//getResNum for the UV.
public int getResidueNum(Vector2 uv)
{
int result;
Debug.Log("Splitting.cs: getResidueNum(uv): " + uv);
if (DNA_Panel == null)
{
DNA_Panel = DNAPanelController.Instance.DNA_Panel;
}
if (DNA_Panel.GetComponent <Renderer>().enabled)
{
if (seqModel == null)
{
seqModel = new SequenceModel();
}
int DNASeqNum = DNAPanelController.Instance.getSeqPos(uv);
string nuc = DNAPanelController.Instance.getNucAcidForUV(uv);
Debug.Log("Pos: " + DNASeqNum + ", DNA: " + nuc + ", seqModel: " + seqModel);
string nucStr = nuc.Split(':')[0];
//string niceName, int pos, Nuc n, Seq type
int pos = seqModel.getPeptidePos("Rattus norvegicus", DNASeqNum, Nucleotide.StrToNuc(nucStr), Seq.DNA);
// residueSeq[x].name;
return(pos);
}
else
{
//do it
Debug.Log("RNA panel");
}
return(0);
}
void OnTriggerExit(Collider other)
{
if (other.tag == "Nucleotide")
{
waiting = null;
}
}
public NucleotideCouple buildHalfCoupleChainFromOneSingle(Nucleotide chain)
{
if (chain.isPaired)
{
return(null);
}
chain = getHeadOfSingleChain(chain);
Nucleotide nhead = chain;
NucleotideCouple n = (Instantiate(couplePrefab) as GameObject).GetComponent <NucleotideCouple>();
NucleotideCouple head = n;
n.setLeftColor(chain.getColor());
n.setType(chain.type, Nucleotide.Type.Empty);
n.needHelix = false;
while (chain.next)
{
chain = chain.next;
n.next = (Instantiate(couplePrefab) as GameObject).GetComponent <NucleotideCouple>();
n.next.setLeftColor(chain.getColor());
n.next.setType(chain.type, Nucleotide.Type.Empty);
n.next.prev = n;
n.next.needHelix = false;
n.next.transform.rotation = nhead.transform.rotation;
n = n.next;
}
head.transform.rotation = nhead.transform.rotation;
head.transform.position = nhead.transform.position;
head.broadcastUpdateTransform();
destroySingleChain(chain);
return(head);
}
public static int[][] GetWeightMatrix(Nucleotide[][] map)
{
var w = new int[map.Length][];
for (int i = 0; i < map.Length; i++)
w[i] = new int[map.Length];
if (map.Length < 100)
{
for (int i = 0; i < map.Length; i++)
for (int j = 0; j < i; j++)
{
var a = Alignment.Align(map[i], map[j], i, j);
w[i][j] = a.Weight;
w[j][i] = a.Weight;
}
}
else
{
Parallel.ForEach(Enumerable.Range(0, map.Length),
new ParallelOptions {MaxDegreeOfParallelism = 8},
i =>
{
for (int j = 0; j < i; j++)
{
var a = Align(map[i], map[j], i, j);
w[i][j] = a.Weight;
w[j][i] = a.Weight;
}
});
}
return w;
}
public BasicSmEncoding(string symbols, string name, MoleculeType moleculeType, bool hasGaps, bool hasAmbiguity, bool hasTerminations)
{
Name = name;
HasGaps = hasGaps;
HasAmbiguity = hasAmbiguity;
HasTerminations = hasTerminations;
// Load the symbols into items
string trimmed = symbols.Trim().ToUpper(CultureInfo.InvariantCulture); // should be no leading or trailing whitespace, but why take chances?
_symbols = new ISequenceItem[trimmed.Length];
byte i = 0; // index into mappings
foreach (char c in trimmed)
{
if (moleculeType == MoleculeType.DNA || moleculeType == MoleculeType.RNA || moleculeType == MoleculeType.NA)
{
Nucleotide item = new Nucleotide(i, c, c.ToString());
_symbols[i] = item;
_values.Add(c, item);
}
else if (moleculeType == MoleculeType.Protein)
{
AminoAcid item = new AminoAcid(i, c, c.ToString());
_symbols[i] = item;
_values.Add(c, item);
}
i++;
}
}
/// <summary>
/// Создаёт мотив по выровненным цепочкам.
