SNPAudio {
  var <>numChannels;//number of channels to use
  var <snpSynths;
  var <>snpDict;//the SNPDict to use
  var <>playTime;//calculated play time of a single SNP, defined by playTime setup on init
  var <>includeUnknown;//wether to include SNPs with unknown resolvers (aka. SNPS with only bases set)
  var <>ignoreSNPs = #[];//Array of Symbols of chromosomes to ignore (1-22,X,Y,MT)
  var <keys;//Array storing normalized settings for each chromosome
  var <keyToFrq;//Dictionary with normalized frequency ranges for 8 different chromosome lengths
  var <isPlaying = false;//boolean indicating the state of playing
  var <currentStep = 0.0;//storage for the position up to which sonification should take place
  var <lastStep = 0.0;//storage for the last played step (SNP position) aka. current position playing
  var <lengthOfSNP = 1.0;//distance between two SNPs in ms
  var <speakerSetup;//Array holding the chromosome numbers for each speaker
  var <synthGroup;//Group for the Synths
  var <fxGroup;//Group for effects
  var <compressionGroup;//Group for compression Synths
  var <recordingGroup;//Group for recording Synths
  var <sonBus;//Bus for Synth->compression
  var <fxBus;//Bus for chromosome based effects
  var <recBus;//Bus for compression->recording/out
  var <record =false;//boolean indicating wether to record or not (default off)
  var <>recPath;//String representing directory to use for recording
  var <recordingBuffer;//the recording buffer to use, wehen recording
  var <baseTone = #[110.00, 65.4, 98.00, 73.42];//the fundamentals from which 8 octaves will be calculated: A (A2), C (C2), G (G2), T (D2)
  var <gui; //TODO: set in constructor

  *new{
    arg snpDict, numChannels = 2, playTime, includeUnknown = false, ignoreSNPs, setRecord = false, recordPath;
    ^super.new.sonificatorInit(snpDict, numChannels, playTime, includeUnknown, ignoreSNPs, setRecord, recordPath);
  }

  sonificatorInit{
    arg snpDict, numChannels, playTime, includeUnknown, ignoreSNPs, setRecord, recordPath;
    this.snpDict = snpDict;
    this.numChannels_(numChannels);
    this.playTime = playTime;
    lengthOfSNP = this.calcSNPTime(playTime);
    this.includeUnknown = includeUnknown;
    if(ignoreSNPs.notNil && ignoreSNPs.isArray,{
      this.ignoreSNPs = ignoreSNPs;
    });
    this.initKeyRange.value;
    this.setupSpeakers(numChannels, true);
    this.setupGroups(numChannels);
    this.setupBusses(numChannels);
    this.addSNPSynths.value;
    this.addCompressionSynths;
    // TODO: add effects Synths based on chromosome areas
    if(setRecord,{//if recording should be set up
      if(recordPath.notNil && recordPath.isString,{//first check if recordingPath is set
        if(recordPath[recordPath.size-1]!="/",{//compensate for missing trailing slash
          recPath = (recordPath++"/");
        },{
          recPath = recordPath;
        });
        if(File.exists(recPath),{//if path exists, init recording to file
          recPath = recordPath;
          record = setRecord;
          this.setupRecording(numChannels); 
        },{
          ("Path does not exist: "++recPath.asString).postln;
          ("Update recPath!")
        });
      },{
        ("Recording path invalid: "++recPath.asString).postln;
      });
    });
  }

  setupBusses{//setup the busses for compression and recording
    arg channels;
    sonBus = Bus.audio(Server.local, channels);
    recBus = Bus.audio(Server.local, channels);
  }

  setupGroups{//setup Groups (for Synths, compression and recording)
    arg channels;
    synthGroup = Group.new;
//    fxGroup = Group.after(synthGroup);
    compressionGroup = Group.after(synthGroup);
    recordingGroup = Group.after(compressionGroup);
    NodeWatcher.register(synthGroup);
//    NodeWatcher.register(fxGroup);
    NodeWatcher.register(compressionGroup);
    NodeWatcher.register(recordingGroup);
  }

