/// <summary>
/// Method for calculating and displaying
/// </summary>
/// <param name="orf"></param>
/// <param name="amino"></param>
private void CalculateAndDisplayORF(List <string> orf, List <string> amino)
{
Data = new DataTable();
int columnIdx = 0;
Data.Columns.Add(new DataColumn("CPB"));
foreach (var k in ORF.aminoORFseq)
{
Data.Columns.Add(new DataColumn(columnIdx.ToString()));
columnIdx++;
}
// CPBcalculator method initialization
try
{
OriginalCPBscoreTextBox.Text = ORF.CPBcalculator(ORF.orfSeq).ToString();
// datagrid filling
ORF.aminoORFseq.Insert(0, "");
ORF.orfSeq.Insert(0, OriginalCPBscoreTextBox.Text);
Data.Rows.Add(ORF.aminoORFseq.ToArray());
Data.Rows.Add(ORF.orfSeq.ToArray());
ORF.aminoORFseq.RemoveAt(0);
ORF.orfSeq.RemoveAt(0);
OptimizationDataGrid.ItemsSource = Data.DefaultView;
GeneticCode.UploadGeneticCode();
ORF.aminoAcidCounts = ORF.aminoORFseq.GroupBy(i => i)
.ToDictionary(i => i.Key, i => i.Count());
NcScoreTextBox.Text = ORF.NcCalculator(ORF.orfSeq, ORF.aminoAcidCounts).ToString();
}
catch
{
string message = "Something went wrong. Please verify your FASTA file for incorrect codons or check your ranking.";
ModernDialog.ShowMessage(message.ToString(), "Error", MessageBoxButton.OK);
}
}
public Zombie(GeneticCode code)
{
this.code = code;
setFuel(200);
addBehaviours();
updateWeights();
}
public float[] Hear()
{
float[] output = new float[8 * 3];
var sounds = SoundManager.instance.GetHearable(this);
int i = 0;
foreach (var item in sounds)
{
if (sounds.Count - i < 8)
{
i++;
continue;
}
else
{
output[i] = GetAngle(item.Value);
output[i + 1] = GeneticCode.ToInt(item.Value.wave);
output[i + 2] = item.Key;
i++;
}
}
return(output);
}
protected NucleotideSequence(string sequence, AlphabetType alphabet, GeneticCode geneticCode = GeneticCode.Standard, IEnumerable <string> tags = null)
: this(sequence, alphabet, geneticCode)
{
if (tags != null)
{
_tags = new HashSet <string>(tags);
}
}
public void Decoding_string_should_ignore_prefixed_operators()
{
Func<string, string> g = s => GenoTypes().Single(x => x.Value.Equals(s)).Key;
Func<string> generateBits = () => string.Format("{0}{1}{2}{3}", g("/"), g("7"), g("+"), g("4"));
var sut = new GeneticCode(new Random());
Assert.Equal("7+4", sut.Decode(generateBits()));
}
public GeneticCode[] MutateNumber(int times)
{
GeneticCode[] gCodes = new GeneticCode[times];
gCodes[0] = this;
for (int i = 1; i < times; i++)
{
gCodes[i] = new GeneticCode(gCodes[i - 1]);
}
return(gCodes);
}
private static GeneticCode DuplicateGeneticCode(GeneticCode oGeneticCode)
{
GeneticCode newGeneticCode = new GeneticCode();
float mutationChance = oGeneticCode.GetMutationChance();
float noise = oGeneticCode.GetNoise();
float noiseChance = oGeneticCode.GetNoiseChance();
List <byte> newGeneticCodeList = new List <byte>();
List <byte> oldGeneticCodeList = oGeneticCode.GetGeneticCodeList();
//Debug.Log("Mutation Chance " + mutationChance);
int randomInsert = Random.Range(0, oldGeneticCodeList.Count);
//randomInsert = 1;
//Debug.Log("Random Insert at = " + randomInsert);
byte randomValue = (byte)(Random.Range(0, 255));
randomValue = 10;
//Debug.Log("Random Value = " + randomValue);
for (int i = 0; i < oldGeneticCodeList.Count; i++)
{
bool addNoise = false;
if (Random.Range(0f, 1f) > noiseChance)
{
addNoise = true;
}
if (Random.Range(0f, 1f) < mutationChance)
{
Debug.Log("Random Insertion @ " + i);
newGeneticCodeList.Add((byte)(Random.Range(0, 255)));
Debug.Log("Safely inserted");
}
byte byteToAdd = oldGeneticCodeList[i];
if (addNoise)
{
//Debug.Log("Adding noise to " + byteToAdd);
byteToAdd = (byte)(byteToAdd * Random.Range(-noise, +noise));
//Debug.Log("Added noise : " + byteToAdd);