/// </summary>
public static Motiff ExtractMotiff(Nucleotide[][] map, int[] mapFactor = null)
{
bool started = false;
var len = map.Max(p => p.Length);
var freq = new List<int[]>();
if (mapFactor == null)
mapFactor = Enumerable.Repeat(1, map.Length).ToArray();
var cnt = mapFactor.Sum();
for (int i = 0; i < len; i++)
{
var tmp = new int[4];
for (int k = 0; k < map.Length; k++)
{
var m = map[k];
if (m.Length <= i || (int) m[i] > 3)
continue;
tmp[(int) m[i]] += mapFactor[k];
}
if (!started)
{
if (tmp.Sum() > cnt / 2)
started = true;
else
continue;
}
freq.Add(tmp);
}
var drop = freq.ToArray().Reverse().TakeWhile(p => p.Sum() < cnt / 2).Count();
freq.RemoveRange(freq.Count - drop, drop);
return new Motiff(cnt, freq.ToArray(), new string(freq.Select(p => GetMaskChar(p, cnt)).ToArray()));
}
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();
}
static void Main(string[] args)
{
/*MemoryCache.Default.Add(
* "complement", new byte[] {
* 0, 8, 4, 12, 2,
* 10, 9, 14, 1, 6,
* 5, 13, 3, 11, 7, 15
* }, new CacheItemPolicy() { Priority = CacheItemPriority.NotRemovable }
* );*/
Stopwatch timer = Stopwatch.StartNew();
Nucleotide complement = Nucleotide.Zero;
for (int i = 0; i < 1000; ++i)
{
for (byte j = 0; j < 16; ++j)
{
//complement = (byte)Constants.COMPLEMENTS[(Nucleotide)j];
//complement = ((byte[])MemoryCache.Default.Get("complement"))[j];
complement = (Nucleotide)bytes[j];
}
}
timer.Stop();
Console.WriteLine(timer.Elapsed);
Console.WriteLine(timer.ElapsedMilliseconds);
Console.WriteLine(timer.ElapsedTicks);
Console.ReadLine();
}
public Style getStyle(Nucleotide nuc)
{
var index = nuc.value.lerp(0, Enum.GetValues(typeof(Style)).Length - 1);
foreach (Style style in Enum.GetValues(typeof(Style)))
{
if ((int)style == Math.Floor(index))
{
return(style);
}
}
if (nuc.value <= .33)
{
return(Style.FillAndStroke);
}
else if (nuc.value <= .66 && nuc.value >= .34)
{
return(Style.Fill);
}
else
{
return(Style.Stroke);
}
}
public NucleotideCouple buildCoupleFromOneSingle(Nucleotide n, bool reverse = false)
{
if (n.isPaired)
{
return(null);
}
GameObject couple = Instantiate(couplePrefab) as GameObject;
couple.transform.position = n.transform.position;
couple.transform.rotation = n.transform.rotation;
if (!reverse)
{
couple.gameObject.GetComponent <NucleotideCouple>().setType(n.type, getPairType(n.type));
Color c = n.getColor();
couple.gameObject.GetComponent <NucleotideCouple>().setLeftColor(c);
couple.gameObject.GetComponent <NucleotideCouple>().setRightColor(Color.white);
}
else
{
couple.gameObject.GetComponent <NucleotideCouple>().setType(getPairType(n.type), n.type);
Color c = n.getColor();
couple.gameObject.GetComponent <NucleotideCouple>().setRightColor(c);
couple.gameObject.GetComponent <NucleotideCouple>().setLeftColor(Color.white);
}
couple.gameObject.GetComponent <NucleotideCouple>().tag = "NucleotideCouple";
Destroy(n.gameObject);
return(couple.gameObject.GetComponent <NucleotideCouple>());
}
public float GetScore(Nucleotide[] nucs)
{
if (nucs.Length != Length)
throw new ArgumentException("nucs.Len != " + Length);