  setupRecording{//create a buffer and a recording SynthDef, leaving file open for writing
    arg channels;
    ("Setting up recording to file.").postln;
    recordingBuffer = Buffer.alloc(Server.local, 262144, channels);
    recordingBuffer.write(recPath++"SNPSonification-"++(Date.seed).asString++"_("++channels.asString++"_chan).aiff".standardizePath, "aiff", "float32", 0, 0, true);
    SynthDef(\recordSNP,{
      arg buffer;
      DiskOut.ar(buffer, In.ar(recBus, channels));
    }).add;
  }

  setupSpeakers{//setup speakers for stereo and circular multichannel
    arg channels, printOuts = false;
    switch(channels.asInt,
      2,{speakerSetup = [[8,16,24,6,14,22,4,12,20,2,10,18],[7,15,23,1,9,17,3,11,19,5,11,21]];},
      4,{speakerSetup = [[3,7,11,15,19,23],[4,8,12,16,20,24],[2,6,10,14,18,22],[1,5,9,13,17,21]];},
      6,{speakerSetup = [[5,11,17,23],[6,12,18,24],[4,10,16,22],[2,8,14,20],[1,7,13,19],[3,9,15,21]];},
      8,{speakerSetup = [[7,15,23],[8,16,24],[6,14,22],[4,12,20],[2,10,18],[1,9,17],[3,11,19],[5,13,21]];},
      12,{speakerSetup = [[11,23],[12,24],[10,22],[8,20],[6,18],[4,16],[2,14],[1,13],[3,15],[5,17],[7,19],[9,21]];},
      {"Invalid number of speakers set! Fix this by calling setupSpeakers(nSpeakers) on this object or this will break. Seriously!".postln;}
    );
    if(printOuts,{//print the speaker setup
      speakerSetup.do({
        arg item, i;
        ("Speaker "++(i+1).asString++" has chromosomes: ").post; 
        item.do({
          arg chromosome;
          (chromosome.asString++" ("++keys[chromosome-1].asString++") ").post;
        });
        "".postln;
      });
    });
  }

  initKeyRange{//init 8 octave spanning frequency set, map SNPs to frequencies
    keys = round(SNPInfo.chromosomesFactor[0..SNPInfo.chromosomesFactor.size-2].normalizeSum*10, 0.125);
    keys.add(0.0);
    keyToFrq = Dictionary.new(8);
    8.do({//setup for 8 octaves
      arg item, i;
      switch(i,
        0, {keyToFrq.put(0.000, this.calcFrqCombination(baseTone));},
        1, {keyToFrq.put(0.125, this.calcFrqCombination(baseTone*2.pow(i)));},
        2, {keyToFrq.put(0.250, this.calcFrqCombination(baseTone*2.pow(i)));},
        3, {keyToFrq.put(0.375, this.calcFrqCombination(baseTone*2.pow(i)));},
        4, {keyToFrq.put(0.500, this.calcFrqCombination(baseTone*2.pow(i)));},
        5, {keyToFrq.put(0.625, this.calcFrqCombination(baseTone*2.pow(i)));},
        6, {keyToFrq.put(0.750, this.calcFrqCombination(baseTone*2.pow(i)));},
        7, {keyToFrq.put(0.875, this.calcFrqCombination(baseTone*2.pow(i)));}
      );
    });
  }

  calcFrqCombination{//calculate tones for bases and their combinations for a given set of notes from the same octave
    arg baseTones;
    ^Dictionary.newFrom(List[
      SNPInfo.a, baseTones[0], 
      SNPInfo.c, baseTones[1], 
      SNPInfo.g, baseTones[2], 
      SNPInfo.t, baseTones[3], 
      SNPInfo.a-SNPInfo.c, (baseTones[0]+baseTones[1])/2, 
      SNPInfo.a-SNPInfo.g, (baseTones[0]+baseTones[2])/2, 
      SNPInfo.a-SNPInfo.t, (baseTones[0]+baseTones[3])/2, 
      SNPInfo.c-SNPInfo.g, (baseTones[1]+baseTones[2])/2, 
      SNPInfo.c-SNPInfo.t, (baseTones[1]+baseTones[3])/2, 
      SNPInfo.g-SNPInfo.t, (baseTones[2]+baseTones[3])/2]
    );
  }