}
newGeneticCodeList.Add(oldGeneticCodeList[i]);
}
Debug.Log("Exited");
newGeneticCode.SetGeneticCodeList(newGeneticCodeList);
//newGeneticCodeList = new List<byte>();
return(newGeneticCode);
}
public static Population NewPopulation(float target, int size, Random randomness)
{
var decoder = new GeneticCode(randomness);
return new Population(target,
Enumerable.Range(0, size)
.Select(id =>
Chromosome.New(target,
decoder)),
randomness,
bits => decoder.Decode(bits));
}
protected NucleotideSequence(string sequence, AlphabetType alphabet, GeneticCode geneticCode)
{
NucleotideAlphabet = new NucleotideAlphabet(alphabet, geneticCode);
ActiveAlphabet = alphabet;
GeneticCode = geneticCode;
var trimmedSequence = sequence.Trim();
VerifyAndInitializeNucleotides(trimmedSequence);
Sequence = trimmedSequence;
}
public Human(GeneticCode code)
{
this.code = code;
type = HumanType.Child;
firstUpdate = true;
secondsUntilMaturity = 5f + (Random.value * 10f);
state = HumanState.Idle;
setFuel(200);
addBehaviours();
updateWeights();
World.world.updateHumanState(getID());
}
public void SpawnCreature(GeneticCode GCode)
{
if (creatures.Count < MaxCreature)
{
Creature newCreature = Instantiate(toInst);
newCreature.Init(BrainMaker.OneSizeBrain(newCreature), GCode, new Vector2(0, 0), new Vector2(1, 0));
creatures.Add(newCreature);
}
}
protected NucleotideSequence(string sequence, AlphabetType alphabet, GeneticCode geneticCode, Dictionary <Nucleotide, long> symbolCounts, IEnumerable <string> tags)
{
NucleotideAlphabet = new NucleotideAlphabet(alphabet, geneticCode);
ActiveAlphabet = alphabet;
GeneticCode = geneticCode;
Sequence = sequence;
SymbolCounts = symbolCounts;
if (tags != null)
{
_tags = new HashSet <string>(tags);
}
}
public GeneticCode(GeneticCode parent)
{
genes = new List <Gene>();
foreach (var g in parent.GetGenes())
{
foreach (var m in g.Mutate())
{
genes.Add(m);
}
}
fillerCode = parent.MutateFiller();
decoded = true;
}
public void Init(Brain brain, GeneticCode GCode, Vector2 pos, Vector2 ang)
{
this.brain = brain;
Genotype = GCode;
stats = new Stats(new List <StatGene>());
stomac = new Stomac(this);
stats = new Stats(Genotype.GetGenes(), this);
brain.owner = this;
position = pos;
orientation = ang;
}
public void SpawnCreature(Brain brain, GeneticCode GCode)
{
if (creatures.Count < MaxCreature)
{
Creature newCreature = Instantiate(toInst);
newCreature.Init(brain, GCode, new Vector2(0, 0), new Vector2(1, 0));
creatures.Add(newCreature);
}
//creatures.Add()
}
public NucleotideAlphabet(AlphabetType nucleotideAlphabet, GeneticCode geneticCode)
{
if (nucleotideAlphabet == AlphabetType.ExtendedProtein || nucleotideAlphabet == AlphabetType.StandardProtein)
{
throw new ArgumentException(String.Format(AlphabetDataProvider.InvalidNucleotideAlphabet, nucleotideAlphabet));
}
GeneticCode = geneticCode;
AllowedSymbols = AlphabetDataProvider.GetAllowedNucleotideSymbols(nucleotideAlphabet);
ComplementTable = AlphabetDataProvider.GetComplementTable(nucleotideAlphabet);
TranscriptionTable = AlphabetDataProvider.GetTranscriptionTable(nucleotideAlphabet);
TranslationTable = AlphabetDataProvider.GetTranslationTable(geneticCode, nucleotideAlphabet);
GcContentSymbols = AlphabetDataProvider.GcContentSymbols(nucleotideAlphabet);
}
public void spawnChild(uint motherID, Vector2 location, GeneticCode code)
{
Boid mother = getBoid(motherID);
float fuel = mother.getFuel();
mother.setFuel(fuel * 0.75f);
Boid child = new Human(code);
child.setPosition(location);
child.setFuel(fuel * 0.5f);
boidsToAdd.Add(child);
humansAlive++;
}
public GeneticCode(GeneticCode a, float mutationRate)
{
data = new List <float>();
