From c0eed84e4d0dfec58d485b97f8ee96ea3467894a Mon Sep 17 00:00:00 2001
From: David Runge <dave@sleepmap.de>
Date: Mon, 30 Mar 2015 19:33:40 +0200
Subject: SNPAudio.sc: Moving/Renaming SNPSonificator.sc to SNPAudio.sc

---
 SNPAudio.sc       | 399 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 SNPSonificator.sc | 399 ------------------------------------------------------
 2 files changed, 399 insertions(+), 399 deletions(-)
 create mode 100644 SNPAudio.sc
 delete mode 100644 SNPSonificator.sc

diff --git a/SNPAudio.sc b/SNPAudio.sc
new file mode 100644
index 0000000..a86a750
--- /dev/null
+++ b/SNPAudio.sc
@@ -0,0 +1,399 @@
+SNPSonificator {
+  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);
+  }
+}
diff --git a/SNPSonificator.sc b/SNPSonificator.sc
deleted file mode 100644
index a86a750..0000000
--- a/SNPSonificator.sc
+++ /dev/null
@@ -1,399 +0,0 @@
-SNPSonificator {
-  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);
-  }
-}
-- 
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