private void PrepareDataForVisualisation()
{
DataManager.DataStruct data = DataManager.getInstance().GetData();
genomeSize = gameObject.GetComponent <LogicManager>().GetGenomeSize();
int totalCutPositionsInFullDigest = 0;
for (int i = 0; i < data._enzymes.Length; i++)
{
totalCutPositionsInFullDigest += data._enzymes[i].cutPositions.Length;
}
finalDataForVisualisation = new DataManager.CutPosition[totalCutPositionsInFullDigest];
int arrayIndex = 0;
for (int i = 0; i < data._enzymes.Length; i++)
{
for (int y = 0; y < data._enzymes[i].cutPositions.Length; y++)
{
finalDataForVisualisation[arrayIndex].position = data._enzymes[i].cutPositions[y];
finalDataForVisualisation[arrayIndex].enzymeIndexID = data._enzymes[i].indexID;
arrayIndex++;
}
}
//Order the array based on cut position
Array.Sort(finalDataForVisualisation, (x, y) => x.position.CompareTo(y.position));
isDataPrepared = true;
}
private void PopulateTextFields()
{
DataManager.DataStruct data = DataManager.getInstance().GetData();
UIManager.getInstance().numberOfEnzymesTextField.text = "Number of Enzymes = " + data._enzymes.Length;
for (int i = 0; i < data._enzymes.Length; i++)
{
UIManager.getInstance().enzymeTextFields[i].text = data._enzymes[i].name + ": ";
for (int x = 0; x < data._enzymes[i].numberOfFragments; x++)
{
UIManager.getInstance().enzymeTextFields[i].text += data._enzymes[i].fragmentSizes[x] + ", ";
}
}
UIManager.getInstance().numberOfMultiDigestsTextField.text = "Number of MultiDigests = " + data._digests.Length;
for (int i = 0; i < data._digests.Length; i++)
{
string s = "";
for (int y = 0; y < data._digests[i].enzymesInDigest.Length; y++)
{
s += DataManager.getInstance().GetEnzymeName(data._digests[i].enzymesInDigest[y]);
if (y < data._digests[i].enzymesInDigest.Length - 1)
{
s += " & ";
}
}
UIManager.getInstance().multiDigestTextFields[i].text = s + ": "; //+ multiDigestTextFields[i].text;
for (int x = 0; x < data._digests[i].numberOfFragments; x++)
{
UIManager.getInstance().multiDigestTextFields[i].text += data._digests[i].fragmentSizes[x] + ", ";
}
}
}
public void DataReview()
{
string textToShow = "";
string enzymeNames = "Enzymes:";
DataManager.DataStruct data = DataManager.getInstance().GetData();
for (int i = 0; i < data._enzymes.Length; i++)
{
enzymeNames += data._enzymes[i].name;
textToShow += data._enzymes[i].name + ": ";
for (int x = 0; x < data._enzymes[i].fragmentSizes.Length; x++)
{
textToShow += data._enzymes[i].fragmentSizes[x];
if (x < data._enzymes[i].fragmentSizes.Length - 1)
{
textToShow += ", ";
}
}
if (i < data._enzymes.Length - 1)
{
enzymeNames += ", ";
}
textToShow += "\n";
}
textToShow = "Review Data:\n\n" + enzymeNames + "\n\nSingle-enzyme digest fragments:\n" + textToShow + "\nMulti-enzyme Digests:\n";
for (int i = 0; i < data._digests.Length; i++)
{
textToShow += data._digests[i].name + ": ";
for (int x = 0; x < data._digests[i].fragmentSizes.Length; x++)
{
textToShow += data._digests[i].fragmentSizes[x];
if (x < data._digests[i].fragmentSizes.Length - 1)
{
textToShow += ", ";
}
}
textToShow += "\n";
}
reviewDataParent.transform.Find("Text").GetComponent <Text>().text = textToShow;
}
public void DisplayFullData()
{
DataManager.DataStruct data = DataManager.getInstance().GetData();
arrayLengthsText.text = "Data\nEnzymes Array Length = " + data._enzymes.Length + "\nDigests Array Length = " + data._digests.Length;
for (int i = 0; i < data._enzymes.Length; i++)
{
int arrayIndex = i;
string enzymeName = data._enzymes[i].name;
int enzymeIndex = data._enzymes[i].indexID;
int numberOfFragments = data._enzymes[i].numberOfFragments;
string fragmentSizes = "";
for (int x = 0; x < data._enzymes[i].numberOfFragments; x++)
{
fragmentSizes += data._enzymes[i].fragmentSizes[x] + ", ";
}
string cutPositions = "";
if (data._enzymes[i].cutPositions != null)
{
for (int x = 0; x < data._enzymes[i].cutPositions.Length; x++)
{
