public void BuildTexture() //, ParseDNA parseDNA) {
//this.DNA_Model = parseDNA;
{
Debug.Log("inside build texture");
string[] val = DNA_Model.data[key];
string sequence = val[1];
var texture = new Texture2D(textureX, textureY, TextureFormat.BGRA32, true);
GetComponent <Renderer>().material.mainTexture = texture;
texture.SetPixel(textureX, textureY, Color.black); // mark the end of this texture.
Debug.Log("sequence: " + sequence);
for (int i = 0; i < sequence.Length; i++)
{
Nuc n = Nucleotide.CharToNuc(sequence[i]);
texture.SetPixel(i % textureX, i / textureX, Nucleotide.defaultColor[n]);
}
texture.filterMode = FilterMode.Point;
texture.Apply();
}
public virtual Nuc[] RandomDNA(int length)
{
Nuc[] array = new Nuc[length];
for (int i = 0; i < length; i++)
{
array[i] = GetRandomNuc();
}
return(array);
}
//NOTICE: VERY SIMILAR TO GETPEPTIDE. @todo: create a common helper function for these two functions.
public int getPeptidePos(string name, int pos, Nuc n, Seq type)
{
Debug.Log("getPeptidePos");
int index;
int offset = 0;
FASTAModel m = registerModel(type); //lol
if (m.GetType() == typeof(RNAModel))
{
offset = (m as RNAModel).exonStartIndices[0];
}
else //dna model, uses start index.
{
offset = (m as DNAModel).indexStart;
}
string key = name + "," + name + ":" + type.ToString() + "," + Seq.AA.ToString();
if (currentAlignment == null || !currentAlignment.id.Equals(key))
{
Consensus alignment;
Debug.Log("getPeptidePos, key: " + key);
if (alignments.TryGetValue(key, out alignment))
{
currentAlignment = alignment;
}
else //make the alignment object.
{
if (proteinSeq == null)
{
registerProteinModel();
}
alignment = seqAligner.alignTo3DProtein(name, type, proteinSeq._3DSeq);
alignment.id = key;
alignments[key] = alignment; //warning, overwrite the old val at the given key!
}
currentAlignment = alignment;
index = alignment.getResNum(pos - offset, n);
}
else
{
index = currentAlignment.getResNum(pos - offset, n);
if (index == -1)
{
Debug.Log("incorrect!!");
}
}
return(index);
}
public int getResNum(int pos, Nuc n)
{
if (nucXaa.Count == 0)
{
AAConsensusNucList();
}
Debug.Log("pos: " + pos);
Debug.Log("nucXaa[0]: " + nucXaa[0]);
Debug.Log(" nucXaa[0].Length: " + nucXaa[0].Length);
string nuc = Char.ToString(nucXaa[0][pos]);
if (Nucleotide.NucToStr(n).Equals(nuc)) //matches our data struct, implying correct alignment
{
return(pos / 3);
}
else
{
//something wrong
//NOTE: it could be the case that the alignment went like so:
// 012 345 678 9
// ATG | GAG | --- | GTA | GGT | //sequence mRNA
// M | somehting | L | something | something //sequence according to 3D protein
// ^
// therefore getResNum(6, G) now refers to ---, L. instead of G of the original pos 6.
// such cases all fall into this branch.
string _1stStr = nucXaa[0];
int numDashes = 0;
for (int i = 0; i < pos; i++)
{
if (_1stStr[i].Equals('-'))
{
numDashes++;
}
if (i == pos - 1 && numDashes % 3 != 0) //eg : --- | -- - |
{
numDashes = ((numDashes / 3) + 1) * 3; // ^
}
}
Debug.Log("numDashes: " + numDashes);
nuc = Char.ToString(nucXaa[0][pos + numDashes]);
if (Nucleotide.NucToStr(n).Equals(nuc))
{
return((pos + numDashes) / 3);
}
Debug.Log("residue can't be found in Consensus for the given seq position in RNA.");
return(-1);
}
}
public virtual void Mutate(int chromosome, int index, Nuc newNuc)
{
if (Count() - 1 > chromosome)
{
return;
}
var chr = Chromosomes.ElementAt(chromosome);
if (chr.Length < index)
{
return;
}
chr[index] = newNuc;
}
private void button1_Click(object sender, EventArgs e)
{
if (textBox1.Text.IsEmpty())
{
Log("请输入设备IP");
return;
}
constrant = new Constrant();
constrant.Init(textBox1.Text);
nuc = new Nuc(constrant);
button1.Enabled = false;
groupBox1.Enabled = true;
groupBox2.Enabled = true;
groupBox3.Enabled = true;
groupBox4.Enabled = true;
}
//niceName: rattus, mus musculus, etc.
