair{//for known base pairs, create a resolver
    arg base;
    base = base.asSymbol;
    switch(base,
      \AC,{^[\AA, \CC]},
      \AG,{^[\AA, \GG]},
      \AT,{^[\AA, \TT]},
      \CG,{^[\CC, \GG]},
      \CT,{^[\CC, \TT]},
      \GT,{^[\GG, \TT]},
      {^[\none, \none]}
    );
  }

  *isUnknownBasePair{//check if it's an unknown pair
    arg base;
    if(unknownBasePair.includes(base.asSymbol),{//if the base is part of the unknown base pairs
      ^true;
    },{
      ^false;
    });
  }

  *isBase{//check if it's a single base
    arg base;
    if(baseSingle.includes(base.asSymbol),{//if the base is part of the unknown base pairs
      ^true;
    },{
      ^false;
    });
  }

  *isBasePair{//check if it's a (known) base pair
    arg base;
    if(basePair.includes(base.asSymbol),{//if the base is part of the unknown base pairs
      ^true;
    },{
      ^false;
    });
  }

  //returns a hex color value for a base/ base pair
  *getColorFromBase{
    arg base;
    if(this.isBase(base.asSymbol),{
      switch(base.asSymbol,
        \A, {^colorA},
        \C, {^colorC},
        \G, {^colorG},
        \T, {^colorT}
      );
    },{
      switch(base.asSymbol,
        \AA, {^colorA},
        \CC, {^colorC},
        \GG, {^colorG},
        \TT, {^colorT},
        {
          if((base.asString.size==2 && this.isBase(base.asString[0]) && this.isBase(base.asString[1])),{
            ^Color.fromHexString(this.getColorFromBase(base.asString[0])).blend(Color.fromHexString(this.getColorFromBase(base.asString[1]))).hexString;
            }
          );
        }
      );
    });
  }
}