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 AllPairsSuffixPrefixResule AllPairsSuffixPrefix(SortedElement[] sortedElements, Edge root)
{
var patternsCount = sortedElements.Length;
var overlapMatrix = new int[patternsCount, patternsCount];
var addedPatterns = new bool[sortedElements.Length];
var startIndex = 0;
var currentIndex = startIndex;
addedPatterns[startIndex] = true;
var patternQueue = new int[patternsCount];
var overlapQueue = new int[patternsCount];
var kmer = 0;
var kmerMax = 1;
var localValue = -1;
var localIndex = -1;
for (int i = 0; i < sortedElements.Length - 1; i++)
{
patternQueue[i] = currentIndex;
kmer = 0;
for (int j = 0; j < sortedElements[0].Chars.Length; j++)
{
var sufStart = j;
var sufLength = sortedElements[0].Chars.Length - j;
var misslimit = (int)(sufLength * 0.05);
FindAllPairs(sortedElements[currentIndex], sufStart, sufLength, 0, 0, root, 0, misslimit, overlapMatrix, currentIndex, ref kmer, addedPatterns);
if (kmer >= kmerMax)
{
break;
}
}
localValue = -1;
localIndex = -1;
for (int j = 0; j < patternsCount; j++)
{
if (overlapMatrix[currentIndex, j] > localValue && !addedPatterns[j])
{
localIndex = j;
localValue = overlapMatrix[currentIndex, j];
}
}
overlapQueue[i] = localValue;
currentIndex = localIndex;
addedPatterns[currentIndex] = true;
}
addedPatterns[startIndex] = false;
localValue = -1;
kmer = 0;
for (int j = 0; j < sortedElements[0].Chars.Length; j++)
{
var sufStart = j;
var sufLength = sortedElements[0].Chars.Length - j;
var misslimit = (int)(sufLength * 0.05);
FindAllPairs(sortedElements[currentIndex], sufStart, sufLength, 0, 0, root, 0, misslimit, overlapMatrix, currentIndex, ref kmer, addedPatterns);
if (kmer >= kmerMax)
{
break;
}
}
for (int j = 0; j < patternsCount; j++)
{
if (overlapMatrix[currentIndex, j] > localValue && !addedPatterns[j])
{
localValue = overlapMatrix[currentIndex, j];
}
}
patternQueue[patternsCount - 1] = currentIndex;
overlapQueue[patternsCount - 1] = localValue;
overlapMatrix[currentIndex, startIndex] = localValue;
return(new AllPairsSuffixPrefixResule()
{
OverlapMatrix = overlapMatrix, OverlapQueue = overlapQueue, PatternQueue = patternQueue
});
}
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;
}
}
}