//int pos: the position we are interested in
//Nuc n : whether it's A|T|C|G
//Seq type: DNA or RNA. shouldn't be AA.
public string getPeptide(string name, int pos, Nuc n, Seq type)
{
string result;
string key = name + "," + name + ":" + type.ToString() + "," + Seq.AA.ToString();
int index;
int offset = 0;
FASTAModel m = registerModel(type); //could be either DNA or RNA.
if (m.GetType() == typeof(RNAModel))
{
offset = (m as RNAModel).exonStartIndices[0];
}
else //dna model, uses start index.
{
offset = (m as DNAModel).indexStart;
}
Consensus alignment;
if (!alignments.TryGetValue(key, out alignment)) //alignment is null, create one.
{
if (proteinSeq == null)
{
registerProteinModel();
}
Debug.Log("inside getPeptide");
alignment = seqAligner.alignTo3DProtein(name, type, proteinSeq._3DSeq);
alignment.id = key;
alignments[key] = alignment;
}
else
{
// (alignment != null)
}
index = alignment.getResNum(pos - offset, n);
if (index == -1)
{
return("-");
}
result = proteinSeq._3DSeq[index].name;
return(result);
}
public void BuildCDSTexture(List <string> cds)
{
Debug.Log("inside build CDS texture");
string sequence1 = cds[0];
string sequence2 = cds[1];
var texture = new Texture2D(textureX, textureY, TextureFormat.BGRA32, true);
GetComponent <Renderer>().material.mainTexture = texture;
//@todo: get new textureX, textureY values from alignment.
texture.SetPixel(textureX, textureY, Color.black); // mark the end of this texture.
Debug.Log("sequence2: " + sequence2);
if (sequence1.Length != sequence2.Length)
{
throw new Exception("two sequences from alignment are not the same length.");
}
for (int i = 0; i < sequence1.Length; i++)
{
Nuc n1 = Nucleotide.CharToNuc(sequence1[i]);
Nuc n2 = Nucleotide.CharToNuc(sequence2[i]);
if (n1 == n2)
{
texture.SetPixel(i % textureX, i / textureX, Nucleotide.litColor[n1]);
}
else
{
texture.SetPixel(i % textureX, i / textureX, Nucleotide.dimColor[n1]);
}
}
texture.filterMode = FilterMode.Point;
texture.Apply();
}
public static string NucToStr(Nuc n)
{
//PetType pet = (PetType)Enum.Parse(typeof(PetType), value); // See if the conversion succeeded: if (pet == PetType.Dog)
return(n.ToString());
}
public virtual ActionMethod SelectAction(Nuc[] tr)
{
Nuc f = tr[0];
Nuc s = tr[1];
Nuc t = tr[2];
if (f == Nuc.A)
{
if (s == Nuc.A)
{
var r = new ActionMethod(MoveAction);
if (t == Nuc.A)
{
ActionIndex = 1;
}
else if (t == Nuc.T)
{
ActionIndex = 2;
}
else if (t == Nuc.C)
{
ActionIndex = 3;
}
else
{
ActionIndex = 4;
}
return(r);
}
else if (s == Nuc.T)
{
var r = new ActionMethod(MoveAction);
if (t == Nuc.A)
{
ActionIndex = 5;
}
else if (t == Nuc.T)
{
ActionIndex = 6;
}
else if (t == Nuc.C)
{
ActionIndex = 7;
}
else
{
ActionIndex = 8;
}
return(r);
}
else if (s == Nuc.C)