if (_cache == null)
_cache = new ProbMotifCache(_data);
var norm = _cache.NormFactor;
var max = 0.0;
foreach (var ds in _cache.DataInversions)
{
var cur = 1.0;
for (int i = 0; i < Length; i++)
{
var nicId = (int)nucs[i];
var d = ds[i];
if (nicId < 4)
cur *= d[nicId];
else
if (nicId == (int) Nucleotide.Any)
cur *= 0.1;
else
throw new NotSupportedException();
}
if (cur > max)
max = cur;
}
return (float)(max*norm);
}
public void SparseSequenceClone()
{
SparseSequence sparseSeq = new SparseSequence(Alphabets.DNA);
sparseSeq.Count = 50;
sparseSeq[0] = Alphabets.DNA.C;
sparseSeq[5] = Alphabets.DNA.G;
sparseSeq[30] = Alphabets.DNA.C;
sparseSeq[44] = Alphabets.DNA.A;
sparseSeq[45] = new Nucleotide('A', "Nucleotide A");
CompoundNucleotide cn = new CompoundNucleotide('M', "Compound");
cn.Add(new Nucleotide('A', "Item A"), 30);
cn.Add(new Nucleotide('C', "Item C"), 20);
sparseSeq[46] = cn;
Assert.AreEqual(sparseSeq.Count, 50);
Assert.AreEqual(sparseSeq.Alphabet, Alphabets.DNA);
Assert.AreSame(sparseSeq[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[5], Alphabets.DNA.G);
Assert.AreSame(sparseSeq[30], Alphabets.DNA.C);
Assert.AreSame(sparseSeq[44], Alphabets.DNA.A);
Assert.AreEqual(sparseSeq[45].Symbol, 'A');
Assert.AreSame(sparseSeq[46], cn);
Assert.AreNotSame(sparseSeq[46], Alphabets.DNA.AC);
for (int i = 0; i < sparseSeq.Count; i++)
{
if (i != 0 && i != 5 && i != 30 && i != 44 && i != 45 && i != 46)
{
Assert.IsNull(sparseSeq[i]);
}
}
SparseSequence sparseSeqClone = sparseSeq.Clone();
Assert.AreEqual(sparseSeqClone.Count, 50);
Assert.AreEqual(sparseSeqClone.Alphabet, Alphabets.DNA);
Assert.AreSame(sparseSeqClone[0], Alphabets.DNA.C);
Assert.AreSame(sparseSeqClone[5], Alphabets.DNA.G);
Assert.AreSame(sparseSeqClone[30], Alphabets.DNA.C);
Assert.AreSame(sparseSeqClone[44], Alphabets.DNA.A);
Assert.AreNotSame(sparseSeqClone[46], cn);
Assert.AreNotSame(sparseSeqClone[46], Alphabets.DNA.AC);
Assert.AreEqual(sparseSeqClone[46].Symbol, 'M');
cn = sparseSeqClone[46] as CompoundNucleotide;
IList <ISequenceItem> sequenceItems = cn.SequenceItems;
Assert.AreEqual(sequenceItems.Count, 2);
Assert.IsTrue(sequenceItems.First(I => I.Symbol == 'A') != null);
Assert.IsTrue(sequenceItems.First(I => I.Symbol == 'C') != null);
for (int i = 0; i < sparseSeqClone.Count; i++)
{
if (i != 0 && i != 5 && i != 30 && i != 44 && i != 45 && i != 46)
{
Assert.IsNull(sparseSeqClone[i]);
}
}
}
private void buildNucleotide()
{
Nucleotide n = (Instantiate(prefab) as GameObject).GetComponent <Nucleotide>();
n.setType(type);
n.transform.position = this.transform.position;
n.transform.rotation = this.transform.rotation;
}
public float GetScore(Nucleotide[] nucs)
{
if(nucs.Length != Length)
throw new ArgumentException("nucs.Len != " + Length);
return _data.Select(ds => ds.Zip(nucs, (a, b) => (a == b || a == Nucleotide.Any) ? 1 : 0).Sum())
.Concat(new[] {0})
.Max()/(float)Length;
}
/// <summary>
/// Lookup an amino acid based on a triplet of nucleotides. U U U for instance
/// will result in Phenylalanine.