  addSNPSynths{//Synthdefs for base pairs, single bases and the MT SNPs
    "Adding SynthDef for base pairs -> \base_pair".postln;
    SynthDef(\base_pair, {|out=0, freq=#[0.0,0.0,0.0] ,amplitude=0.6, attackTime = 0.01, releaseTime = 0.3, curve = -4| 
    var env = EnvGen.kr(
        Env.perc(attackTime,releaseTime,amplitude,curve),doneAction:2//free the enclosing Synth when done
      );
    Out.ar(
      sonBus.index+out,//speaker to play on
      SinOsc.ar(//sine tone for the base pair
        freq[0],0,env,
        SinOsc.ar(//sine tone for the first (lower) resolver
          freq[1],0,env*0.5
        )+
        SinOsc.ar(//sine tone for the second (upper) resolver
          freq[2],0,env * 0.5
        )
      )
    );}, variants: (//variants for 23 first chromosomes
      1: [amplitude: 0.10, attackTime:0.01, releaseTime:0.7, curve:-4],//0.125
      2: [amplitude: 0.10, attackTime:0.01, releaseTime:0.7, curve:-4],//0.125
      3: [amplitude: 0.08, attackTime:0.01, releaseTime:0.6, curve:-4],//0.250
      4: [amplitude: 0.08, attackTime:0.01, releaseTime:0.6, curve:-4],//0.250
      5: [amplitude: 0.08, attackTime:0.01, releaseTime:0.6, curve:-4],//0.250
      6: [amplitude: 0.08, attackTime:0.01, releaseTime:0.6, curve:-4],//0.250
      7: [amplitude: 0.08, attackTime:0.01, releaseTime:0.6, curve:-4],//0.250
      8: [amplitude: 0.08, attackTime:0.01, releaseTime:0.6, curve:-4],//0.250
      9: [amplitude: 0.08, attackTime:0.01, releaseTime:0.6, curve:-4],//0.250
      10: [amplitude: 0.06, attackTime:0.01, releaseTime:0.5, curve:-2],//0.375
      11: [amplitude: 0.06, attackTime:0.01, releaseTime:0.5, curve:-2],//0.375
      12: [amplitude: 0.06, attackTime:0.01, releaseTime:0.5, curve:-2],//0.375
      13: [amplitude: 0.06, attackTime:0.01, releaseTime:0.5, curve:-2],//0.375
      14: [amplitude: 0.06, attackTime:0.01, releaseTime:0.5, curve:-2],//0.375
      15: [amplitude: 0.06, attackTime:0.01, releaseTime:0.5, curve:-2],//0.375
      16: [amplitude: 0.04, attackTime:0.01, releaseTime:0.5, curve:-2],//0.500
      17: [amplitude: 0.04, attackTime:0.01, releaseTime:0.5, curve:-2],//0.500
      18: [amplitude: 0.04, attackTime:0.01, releaseTime:0.5, curve:-2],//0.500
      19: [amplitude: 0.04, attackTime:0.01, releaseTime:0.5, curve:-2],//0.750
      20: [amplitude: 0.05, attackTime:0.01, releaseTime:0.5, curve:-2],//0.625
      21: [amplitude: 0.05, attackTime:0.01, releaseTime:0.5, curve:-2],//0.875
      22: [amplitude: 0.05, attackTime:0.01, releaseTime:0.5, curve:-2],//0.875
      23: [amplitude: 0.05, attackTime:0.01, releaseTime:0.5, curve:-2]//0.875
    )).add;
    "Adding SynthDef for single bases -> \base_single".postln;
    SynthDef(\base_single, {|out=0, freq=#[0.0,0.0] ,amplitude=0.6, attackTime = 0.01, releaseTime = 0.3, curve = -4|
      var env = EnvGen.kr(
        Env.perc(attackTime,releaseTime,amplitude,curve),doneAction:2//free the enclosing Synth when done
      );
      Out.ar(
        sonBus.index+out,
        Saw.ar(//sine tone for the base
          freq[0],env,SinOsc.ar(//sine tone for the resolver
            freq[1],0,env*0.5
          )
        )
      );},variants: (//variants for X and Y chromosomes
        23:[amplitude: 0.07, attackTime: 0.01, releaseTime: 0.5, curve: -4],//0.250 -> X
        24:[amplitude: 0.10, attackTime: 0.01, releaseTime: 0.7, curve: -4]//0.75 ->Y
    )).add;
    "Adding SynthDef for MT bases -> \base_mt".postln;
    SynthDef(\base_mt, {|startPosition = 0, freq = #[0.0,0.0], attackTime = 0.01, releaseTime = 1.5, amplitude = 0.4, curve = -4 |
      var mtSynth, panAround; 
      var env = EnvGen.kr(
        Env.perc(attackTime,releaseTime,amplitude,curve),doneAction:2//free the enclosing Synth when done
      );
      mtSynth = Saw.ar(//sine tone for the base
        freq[0],env,SinOsc.ar(//sine tone for the resolver
          freq[1],0,env*0.5
        )
      );
      panAround = PanAz.ar(
        numChannels,//span the whole number of channels available
        mtSynth,//use the MT Synth as input
        LFSaw.kr(2,0),//pan around TODO: + startPosition
        0.5,//control level
        2,//width of sound
        startPosition//random starting point
      );
      Out.ar(sonBus, panAround);
    }).add;
  }