{
var r = new ActionMethod(FightAction);
if (t == Nuc.A)
{
ActionIndex = 1;
}
else if (t == Nuc.T)
{
ActionIndex = 2;
}
else if (t == Nuc.C)
{
ActionIndex = 3;
}
else
{
ActionIndex = 4;
}
return(r);
}
else
{
var r = new ActionMethod(FightAction);
if (t == Nuc.A)
{
ActionIndex = 5;
}
else if (t == Nuc.T)
{
ActionIndex = 6;
}
else if (t == Nuc.C)
{
ActionIndex = 7;
}
else
{
ActionIndex = 8;
}
return(r);
}
}
else if (f == Nuc.T)
{
if (s == Nuc.A)
{
var r = new ActionMethod(WatchAction);
if (t == Nuc.A)
{
ActionIndex = 1;
}
else if (t == Nuc.T)
{
ActionIndex = 2;
}
else if (t == Nuc.C)
{
ActionIndex = 3;
}
else
{
ActionIndex = 4;
}
return(r);
}
else if (s == Nuc.T)
{
var r = new ActionMethod(WatchAction);
if (t == Nuc.A)
{
ActionIndex = 5;
}
else if (t == Nuc.T)
{
ActionIndex = 6;
}
else if (t == Nuc.C)
{
ActionIndex = 7;
}
else
{
ActionIndex = 8;
}
return(r);
}
if (s == Nuc.C)
{
var r = new ActionMethod(ActivateAction);
if (t == Nuc.A)
{
ActionIndex = 1;
}
else if (t == Nuc.T)
{
ActionIndex = 2;
}
else if (t == Nuc.C)
{
ActionIndex = 3;
}
else
{
ActionIndex = 4;
}
return(r);
}
else if (s == Nuc.G)
{
var r = new ActionMethod(ActivateAction);
if (t == Nuc.A)
{
ActionIndex = 5;
}
else if (t == Nuc.T)
{
ActionIndex = 6;
}
else if (t == Nuc.C)
{
ActionIndex = 7;
}
else
{
ActionIndex = 8;
}
return(r);
}
}
else if (f == Nuc.C)
{
if (s == Nuc.A)
{
var r = new ActionMethod(Duplicate);
if (t == Nuc.A)
{
ActionIndex = 1;
}
else if (t == Nuc.T)
{
ActionIndex = 2;
}
else if (t == Nuc.C)
{
ActionIndex = 3;
}
else
{
ActionIndex = 4;
}
return(r);
}
else if (s == Nuc.T)
{
var r = new ActionMethod(Duplicate);
if (t == Nuc.A)
{
ActionIndex = 5;
}
else if (t == Nuc.T)
{
ActionIndex = 6;
}
else if (t == Nuc.C)
{
ActionIndex = 7;
}
else
{
ActionIndex = 8;
}
return(r);
}
}
ActionIndex = 0;
return(new ActionMethod(SleepAction));
}
public virtual int Skip(Nuc[] tr)
{
if (tr.Length != 3)
{
return(0);
}
Nuc f = tr[0];
Nuc s = tr[1];
Nuc t = tr[2];
if (f == Nuc.A)
{
if (s == Nuc.A)
{
return(1);
}
else if (s == Nuc.T)
{
return(2);
}
else if (s == Nuc.C)
{
return(3);
}
else if (s == Nuc.G)
{
return(4);
}
else
{
return(0);
}
}
else if (f == Nuc.T)
{
if (s == Nuc.A)
{
return(5);
}
else if (s == Nuc.T)
{
return(6);
}
else if (s == Nuc.C)
{
return(7);
}
else if (s == Nuc.G)
{
return(8);
}
else
{
return(0);
}
}
else if (f == Nuc.C)
{
if (s == Nuc.A)
{
return(-1);
}
else if (s == Nuc.T)
{
return(-2);
}
else if (s == Nuc.C)
{
return(-3);
}
else if (s == Nuc.G)
{
return(-4);
}
else
{
return(0);
}
}
else if (f == Nuc.G)
{
if (s == Nuc.A)
{
return(-5);
}
else if (s == Nuc.T)
{
return(-6);
}
else if (s == Nuc.C)
{
return(-7);
}
else if (s == Nuc.G)
{
return(-8);
}
else
{
return(0);
}
}
return(0);
}