/// </summary>
public static AminoAcid Lookup(Nucleotide n1, Nucleotide n2, Nucleotide n3)
{
StringBuilder source = new StringBuilder();
source.Append(n1.Symbol);
source.Append(n2.Symbol);
source.Append(n3.Symbol);
return(codonMap[source.ToString()]);
}
public StrictMotif(Nucleotide[] data)
{
Length = data.Length;
_data = new Nucleotide[4][];
_data[0] = data;
_data[1] = data.Reverse().ToArray();
_data[2] = data.Select(p => p.Inverse()).ToArray();
_data[3] = _data[2].Reverse().ToArray();
}
public virtual long NucleotideCount(Nucleotide nucleotide)
{
if (!AllowedSymbols.Contains(nucleotide))
{
throw new ArgumentException(String.Format(InvalidNucleotideForAlphabetType, nucleotide, ActiveAlphabet));
}
return(!SymbolCounts.ContainsKey(nucleotide) ? 0 : SymbolCounts[nucleotide]);
}
public void setType(Nucleotide.Type t)
{
if (!this.attach)
{
this.attach = (Instantiate(nucleotidePrefab, this.transform.position, this.transform.rotation) as GameObject).GetComponent <Nucleotide>();
}
this.attach.attach();
this.attach.setType(t);
}
public static SuffixArray BuildOne(Nucleotide[] fragments)
{
var tmp = new byte[fragments.Length + 1];
for (int i = 0; i < fragments.Length; i++)
tmp[i] = (byte)fragments[i];
tmp[tmp.Length - 1] = (byte)Nucleotide.End;
var sfx = new SuffixArray(tmp);
return sfx;
}
void OnTriggerExit(Collider other)
{
if (this.attach && other.gameObject.GetComponent <Nucleotide>() == this.attach)
{
this.attach.detach();
this.attach = null;
this.parent.detach(this);
}
}
public void cutPrev()
{
if (this.prev)
{
this.prev.nextBond.SetActive(false);
this.prev.next = null;
}
this.prevBond.SetActive(false);
this.prev = null;
}
/// <summary>
/// Indication of whether or not an ISequenceItem is in the encoding. This is
/// a simple lookup and will only match exactly with items of this encoding. It
/// will not compare items from other encodings that match the same nucleotide.
/// </summary>
public bool Contains(ISequenceItem item)
{
Nucleotide nucleo = item as Nucleotide;
if (nucleo == null)
{
return(false);
}
return(values.Contains(nucleo));
}
public NucleotideCouple buildCoupleChainFromOneSingleAnimation(Nucleotide chain, float timeGap = 0.8F)
{
NucleotideCouple head = buildHalfCoupleChainFromOneSingle(chain);
if (head == null)
{
return(null);
}
StartCoroutine(fillHalfCoupleChainRoutine(head, timeGap));
return(head);
}
public Nucleotide getTailOfSingleChain(Nucleotide n)
{
Nucleotide tail = n;
while (tail.next)
{
tail = tail.next;
}
return(tail);
}
public Nucleotide getHeadOfSingleChain(Nucleotide n)
{
Nucleotide head = n;
while (head.prev)
{
head = head.prev;
}
return(head);
}
/// <summary>
/// Выравнивание двух последовательностей.
/// Учитывает перестановки A-T и G-C, а также реверсии.
/// </summary>
public static AlignmentResult Align(Nucleotide[] a0, Nucleotide[] b0, int id1 = 0, int id2 = 0)
{
var bestDir = Direction.Straight;
var bestMask = string.Empty;
int bestWeight = -1;
int bestShift1 = 0;
int bestShift2 = 0;
var tmp = new StringBuilder(Math.Max(a0.Length, b0.Length));
foreach (Direction direction in Enum.GetValues(typeof(Direction)))
{
var a = a0;
var b = b0.GetChain(direction);
for (int s = 0; s < b.Length + a.Length - 1; s++) // s - смещение a относительно b
{
int w = 0;
var sa = Math.Max(0, a.Length - s - 1); // откуда начинать отсчёт от a
var sb = Math.Max(0, s + 1 - a.Length); // откуда начинать отсчёт от b
var len = Math.Min(a.Length - sa, b.Length - sb);
for (int i = 0; i < len; i++) // безим по смещённым последовательностям
{
var na = a[sa + i];
var nb = b[sb + i];
if (na == nb)
{
tmp.Append(na);
w++;
}
else
tmp.Append("?");
}
if (w > bestWeight)
{
bestWeight = w;
bestMask = tmp.ToString();
bestDir = direction;
bestShift1 = sa;
bestShift2 = sb;
}
tmp.Clear();
}
}
if (bestMask.StartsWith("?"))