  addCompressionSynths{
    "Adding SynthDef for compression -> \compressor".postln;
    SynthDef(\compressor, {|inBus|
      var in,compressed;
      in = In.ar(inBus,numChannels);
      compressed = Compander.ar(
        in,//signal in
        in,//control signal
        0.5,//threshold
        1,//slopeBelow
        0.3,//slopeAbove
        0.002,//clampTime
        0.01//relaxTime
      );
      ReplaceOut.ar(0, compressed*0.1);
      Out.ar(recBus, compressed*0.1);
    }).add;
  }

  startDSPSynths{//start compression and possibly recording Synths
    ("Starting compression Synth.").postln;
    Synth(\compressor, [inBus:sonBus], compressionGroup);//play compression Synth
    compressionGroup.run(true);//explicitely turn on compressionGroup (needed for pause/play)
    if(record,{//if recording, play recording Synth
      ("Starting recording Synth for recording to file.").postln;
      Synth(\recordSNP, [buffer: this.recordingBuffer], recordingGroup);
    },{//FIXME: Do we have to explicitely deactivate recordingGroup when not used?
      recordingGroup.run(false);
    });
  }

  stopDSPSynths{//stop compression and possibly recording Synths
    Routine{
      2.wait;
      if(record,{
        ("Stopping recording to file.").postln;
        recordingBuffer.close;
        recordingBuffer.free;
        if(recordingGroup.isRunning,{
          recordingGroup.run(false);
        });
      });
      1.wait;
      if(compressionGroup.isRunning,{
        ("Stopping compressor Synth.").postln;
        compressionGroup.run(false);
      });
    }.play;
  }

