public void Add(SortedElement s)
{
if (SortedElementsList.Count == 0)
{
SortedElementsList.Add(s);
}
else
{
var start = 0;
var end = SortedElementsList.Count;
while (end > start)
{
var n = start + ((end - start) / 2);
if (BwtComparer.Compare(s.Chars, SortedElementsList[n].Chars) == 1)
{
end = n;
}
else
{
start = n + 1;
}
}
SortedElementsList.Insert(start, s);
}
}
private static void FindAllPairs(SortedElement src, int sufStart, int sufLength, int v, int localPosition, Edge currentNode, int missmatch, int misslimit,
int[,] overlapMatrix, int indexOverlap, ref int kmer, bool[] addedPatterns)
{
while (true)
{
if (sufLength == v)
{
for (int i = currentNode.StartIndex; i < currentNode.EndIndex + 1; i++)
{
if (overlapMatrix[indexOverlap, i] < v)
{
if (i != indexOverlap && !addedPatterns[i])
{
overlapMatrix[indexOverlap, i] = v;
kmer++;
}
}
}
return;
}
if (localPosition <= currentNode.LengthString - 1)
{
if (src.Chars[v + sufStart] != currentNode.Src.Chars[currentNode.StartString + localPosition])
{
missmatch++;
}
if (missmatch > misslimit)
{
return;
}
localPosition++;
v++;
}
else
{
for (int j = 0; j < 4; j++)
{
var mistemp = missmatch;
if (src.CodeChars[sufStart + v] != j)
{
mistemp++;
}
if (currentNode.Childs[j] != null && mistemp <= misslimit)
{
var v1 = v + 1;
FindAllPairs(src, sufStart, sufLength, v1, 1, currentNode.Childs[j], mistemp, misslimit, overlapMatrix,
indexOverlap, ref kmer, addedPatterns);
}
}
return;
}
}
}
private static void EditErrorsInSortedElement(int[] overlapVector, SortedElement[] sortedElements,
SortedElement currentElement)
{
var length = currentElement.Chars.Length;
var sortderList = Sort(overlapVector);
var minIndex = sortderList[0];
var minValue = overlapVector[minIndex];
for (int j = 0; j < minValue; j++)
{
if (currentElement.Chars[length - 1 - j] != sortedElements[minIndex].Chars[minValue - 1 - j])
{
currentElement.Chars[length - 1 - j] = sortedElements[minIndex].Chars[minValue - 1 - j];
currentElement.CodeChars[length - 1 - j] = sortedElements[minIndex].CodeChars[minValue - 1 - j];
break;
}
}
}
public void Update(SortedElement s)
{
SortedElementsList.RemoveAt(s.PositionInList);
Add(s);
UpdateIndexes();
}
private static void CreatePrefix(Edge root, SortedElement sortedElement)
{
var inputArr = sortedElement.Chars;
var codes = sortedElement.CodeChars;
var length = inputArr.Length;
var curentEdge = root;
for (int j = 0; j < length; j++)
{
Edge searchElement = null;
var cCode = codes[j];
if (curentEdge.Childs[cCode] != null)
{
searchElement = curentEdge.Childs[cCode];
}
if (searchElement == null)
{
var newEdge = new Edge();
newEdge.LengthString = length - j;
newEdge.StartString = j;
newEdge.StartIndex = sortedElement.PositionInList;
newEdge.EndIndex = sortedElement.PositionInList;
newEdge.Src = sortedElement;
curentEdge.Childs[codes[j]] = newEdge;
break;
}
else
{
var minL = Math.Min(searchElement.LengthString, length - j);
var copyL = 1;
var charsInEdge = searchElement.Src.Chars;
var codesCharsInEdge = searchElement.Src.CodeChars;
for (int k = 1; k < minL; k++)
{
if (charsInEdge[searchElement.StartString + k] == inputArr[j + k])
{
copyL++;
}
else
{
break;
}
}
if (copyL < searchElement.LengthString)
{
var newEdge = new Edge();
newEdge.StartString = searchElement.StartString + copyL;
newEdge.LengthString = searchElement.LengthString - copyL;
newEdge.CopyChilds(searchElement.Childs);
newEdge.EndIndex = searchElement.EndIndex;
newEdge.StartIndex = searchElement.StartIndex;
newEdge.Src = searchElement.Src;
searchElement.CleanChild();
searchElement.Childs[codesCharsInEdge[newEdge.StartString]] = newEdge;
searchElement.LengthString = copyL;
}
searchElement.EndIndex = sortedElement.PositionInList;
j = j + copyL - 1;
curentEdge = searchElement;
}
}
}