{
var cnt = bestMask.TakeWhile(p => p == '?').Count();
bestShift1 += cnt;
bestShift2 += cnt;
bestMask = bestMask.Trim('?');
}
else
bestMask = bestMask.TrimEnd('?');
return new AlignmentResult(bestWeight, bestMask, bestDir, bestShift1, bestShift2, id1, id2);
}
public void getResidueForUV(Vector2 uv)
{
Debug.Log("Splitting.cs: getResidueForUV(uv): " + uv);
if (DNAPanelController.Instance.DNA_Panel == null)
{
//do it
Debug.Log("RNA panel");
if (seqModel == null)
{
seqModel = new SequenceModel();
}
int RNASeqNum = RNAPanelController.Instance.getSeqPos(uv);
string nuc = RNAPanelController.Instance.getNucAcidForUV(uv);
Debug.Log("Pos: " + RNASeqNum + ", RNA: " + nuc + ", seqModel: " + seqModel);
string nucStr = nuc.Split(':')[0];
//string niceName, int pos, Nuc n, Seq type
int num = seqModel.getPeptidePos("Rattus norvegicus", RNASeqNum, Nucleotide.StrToNuc(nucStr), Seq.RNA);
Debug.Log("peptidePos: " + num);
if (ProteinFocus != null)
{
GameObject.Destroy(ProteinFocus);
}
updateSplit(num);
Residue r = residueSeq[num];
string resName = r.name;
RNAPanelController.Instance.setSeqPos(resName);
}
else
{
if (DNAPanelController.Instance.DNA_Panel.GetComponent <Renderer>().enabled)
{
if (seqModel == null)
{
seqModel = new SequenceModel();
}
int DNASeqNum = DNAPanelController.Instance.getSeqPos(uv);
string nuc = DNAPanelController.Instance.getNucAcidForUV(uv);
Debug.Log("Pos: " + DNASeqNum + ", DNA: " + nuc + ", seqModel: " + seqModel);
string nucStr = nuc.Split(':')[0];
//string niceName, int pos, Nuc n, Seq type
int num = seqModel.getPeptidePos("Rattus norvegicus", DNASeqNum, Nucleotide.StrToNuc(nucStr), Seq.DNA);
Debug.Log("peptidePos: " + num);
}
}
}
public string SingleChain2String(Nucleotide chain)
{
Nucleotide n = getHeadOfSingleChain(chain);
string result = "1";
while (n)
{
result += Type2Char(n.type);
n = n.next;
}
return(result);
}
public void destroySingleChain(Nucleotide chain)
{
Nucleotide prev, head = getHeadOfSingleChain(chain);
while (head)
{
prev = head;
head = head.next;
Destroy(prev.gameObject);
}
Debug.Log("Destroyed");
}
public int getLengthOfSingleChain(Nucleotide n)
{
Nucleotide head = getHeadOfSingleChain(n);
int cnt = 1;
while (n.next)
{
cnt += 1;
n = n.next;
}
return(cnt);
}
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 bool addPrev(Nucleotide n)
{
if (n.next != null)
{
return(false);
}
n.nextBond.SetActive(true);
n.next = this;
this.prevBond.SetActive(true);
this.prev = n;
broadcastUpdateTransform();
return(true);
}
public double CalcMaxScore(Nucleotide[] data, CalcMode? mode = null)
{
var ret = 0.0;
foreach (Direction direction in Enum.GetValues(typeof (Direction)))
{
var b = data.GetChain(direction);
for (int i = 0; i < data.Length - Length; i++)
{
var tmp = CalcScore(b, i, mode);
if (tmp > ret)
ret = tmp;
}
}
return ret;
}
void OnTriggerEnter(Collider other)
{
if (other.tag == "Nucleotide")
{
Nucleotide n = other.gameObject.GetComponent <Nucleotide>();
if (waiting)
{
NucleotideDirector.getInstance().buildCoupleChainFromTwoSingles(waiting, n, transform.position);
waiting = null;
}
else
{
waiting = n;
}
}
}
public static string NucleotideAbbrString(Nucleotide nuc)
{
switch (nuc)
{
case Nucleotide.Adenine:
return("A");
case Nucleotide.Cytosine:
return("C");
case Nucleotide.Guanine:
return("G");
case Nucleotide.Thymine:
return("T");
}
return("");
}
public void updateTransform(Vector3 position, Quaternion rotation, Nucleotide from)
