//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);
}
// translate(mRNA) <== pairwise-align ==> 3D Seq
// Consensus object will be loaded with the aa seq to aa seq (from 3d protein) alignments
// The first aa seq will actually have to map back to mRNA nucleotides. But that's job of Consensus.
// Not sure if it's the best way to do this however. Open to better ideas.
public Consensus alignTo3DProtein(string name, Seq type, List <Residue> _3DSeq)
{
if (pam100 == null)
{
populatePAM();
}
FASTAModel model = getFASTAModel(type);
string key = model.niceName[name];
string seq = model.data[key][1];
id = name + "," + name + ":" + type.ToString() + "," + Seq.AA.ToString();
Consensus c;
if (!seqModel.alignments.TryGetValue(id, out c))
{
c = new Consensus();
//map DNA, AA. onto nucXaa.
List <List <string> > mapping = new List <List <string> >();
List <string> nuc = new List <string>();
List <string> aa = new List <string>();
for (int i = 0; i < seq.Length / 3; i++)
{
string codon = "" + seq[i * 3] + seq[i * 3 + 1] + seq[i * 3 + 2];
string AA3 = GeneticCode.DNAtoAA[codon];
// Debug.Log("AA3: " + AA3);
string oneLetter = AminoAcid.OneLetterCode[AA3];
nuc.Add(codon);
aa.Add(oneLetter);
}
mapping.Add(nuc);
mapping.Add(aa);
c.nucMapAA = mapping;
startPairwise(name, type, name, Seq.AA);
if (c == null)
{
Debug.Log("pairwise algorithm did not work!!!"); //not sure how it follows that if c is null, alg didnt work.
}
c.aas = result;
seqModel.alignments[id] = c;
}
return(c);
}
//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);
}
