//This works
void VisualiseMultiDigest(int multiDigestIndex)
{
for (int i = 0; i < multiDigests[multiDigestIndex].digestCutPositions.Length; i++)
{
visualisation.CreateLine(((float)multiDigests[multiDigestIndex].digestCutPositions[i].position / genomeSize) * 360, enzymes[multiDigests[multiDigestIndex].digestCutPositions[i].enzymeIndexID].name + " " + multiDigests[multiDigestIndex].digestCutPositions[i].position, Color.red);
}
}
void Start()
{
genomeSize = 400;
//Enzymes
int digestNumber = 0;
enzymes = new Enzyme[3];
enzymes[digestNumber].name = "HindIII";
enzymes[digestNumber].indexID = 0;
enzymes[digestNumber].numberOfFragments = 2;
enzymes[digestNumber].fragmentSizes = new int[2] {
382, 18
};
enzymes[digestNumber].cutPositions = CreateCutPositions(enzymes[digestNumber].fragmentSizes);
enzymes[digestNumber].originalCutPositions = new int[enzymes[digestNumber].cutPositions.Length];
enzymes[digestNumber].cutPositions.CopyTo(enzymes[digestNumber].originalCutPositions, 0);
digestNumber = 1;
enzymes[digestNumber].name = "BamHI";
enzymes[digestNumber].indexID = 1;
enzymes[digestNumber].numberOfFragments = 2;
enzymes[digestNumber].fragmentSizes = new int[2] {
235, 165
};
enzymes[digestNumber].cutPositions = CreateCutPositions(enzymes[digestNumber].fragmentSizes);
enzymes[digestNumber].originalCutPositions = new int[enzymes[digestNumber].cutPositions.Length];
enzymes[digestNumber].cutPositions.CopyTo(enzymes[digestNumber].originalCutPositions, 0);
digestNumber = 2;
enzymes[digestNumber].name = "EcoRI";
enzymes[digestNumber].indexID = 2;
enzymes[digestNumber].numberOfFragments = 2;
enzymes[digestNumber].fragmentSizes = new int[2] {
300, 100
};
enzymes[digestNumber].cutPositions = CreateCutPositions(enzymes[digestNumber].fragmentSizes);
enzymes[digestNumber].originalCutPositions = new int[enzymes[digestNumber].cutPositions.Length];
enzymes[digestNumber].cutPositions.CopyTo(enzymes[digestNumber].originalCutPositions, 0);
//MultiDigests
digestNumber = 0;
multiDigests = new Digest[3];
multiDigests[digestNumber].name = "HindIII & BamHI";
multiDigests[digestNumber].numberOfFragments = 4;
multiDigests[digestNumber].fragmentSizes = new int[4] {
235, 120, 27, 18
};
multiDigests[digestNumber].enzymesInDigest = new int[2] {
0, 1
};
multiDigests[digestNumber].digestCutPositions = new CutPosition[multiDigests[digestNumber].numberOfFragments];
digestNumber = 1;
multiDigests[digestNumber].name = "HindIII & EcoRI";
multiDigests[digestNumber].numberOfFragments = 4;
multiDigests[digestNumber].fragmentSizes = new int[4] {
187, 100, 95, 18
};
multiDigests[digestNumber].enzymesInDigest = new int[2] {
0, 2
};
multiDigests[digestNumber].digestCutPositions = new CutPosition[multiDigests[digestNumber].numberOfFragments];
digestNumber = 2;
multiDigests[digestNumber].name = "BamHI & EcoRI";
multiDigests[digestNumber].numberOfFragments = 4;
multiDigests[digestNumber].fragmentSizes = new int[4] {
160, 140, 75, 25
};
multiDigests[digestNumber].enzymesInDigest = new int[2] {
1, 2
};
multiDigests[digestNumber].digestCutPositions = new CutPosition[multiDigests[digestNumber].numberOfFragments];
genomeSize = CalculateGenomeSize(enzymes[0].fragmentSizes);
//Complete all multidigests
#region Instructions
for (int i = 0; i < multiDigests.Length; i++)
{
bool isSuccessful = false;
int attemptNumber = 1;
if (MultiDigestCutPositionsFromSingleDigests(i))
{
isSuccessful = true;
attemptNumber++;
}
else
{
FlipEnzymeCutPositions(enzymes[multiDigests[i].enzymesInDigest[1]].cutPositions).CopyTo(enzymes[multiDigests[i].enzymesInDigest[1]].cutPositions, 0);
ResetCutPositions(multiDigests[i].enzymesInDigest[0]);
if (MultiDigestCutPositionsFromSingleDigests(i))
{
isSuccessful = true;
attemptNumber++;
}
}
if (isSuccessful)
{
//Debug.Log("Success " + i + " Attempt " + attemptNumber);
for (int x = 0; x < multiDigests[i].enzymesInDigest.Length; x++)
{
PrintArray(enzymes[multiDigests[i].enzymesInDigest[x]].name + ": ", enzymes[multiDigests[i].enzymesInDigest[x]].cutPositions);
}
}
else
{
//Debug.Log("multidigest " + i + " Failed");
}
}
#endregion
AlignDigestsBasedOnCommonEnzymes(1, 0);
AlignDigestsBasedOnCommonEnzymes(2, 1);
FlipMultiDigestCutPositions(2);
AlignDigestsBasedOnCommonEnzymes(2, 0);
FlipMultiDigestCutPositions(1);
AlignDigestsBasedOnCommonEnzymes(1, 0);
PrintCutPositionArray("MultiDigest 0: ", multiDigests[0].digestCutPositions);
PrintCutPositionArray("MultiDigest 1: ", multiDigests[1].digestCutPositions);
PrintCutPositionArray("MultiDigest 2: ", multiDigests[2].digestCutPositions);
LoadFinalCutPositonsForEnzymes();
PrintArray(enzymes[0].name + " CutPositions: ", enzymes[0].cutPositions);
PrintArray(enzymes[1].name + " CutPositions: ", enzymes[1].cutPositions);
PrintArray(enzymes[2].name + " CutPositions: ", enzymes[2].cutPositions);
//VisualiseMultiDigest(0);
if (CheckAllMultiDigests())
{
Debug.Log("F*****G DONE IT SON.");
}
else
{
Debug.Log("haha, you thought you were done");
}
for (int i = 0; i < enzymes.Length; i++)
{
for (int x = 0; x < enzymes[i].cutPositions.Length; x++)
{
visualisation.CreateLine(((float)enzymes[i].cutPositions[x] / genomeSize) * 360, enzymes[i].name, Color.red);
}
}
}