for (int i = 0; i < a.getLength(); i++)
{
if (Random.value < mutationRate)
{
data.Add(Random.value);
}
else
{
data.Add(a.getValue(i));
}
}
}
public RnaSequence(string rawBasePairs, AlphabetType alphabet, GeneticCode geneticCode = GeneticCode.Standard, IEnumerable <string> tags = null)
: base(rawBasePairs, alphabet, geneticCode, tags)
{
switch (alphabet)
{
case AlphabetType.AmbiguousRna:
break;
case AlphabetType.StrictRna:
break;
default:
throw new ArgumentException(String.Format(InvalidAlphabetForSequenceType, alphabet, GetType()));
}
}
public ProteinAlphabet(AlphabetType proteinAlphabet, GeneticCode geneticCode = GeneticCode.Standard)
{
switch (proteinAlphabet)
{
case AlphabetType.ExtendedProtein:
break;
case AlphabetType.StandardProtein:
break;
default:
throw new ArgumentException(String.Format(InvalidProteinAlphabet, proteinAlphabet));
}
_activeAlphabet = proteinAlphabet;
_geneticCode = geneticCode;
}
public GeneticCode(GeneticCode a, GeneticCode b, float mutationRate)
{
data = new List <float>();
if (a.getLength() == b.getLength())
{
for (int i = 0; i < a.getLength(); i++)
{
if (Random.value < mutationRate)
{
data.Add(Random.value);
}
else
{
data.Add((a.getValue(i) + b.getValue(i)) / 2.0f);
}
}
}
}
// Start is called before the first frame update
void Start()
{
if (instance == null)
{
instance = this;
}
InitRdm();
Gene.SetMutationConstants(duplication: dupRate, inversion: inverRate, supression: supRate, insertion: inserRate);
creatures = new HashSet <Creature>();
var fill = GeneticCode.GetNewFiller();
SpawnCreature(new GeneticCode("HXHOOOOOHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh", fill));
SpawnCreature(new GeneticCode("HXHVHHHxHXHOhhhxHXHOhhhxHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh", fill));
Tick();
}
public float[] Look()
{
float[] output = new float[8 * 3];
int i = 0;
foreach (var item in GetInRange(this, stats.vDistance, stats.vAngle))
{
if (i >= 8)
{
break;
}
output[i] = GeneticCode.ToInt(item.Value.GetPheno());
output[i + 1] = GetAngle(item.Value);
output[i + 2] = GetDistance(item.Value);
i++;
}
return(output);
}
/// <summary>
/// return percentage of similarity between 2 genomes.
/// </summary>
/// <param name="g1"></param>
/// <param name="g2"></param>
/// <returns></returns>
static public float Compare(GeneticCode g1, GeneticCode g2)
{
if (!g1.decoded)
{
g1.Decode();
}
if (!g2.decoded)
{
g2.Decode();
}
int success = 0;
int fail = 0;
CompareGenes(g1.genes, g2.genes, ref success, ref fail);
CompareFiller(g1.fillerCode, g2.fillerCode, ref success, ref fail);
//Debug.Log(success + "s");
//Debug.Log(fail + "f");
return((float)success / (float)(success + fail));
}
void SetValue()
{
value = GeneticCode.ToInt(geneticString.Substring(TYPELENGTH + 2));
}
void Start()
{
gameObject.AddComponent <MeshFilter>();
currentStage = CurrentStage.expanding;
//Debug.Log("Start being called");
if (geneticCode == null)
{
//Debug.Log(gameObject.name + " is creating a genetic code!");
geneticCode = new GeneticCode();
}
else
{
//Debug.Log(gameObject.name + " already have a genetic code!");
}
parts = new List <GameObject>();
geneticCodeOperator = new GeneticCodeOperator();
geneticBuildingInstructions = new GeneticBuildingInstructions();
#region neural network tests
/*
* neural = new NetworkModel();
* neural.Layers.Add(new NeuralLayer(4, 1, "INPUT"));
* neural.Layers.Add(new NeuralLayer(2, 1, "HIDDEN"));
* neural.Layers.Add(new NeuralLayer(4, 2, "OUTPUT"));
*
* neural.Build();
* //Debug.Log("----Before Training------------");
* neural.Print();
*
* NeuralData X = new NeuralData(4);
* X.Add(1, 1);
* X.Add(1, 1);
* X.Add(1, 0);
* X.Add(1, 1);
*
* NeuralData Y = new NeuralData(4);
