SNPFile{
  var <snpDict;
  var <file;
  var <fileLength;
  var <userID;
  var <testSet = inf;
  *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;
    });
  }

  readFile{//read a SNPDict from file
    var snpFile = File(file, "r"), line = "", counter = 0, procCounter = Array.new(9), tmp, key, sizeOf, snp, res, keyCount = 0.0, unknown, unknownCount = 0.0;
    fileLength = (("wc -l "++file.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace});
    9.do({|item,i| procCounter.add(round((fileLength[0].asFloat/100)*(i+1)*10, 1).asInt)});//calculating procentuals for a simple progression output
    ("Now reading: "++file++" ("++fileLength[0]++" lines).").postln;
    ("==========").postln;
    if(snpFile.isOpen,{
      protect{
        while{(line = snpFile.getLine).notNil }{
          switch(line[0].asString, 
            "*",{//info line
              sizeOf = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab
              snpDict = SNPDict.new(sizeOf[1].asFloat, sizeOf[3].asInt);//init new SNPDict
              snpDict.initLookupFromFile(sizeOf[1].asFloat, sizeOf[2].asFloat);
            },
            ";",{//key line
              key = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab
              snpDict.addPositionLookupFromFile(keyCount, key[1].asFloat);//store to lookup table!
              keyCount = keyCount + 1.0;
            },
            "+",{//SNP line
              tmp = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab
              if(tmp[6].isNil,{
                res = [tmp[5].asSymbol];
              },{
                res = [tmp[5].asSymbol, tmp[6].asSymbol];
              });
              snp = SNP.new(tmp[1], tmp[2], tmp[3], tmp[4], res);
              snpDict.storeSNP(snp, key[1]);
            },
            "|",{//unknown line
              unknown = line.delimit({|ch| ch.isSpace});//delimit by space and/or tab
              snpDict.addUnknownLookupFromFile(unknownCount, unknown[1].asFloat);
              unknownCount = unknownCount + 1.0;
            }
          );
          counter = counter + 1;
          switch(counter,
            procCounter[0],{"=".post;},
            procCounter[1],{"=".post;},
            procCounter[2],{"=".post;},
            procCounter[3],{"=".post;},
            procCounter[4],{"=".post;},
            procCounter[5],{"=".post;},
            procCounter[6],{"=".post;},
            procCounter[7],{"=".post;},
            procCounter[8],{"=".post;}
          );
        };
      "=".postln;
      "Done reading file to RAM.".postln;
      }{
        snpFile.close;
      };
    },{
      ("Couldn't open file for reading: "++file).warn;
    });
    ^snpDict;
  }

  writeFile{//write a SNPDict to file
    arg snpDict;
    var snpFile = File(file, "w"), line = "", counter = 0, tmp, snp, newSameCounter = 0;
    ("Attempting to write SNPDict to file: "++file).postln;
    if(snpFile.isOpen, {
      protect{
        snpFile.write("*\t"++snpDict.snpArr.size.asString++"\t"++snpDict.unknownArr.size.asString++"\t"++snpDict.userID++"\n");//write length of snpArr and unknownArr
        snpDict.snpArr.do({
          arg item;
          snpFile.write(";\t"++item.asString++"\n");
          snpDict.snpAtPosition(item).do({//write all SNPs
            arg snp;
            var res;
            if(snp.resolver.size==2,{
              res = (snp.resolver[0]++"\t"++snp.resolver[1]).asString;
            },{
              res = snp.resolver[0].asString;
            });
            snpFile.write("+\t"++snp.chromosome.asString++"\t"++snp.position.asString++"\t"++snp.id.asString++"\t"++snp.base.asString++"\t"++res++"\n");//write SNP to file 
          });
        });
        snpDict.unknownArr.do({//write all unknown positions
          arg item;
          snpFile.write("|\t"++item.asString++"\n");
        });
      }{
        snpFile.close;
        ("Done writing to file.").postln;
        ^true;
      };
    },{
      ("Couldn't open file for writing: "++file).postln;
      ^false;
    });
  }

  writeUnknownIDToFile{//write the rsids of all unknown SNPs to file
    arg snpDict;
    var snpFile = File("/media/Data/tmp/1/1.unknown.snp", "w");
    ("Attempting to write unknowns to file: "++file).postln;
    if(snpFile.isOpen, {
      protect{
        snpDict.unknownArr.do({
          arg item,i;
          snpDict.noneResolverAtPosition(item).do({
            arg snp,i;
            snpFile.write(snp.id++"\n");
          });
        });
      }
    },{
      ("Couldn't open file for writing: "++file).postln;
      ^false;
    });
  }

  readUnknownIDFromFile{
    arg unknowns;
    var snpFile = File(unknowns, "r"), fileLength, line ="", outArr, counter = 0;
    fileLength = (("wc -l "++unknowns.shellQuote).unixCmdGetStdOut).delimit({|ch| ch.isSpace});
    fileLength.postln;
    outArr = Array.new(fileLength[0].asInt);
    if(snpFile.isOpen, {
      protect{
        while{(line = snpFile.getLine).notNil }{
          outArr.add(line.asSymbol);
          counter = counter + 1;
        }
      }
      ^outArr;
    },{
      ("Couldn't open file for writing: "++file).postln;
      ^false;
    });
  }
}