{
this.transform.position = position;
this.transform.rotation = rotation;
if (prev && from != prev)
{
Quaternion prevRotation = rotation;
Vector3 prevPosition = position + rotation * Vector3.up * gap;
prev.updateTransform(prevPosition, prevRotation, this);
}
if (next && from != next)
{
Quaternion nextRotation = rotation;
Vector3 nextPosition = position + rotation * Vector3.down * gap;
next.updateTransform(nextPosition, nextRotation, this);
}
}
public NucleotideCouple buildCoupleChainFromTwoSingles(Nucleotide c1, Nucleotide c2, Vector3 position = default(Vector3))
{
if (c1.isPaired || c2.isPaired)
{
return(null);
}
if (getLengthOfSingleChain(c1) != getLengthOfSingleChain(c2))
{
return(null);
}
c1 = getHeadOfSingleChain(c1);
if (c1 == getHeadOfSingleChain(c2))
{
return(null);
}
c2 = getTailOfSingleChain(c2);
NucleotideCouple n = (Instantiate(couplePrefab) as GameObject).GetComponent <NucleotideCouple>();
NucleotideCouple head = n;
n.setLeftColor(c1.getColor());
n.setRightColor(c2.getColor());
n.setType(c1.type, c2.type);
while (c1.next)
{
c1 = c1.next;
c2 = c2.prev;
n.next = (Instantiate(couplePrefab) as GameObject).GetComponent <NucleotideCouple>();
n.next.setLeftColor(c1.getColor());
n.next.setRightColor(c2.getColor());
n.next.setType(c1.type, c2.type);
n.next.prev = n;
n = n.next;
}
head.transform.position = position;
head.broadcastUpdateTransform();
destroySingleChain(c1);
destroySingleChain(c2);
return(n);
}
//核苷酸之间氢键角度不知道怎么归位，deHelix先注释掉了
//public void deHelix(NucleotideCouple n)
//{
// if(n.needHelix == true)
// {
// n.needHelix = false;
// }
//}
public NucleotideCouple buildCoupleChainFromOneSingle(Nucleotide n, bool reverse = false)
{
if (n.isPaired)
{
return(null);
}
Nucleotide head = getHeadOfSingleChain(n);
Nucleotide next = head.next;
if (next == null)
{
return(buildCoupleFromOneSingle(head));
}
else
{
NucleotideCouple coupleHead = buildCoupleFromOneSingle(head);
NucleotideCouple couple = coupleHead;
while (next.next)
{
next = next.next;
couple.next = buildCoupleFromOneSingle(next.prev, reverse);
couple.next.prev = couple;
couple = couple.next;
}
couple.next = buildCoupleFromOneSingle(next);
couple.next.prev = couple;
if (!reverse)
{
coupleHead.broadcastUpdateTransform();
}
else
{
couple.next.broadcastUpdateTransform();
}
return(coupleHead);
}
}
/// <summary>
/// Добавление прецедента в мотив.
/// </summary>
public void AddItem(Nucleotide[] nucs, int factor = 1)
{
if(nucs == null || nucs.Length != Length)
throw new ArgumentException("nucs");
for (int i = 0; i < nucs.Length; i++)
{
var nucId = (int) nucs[i];
if (nucId < 4)
{
var d = _data[i];
d[nucId] += factor;
d[4] += factor;
}
else
if (nucId == (int) Nucleotide.Any)
_data[i][4] += factor;
else
throw new NotSupportedException();
}
_cache = null;
}
public MultiAlignmentResult Align()
{
var parent = Nodes[0];
var directions = new Direction[Nodes.Length];
var shifts = new int[Nodes.Length];
var w = Alignment.GetWeightMatrix(Nodes.Select(p => p.NucleoChain).ToArray());
var baseId = w.FirstIndexWhereMax(a => a.Sum());
directions[baseId] = Direction.Straight;
shifts[baseId] = 0;
for (int i = 0; i < Nodes.Length; i++)
{
if(i == baseId)
continue;
var a = Alignment.Align(parent.NucleoChain, Nodes[i].NucleoChain);
directions[i] = a.Direction;
shifts[i] = a.Shift1 - a.Shift2;
}
var minShift = shifts.Min();
Debug.Assert(minShift <= 0);