* Y.Add(1);
* Y.Add(1);
* Y.Add(0);
* Y.Add(0);
*
* neural.Train(X, Y, iterations: 10, learningRate: 0.1);
* //List<double> outputs = neural.Process(X);
*
*/
#endregion
//Debug.Log("----After Training------------");
//for(int i = 0; i < outputs.Count; i++)
//{
// Debug.Log($"Output{i} = {outputs[i]}");
//}
//neural.Print();
//X.Add(2.0f);
//X.Add(3.0f);
//List<double> outputs = neural.Train(X);
//Debug.Log("Output");
//for (int i = 0; i < outputs.Count; i++)
//{
// Debug.Log($"Out{i} = {outputs[i]}");
//}
List <byte> geneticCodeList = geneticCode.GetGeneticCodeList();
geneticCodeOperator.ProcessGeneticCode(gameObject, ref geneticCodeList, geneticBuildingInstructions.GetBuildingInstructions());
geneticCode.SetGeneticCodeList(geneticCodeList);
//read geneticCode
//operateGeneticCode
}
public void SetGeneticCode(GeneticCode _geneticCode)
{
geneticCode = _geneticCode;
}
public override void update(float deltaTime, List <Boid> neighbors, List <Boid> touching)
{
HumanType initialType = type;
HumanState initialState = state;
bool seesZombie = false;
for (int i = 0; i < neighbors.Count; i++)
{
if (neighbors[i].getFaction() == "Zombie")
{
state = HumanState.Hunted;
seesZombie = true;
}
}
if (seesZombie == false)
{
state = HumanState.Idle;
}
for (int i = 0; i < touching.Count; i++)
{
if (touching[i].getFaction() == "Food")
{
addFuel(touching[i].getFuel());
World.world.removeFood(touching[i].getID());
}
else if (type == HumanType.Female && touching[i].getFaction() == "Male")
{
//Become pregnant
type = HumanType.PregnantFemale;
childCode = new GeneticCode(touching[i].getGeneticCode(), code, 0.05f);
secondsUntilBirth = 7f;
}
}
if (getFuel() < 0)
{
World.world.killHuman(getID());
return;
}
else if (getFuel() < 50)
{
state = HumanState.Hungry;
}
if (type == HumanType.PregnantFemale)
{
secondsUntilBirth -= deltaTime;
if (secondsUntilBirth < 0)
{
//Give birth
World.world.spawnChild(getID(), getPosition(), childCode);
type = HumanType.Female;
}
}
else if (type == HumanType.Child)
{
secondsUntilMaturity -= deltaTime;
if (secondsUntilMaturity < 0)
{
//Become an adult
if (Random.value < 0.5f)
{
type = HumanType.Male;
}
else
{
type = HumanType.Female;
}
}
}
secondsAlive += deltaTime;
if (firstUpdate || initialState != state || initialType != type)
{
firstUpdate = false;
updateWeights();
World.world.updateHumanState(getID());
}
return;
}
internal RnaSequence(string safeSequence, AlphabetType alphabet, GeneticCode geneticCode, Dictionary <Nucleotide, long> symbolCounts, IEnumerable <string> tags = null)
: base(safeSequence, alphabet, geneticCode, symbolCounts, tags)
{
}
public override void Express(Creature owner)
{
int value = GeneticCode.ToInt(geneticString.Substring(4));
switch (geneticString.Substring(2, 2))
{
default:
{
break;
}
case "HH":
{
break;
}
case "HV":
{
owner.stats.size += value;
break;
}
case "HO":
{
owner.stats.speed += value;
break;
}
case "HX":
{
owner.stats.GestationTime += value;
break;
}
case "VH":
{
owner.stats.GestationMaturity += value;
break;
}
case "VV":
{
owner.stats.strength += value;
break;
}
case "VO":
{
//owner.stats
break;
}
case "VX":
{
//owner.stats
break;
}
case "OH":
{
//owner.stats
break;
}
case "OV":
{
//owner.stats
break;
}
case "OO":
{
//owner.stats
break;
}
case "OX":
{
//owner.stats
break;
}
case "XH":
{
//owner.stats
break;
}
case "XV":
{
//owner.stats
break;
}
case "XO":
{
//owner.stats
break;
}
case "XX":
{
//owner.stats
break;
}
}
}
void SetType()
{
type = (StatType)GeneticCode.ToInt(geneticString.Substring(0, TYPELENGTH));
}
//Contructor for the brain.
public Brain(Citizen _body, GeneticCode DNA)
{
body = _body;
geneticCode = DNA;
location = body.GetLocation();
}