SNPParser{
  var <placement;
  var <comboDict;
  var <file;
  var <fileLength;
  var <userID;
  var <testSet;

  *new{
    arg aFile, aTestSet = inf;
    ^super.new.init(aFile, aTestSet);
  }

  init{
    arg aFile, aTestSet;
    this.setFileAndUser(aFile);
    testSet = aTestSet;
  }

  setFileAndUser{//set the file (again) to be parsed
    arg aFile;
    var allSlash, allDot;
    file = aFile;
    allSlash = file.findAll("/");
    allDot = file.findAll(".");
    if(allSlash.notNil,{//if there is no slash in the filename
      userID = file[allSlash[allSlash.size-1]+1..allDot[allDot.size-2]-1].asInt;
    },{
      userID = file[0..allDot[allDot.size-2]-1].asInt;
    });
    userID.postln;
  }

  readFile{//parse the file this parser currently is setup with
    var found = false, company = "";
    "Guessing parser.".postln;
    SNPInfo.sCompany.do({
      arg cCompany, i;
      if(file.contains(cCompany.asString),{
        if(SNPInfo.workingSCompany.includes(i),{
          ("Attempting to parse a "++cCompany++" file now.").postln;
          company = cCompany;
          found = true;
        },{
          ("Parsing files from "++cCompany++" is not supported (yet). Get me a coffee to make it work!").postln;
        });
      });
    });
    if(found.not,{
      ("This file might not be supported at all: "++file).postln;
    },{
      switch(company,
        "23andme",{^this.parse23andme},
        {"No no no no no!".postln}
      );
    });
  }

  parse23andme{//parsing a 23andme file: id, chromosome, position, base
    var snpFile = File(file, "r"), line = "", counter = 0.0, tmp, snp, newSameCounter = 0.0;
    fileLength = (("wc -l "++file.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace});
    ("File "++file++" is "++fileLength[0]++" lines long.").postln;
    "Parsing might require some minutes! So kick back an get a coffee, while it lasts.".postln;
    comboDict = SNPDict.new(fileLength[0], userID);
    if(snpFile.isOpen,{
      protect{
        while{(line = snpFile.getLine).notNil}{//FIXME: Reinsert testset
          if(line[0].asString!="#",{//skip commented lines
            tmp = line.delimit({|ch| ch.isSpace});//delimit the line by space and/or tab
            if(tmp[3].asString!="--" && (SNPInfo.isBasePair(tmp[3]) || SNPInfo.isBase(tmp[3]) && (SNPInfo.chromosomesLength[SNPInfo.convertChromosome(tmp[1])-1]>=tmp[2].asFloat)),{//skip empty SNPs and make sure it's either a single base or a base pair and ignore out-of-range SNPs (yes, science is unclear!)
              if(SNPInfo.isBasePair(tmp[3]),{//if it's a base pair, set it up
                snp = SNP.new(tmp[1], tmp[2], tmp[0], tmp[3], SNPInfo.createResolverForPair(tmp[3]));
              },{
                if(SNPInfo.isBase(tmp[3]), {//if it's a single base, set it up
                  snp = SNP.new(tmp[1], tmp[2], tmp[0], tmp[3], \none);
                });
              });
              newSameCounter = newSameCounter + comboDict.storeSNP(snp, SNPInfo.calcPosition(snp.chromosome, snp.position));
              switch(newSameCounter,
                1.0,{"Storing SNPs now: \n==========".postln;},
                100000.0,{"=".post;},
                200000.0,{"=".post;},
                300000.0,{"=".post;},
                400000.0,{"=".post;},
                500000.0,{"=".post;},
                600000.0,{"=".post;},
                700000.0,{"=".post;},
                800000.0,{"=".post;},
                900000.0,{"=".post;},
              );
            });
          });
        counter = counter + 1;
        };
      }{
        snpFile.close;
      };
    },{
      ("Couldn't open file for reading: "++file).warn;
    });
    "=".postln;
    "Sorting lookup tables. This will also take some time!".postln;
    comboDict.orderLookup(2);
    "Done sorting lookup tables.".postln;
    ^comboDict;
  }
}