  playFromTo{//start from a position (if none set, start from the beginning), play to a position (or end, if none set)
    arg fromPosition = 0.0, toPosition = snpDict.positions;//start from position, play to position
    var startTime=0.0;//time to first position (if not playing from the beginning, this stays the same)
    this.startDSPSynths;//start Synths for compression and recording
    isPlaying = true; //set play parameter
    if((fromPosition == 0.0) || (snpDict.positions<fromPosition),{//if playing from start (or out of bounds), calculate start time for the first SNP
      startTime = lengthOfSNP*snpDict.distanceToNextPosition(fromPosition.asFloat);
      currentStep = fromPosition;//set start position
    },{//else start at once 
      currentStep = fromPosition;
    });
    if((toPosition>snpDict.positions) || (toPosition < fromPosition) || (toPosition.isNil),{//if to position is out of bounds or smaller then from, set to total length
      lastStep = snpDict.positions;
    },{//else play up to that position
      lastStep = toPosition;
    });
    ("Starting to play positions: "++currentStep++" - "++lastStep).postln;
    SystemClock.sched(startTime,{//start a SystemClock immediately or with calculated startTime to read from the SNPDict
      arg time;
      var resched = 0.0;
      if((isPlaying) && (snpDict.positions>currentStep) && (currentStep <= lastStep),{//if playing and positions are left, play the position and reschedule SystemClock to the next SNP
//        ("Playing SNP #"++currentStep++" of "++snpDict.positions++".").postln;
        resched = lengthOfSNP*this.playPosition(snpDict.snpAtPosition(snpDict.snpArr[currentStep]), snpDict.snpArr[currentStep]);
        currentStep = currentStep+1.0;
//        ("Rescheduling in "++resched++"s for step #"++currentStep++" of "++snpDict.positions).postln;
        resched;
      },{//end the SystemClock and print out last position
        ("Done playing. Last position: "++(currentStep-1).asString).postln;
        this.stopDSPSynths;
        nil;
      });
    });
  }

  pausePlay{//pause the sonification
    isPlaying = false;
  }

  resumePlay{//resume the sonification from last position played
    isPlaying = true;
    ("current: "++currentStep++" - last: "++lastStep).postln;
    this.playFromTo(currentStep, lastStep);
  }

  playPosition{//play the SNP(s) at a position and return the distance to the next
    arg posDict, position;
    posDict.keysValuesDo{
      arg key, value;
      if(ignoreSNPs.includes(key).not,{//ignore chromosomes if that is set up
        if(includeUnknown,{//if SNPs without resolvers should be ignored, do that
          this.playBase(value);
        },{
          if(value.hasResolver,{
            this.playBase(value);
          });
        });
      });
    };
    ^snpDict.distanceToNextPosition(position);
  }

  playBase{//play the actual base/base pair
    arg snp;
    var baseKey = keyToFrq.at(keys[snp.vecChromosome-1]);
    if(SNPInfo.isBasePair(snp.base),{//play base pairs
      Synth('base_pair.'++snp.vecChromosome.asSymbol, [out: this.findSpeaker(snp.vecChromosome), freq: [baseKey.at(snp.vecBase), baseKey.at(snp.vecResolver[0]), baseKey.at(snp.vecResolver[1])]], synthGroup);
    },{
      if(SNPInfo.isBase(snp.base), {//play single bases
        if(snp.chromosome==\MT, {//play the MT chromosome
          Synth('base_mt', [startPosition: rrand(numChannels,0), freq: [baseKey.at(snp.vecBase), baseKey.at(snp.vecResolver[0])]], synthGroup);
        },{//play parts of the X and the Y chromosome
          Synth('base_single.'++snp.vecChromosome.asSymbol, [out: this.findSpeaker(snp.vecChromosome), freq: [baseKey.at(snp.vecBase), baseKey.at(snp.vecResolver[0])]], synthGroup);
        });
      });
    });
    //update the currently playing base of the chromosome in gui, if it has been spawned
    if(gui.notNil,{
      gui.setIntermediateText(snp.vecChromosome, snp.base);
    });
    baseKey.free;
  }

  findSpeaker{//find the speaker for the chromosome (defined in speakerSetup)
    arg chromosome;
    var speaker = 0;
    speakerSetup.do({
      arg item, i;
      if(item.includes(chromosome),{
        speaker = i;
      });
    });
    ^speaker;
  }

  calcSNPTime{//calculate the clock time for a single SNP
    arg playTime;
    var snpTime;
    snpTime = ((1/SNPInfo.lengthAtOneMs)*playTime)/1000;
    ^snpTime;
  }

  queryTimeAndPosition{//query current time and position
    ("Positions: "++currentStep.asString++" - "++lastStep.asString++".").postln;
    ("Play time: "++(currentStep*lengthOfSNP*1000).asString++"s - "++(lastStep*lengthOfSNP*1000).asString++"s.").postln;
  }

  // create a new SNPGUI instance
  spawnView{
    gui = SNPGUI.new(speakerSetup);
  }
}