var map = new Nucleotide[Nodes.Length][];
var mapFactors = new int[Nodes.Length];
for (int i = 0; i < Nodes.Length; i++)
{
var s = shifts[i] -= minShift;
var chain = Nodes[i].NucleoChain.GetChain(directions[i]);
if (s > 0)
chain = Enumerable.Repeat(Nucleotide.All, s).Concat(chain).ToArray();
map[i] = chain;
mapFactors[i] = Nodes[i].Count;
}
return new MultiAlignmentResult(shifts, directions, map, mapFactors);
}
public double CalcMaxScore(Nucleotide[] data, int startPos, int endPos, CalcMode? mode = null)
{
Debug.Assert(startPos > 0);
var ret = 0.0;
var end = Math.Min(data.Length - Length, endPos);
for (int i = startPos; i < end; i++)
{
var tmp = CalcScore(data, i, mode);
if (tmp > ret)
ret = tmp;
}
return ret;
}
/// <summary>
/// Gets simple distance estimate for 2 nucleotides
/// </summary>
/// <param name="n1">The nucleotide 1.</param>
/// <param name="n2">The nucleotide 2.</param>
/// <returns>Distance estimate</returns>
public override double NucleotideDistance(Nucleotide n1, Nucleotide n2)
{
return this.DistanceMap[new NucleotidePair(n1, n2)];
}
/// <summary>
/// Вычисляет коэффициент близости.
/// Степенной алгоритм:
/// * Если задано All, то берёт наименее вероятный нуклеотид;
/// * Если нуклеотид не встречался, то считает, что совпадения вообще нет.
/// * Если в конкретной позиции при формировании распределения участвовали не все элементарные мотивы, то сокращает вклад степенным алгоритмом.
/// </summary>
/// <returns>1 - точное совпадение, 0 - отсутствие совпадения.</returns>
public double CalcScoreDegree(Nucleotide[] data, int pos)
{
var ret = 1.0;
if (pos < 0 || data.Length <= pos + Length)
return 0;
for (int i = 0; i < Length; i++)
{
var d = data[pos + i];
var c = (double)((d == Nucleotide.All) ? Freq[i].Min() : Freq[i][(byte)d]);
if (c <= 0)
c = 0.1;
var n = Norm[i];
if (n != Count)
c = Math.Pow(c, n/(double) Count);
ret *= c;
}
return ret * CalcDegreeScoreNormFactor;
}
/// <summary>
/// Gets simple distance estimate for 2 nucleotides
/// </summary>
/// <param name="n1">The nucleotide 1.</param>
/// <param name="n2">The nucleotide 2.</param>
/// <returns>Distance estimate</returns>
public override double NucleotideDistance(Nucleotide n1, Nucleotide n2)
{
return n1 == n2 ? 0 : 1;
}
public static IList<Nucleotide> ParseNucleotides(IList<char> data)
{
Nucleotide[] result = new Nucleotide[data.Count];
for (int i = 0; i < data.Count; i++)
{
switch (data[i])
{
case 'A':
result[i] = Nucleotide.Adenine;
break;
case 'G':
result[i] = Nucleotide.Guanine;
break;
case 'C':
result[i] = Nucleotide.Cytosine;
break;
case 'T':
result[i] = Nucleotide.Thymine;
break;
default:
throw new InvalidOperationException(string.Format("The table contents must be valid nucleotides. Row {0} value {1}", i + 1, data[i]));
}
}
return result;
}
public Nucleotide[] GetPack(int start, int count)
{
Debug.Assert(start + count <= Count);
var ret = new Nucleotide[count];
if (count == 0)
return ret;
var byteId = start/4;
var lastByteId = (start + count)/4;
var packId = start%4;
var b = _data[byteId];
var cnt = 0;
for (int i = packId; i < 4; i++)
{
ret[cnt] = (Nucleotide)((b >> (2*(i))) & 0x03);
if (++cnt == count)
break;
}
byteId++;
for (; byteId <= lastByteId && cnt != count; byteId++)
{
b = _data[byteId];
for (int i = 0; i < 4; i++)
{
ret[cnt] = (Nucleotide)(b & 0x03);
if (++cnt == count)
break;
b = (byte) (b >> 2);
}
}
return ret;
}
public double[] CalcMaxScore(Nucleotide[][] data, CalcMode? mode = null)
{
return data.Select(p => CalcMaxScore(p, mode)).ToArray();
}
public double CalcScore(Nucleotide[] data, int pos, CalcMode? mode)
{
switch (mode ?? DefaultCalcMode)
{
case CalcMode.Degree:
return CalcScoreDegree(data, pos);
case CalcMode.Eps:
return CalcScoreEps(data, pos);
case CalcMode.Strict:
return CalcScoreStrict(data, pos);
default:
throw new NotSupportedException();
}
}
/// <summary> /// Gets distance estimate for 2 nucleotides /// </summary> /// <param name="n1">The nucleotide 1.</param> /// <param name="n2">The nucleotide 2.</param> /// <returns>Distance estimate</returns> public abstract double NucleotideDistance(Nucleotide n1, Nucleotide n2);
public Nucleotide[] GetPack(int start, int count)
{
Debug.Assert(start >= 0);
Debug.Assert(count >= 0);
Debug.Assert(start + count <= Count);
var ret = new Nucleotide[count];
if (count == 0)
return ret;
var byteId = start / 4;
var lastByteId = (start + count) / 4;
var packId = start % 4;
var b = _data[byteId];
var cnt = 0;
for (int i = packId; i < 4; i++)
{
ret[cnt] = (Nucleotide)((b >> (2 * (i))) & 0x03);
if (++cnt == count)
break;
}
byteId++;
for (; byteId <= lastByteId && cnt != count; byteId++)
{
b = _data[byteId];
for (int i = 0; i < 4; i++)
{
ret[cnt] = (Nucleotide)(b & 0x03);
if (++cnt == count)
break;
b = (byte)(b >> 2);
}
}
// добавим маску
for (int i = 0; i < ret.Length; i++)
{
var mId = start + i;
if(((_mask[mId/8] >> (mId%8)) & 1) != 1)
ret[i] = Nucleotide.Any;
}
return ret;
}
/// <summary>
/// Gets distance estimate for nucleotide and profile
/// </summary>
/// <param name="nucleotide">The nucleotide.</param>
/// <param name="profileItem">The profile item.</param>
/// <returns>Distance estimate</returns>
public double ProfileItemNucleotideDistance(Nucleotide nucleotide, ProfileItem profileItem)
{
return profileItem.Sum(n => n.Value * this.NucleotideDistance(n.Key, nucleotide));
}
public double CalcScore(Nucleotide[] data, int pos, CalcMode? mode)
{
double ret = 0.0;
var mo = mode ?? DefaultCalcMode;
foreach (var ms in new[] {_posMotiffs, _negMotiffs})
{
var sum = new List<double>();
foreach (var m in ms)
{
switch (mo)
{
case CalcMode.Degree:
sum.Add(m.CalcScoreDegree(data, pos));
break;
case CalcMode.Eps:
sum.Add(m.CalcScoreEps(data, pos));
break;
case CalcMode.Strict:
sum.Add(m.CalcScoreStrict(data, pos));
break;
default:
throw new NotSupportedException();
}
}
var tmp = Mode == DiffMode.Avg ? sum.Average() : sum.Max();
if (ms == _posMotiffs)
ret += tmp;
else
ret -= tmp;
}
return (ret + 1.0)/2.0;
}
public MultiAlignmentResult(int[] shifts, Direction[] directions, Nucleotide[][] map, int[] mapFactors)
{
Shifts = shifts;
Directions = directions;
Map = map;
MapFactors = mapFactors;
Prepare();
}
/// <summary>
/// Вычисляет коэффициент близости.
/// Жёсткий алгоритм:
/// * Если задано All, то берёт наименее вероятный нуклеотид;
/// * Если нуклеотид не встречался, то считает, что совпадения вообще нет.
/// </summary>
/// <returns>1 - точное совпадение, 0 - отсутствие совпадения.</returns>
public double CalcScoreStrict(Nucleotide[] data, int pos)
{
var ret = 1.0;
if (pos < 0 || data.Length <= pos + Length)
return 0;
for (int i = 0; i < Length; i++)
{
var d = data[pos + i];
var c = (d == Nucleotide.All) ? Freq[i].Min() : Freq[i][(byte)d];
if (c == 0)
return 0;
ret *= c;
}
return ret * CalcScoreNormFactor;
}