cutPositions += data._enzymes[i].cutPositions[x] + ", ";
}
}
string originalCutPositions = "";
if (data._enzymes[i].originalCutPositions != null)
{
for (int x = 0; x < data._enzymes[i].originalCutPositions.Length; x++)
{
originalCutPositions += data._enzymes[i].originalCutPositions[x] + ", ";
}
}
enzymesText[i].text = "Enzymes [" + arrayIndex + "]\nName: " + enzymeName + "\nIndexID: " + enzymeIndex + "\nNumber of fragments: " + numberOfFragments + "\nFragment Sizes: " + fragmentSizes + "\nCut Positions: " + cutPositions + "\nOriginal Cut Positions: " + originalCutPositions;
}
}
private bool CalculationAlgorithm()
{
//Initialise DataSet
//DataManager.DataStruct loadedData = DataManager.getInstance().GetData();
loadedData = DataManager.getInstance().GetData();
enzymes = loadedData._enzymes;
multiDigests = loadedData._digests;
genomeSize = CalculateGenomeSize(enzymes[0].fragmentSizes);
//Check data for errors
for (int i = 0; i < enzymes.Length; i++)
{
if (enzymes[i].fragmentSizes.Length == 0)
{
errorMessage = "Enzyme " + enzymes[i].name + " digest has no fragments. Calculation aborted.";
return(false);
}
}
for (int i = 0; i < enzymes.Length; i++)
{
enzymes[i].cutPositions = CreateCutPositions(enzymes[i].fragmentSizes);
enzymes[i].originalCutPositions = new int[enzymes[i].cutPositions.Length];
enzymes[i].cutPositions.CopyTo(enzymes[i].originalCutPositions, 0);
}
for (int i = 0; i < multiDigests.Length; i++)
{
multiDigests[i].digestCutPositions = new DataManager.CutPosition[multiDigests[i].numberOfFragments];
}
#region DEBUGGING!!!
//Enzymes
for (int i = 0; i < enzymes.Length; i++)
{
Debug.Log("_____");
Debug.Log("Enzyme " + i + " | Name = " + enzymes[i].name);
Debug.Log("Enzyme " + i + " | indexID = " + enzymes[i].indexID);
Debug.Log("Enzyme " + i + " | Number Of Fragments = " + enzymes[i].numberOfFragments);
string fragmentSizes = "{ ";
for (int x = 0; x < enzymes[i].fragmentSizes.Length - 1; x++)
{
fragmentSizes += enzymes[i].fragmentSizes[x] + ", ";
}
fragmentSizes += enzymes[i].fragmentSizes[enzymes[i].fragmentSizes.Length - 1] + " }";
Debug.Log("Enzyme " + i + " | Fragment Sizes = " + fragmentSizes);
string cutPositions = "{ ";
for (int x = 0; x < enzymes[i].cutPositions.Length - 1; x++)
{
fragmentSizes += enzymes[i].cutPositions[x] + ", ";
}
cutPositions += enzymes[i].cutPositions[enzymes[i].cutPositions.Length - 1] + " }";
Debug.Log("Enzyme " + i + " | Cut Positions = " + cutPositions);
Debug.Log("Enzyme " + i + " | Cut positions length = " + enzymes[i].cutPositions.Length);
}
//Multi Digests
for (int i = 0; i < multiDigests.Length; i++)
{
Debug.Log("_____");
Debug.Log("MultiDigest " + i + " | Name = " + multiDigests[i].name);
Debug.Log("MultiDigest " + i + " | Number Of Fragments = " + multiDigests[i].numberOfFragments);
string fragmentSizes = "{ ";
for (int x = 0; x < multiDigests[i].fragmentSizes.Length - 1; x++)
{
fragmentSizes += multiDigests[i].fragmentSizes[x] + ", ";
}
fragmentSizes += multiDigests[i].fragmentSizes[multiDigests[i].fragmentSizes.Length - 1] + " }";
Debug.Log("MultiDigest " + i + " | Fragment Sizes = " + fragmentSizes);
string enzymesInDigest = "{ ";
for (int x = 0; x < multiDigests[i].enzymesInDigest.Length - 1; x++)
{
enzymesInDigest += multiDigests[i].enzymesInDigest[x] + ", ";
}
enzymesInDigest += multiDigests[i].enzymesInDigest[multiDigests[i].enzymesInDigest.Length - 1] + " }";
Debug.Log("MultiDigest " + i + " | Enzymes In Digest = " + enzymesInDigest);
}
#endregion
//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 = 1;
}
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 = 2;
}
}
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
{
errorMessage = "Multidigest " + i + " failed to solve";
return(false);
}
}
#endregion
//Final Solve
if (!RandomAlignmentToSolve())
{
//Calculations have failed.
HelperMethods.WriteToFile("Critical Failure");
UIManager.getInstance().ErrorMessage("Critical Failure");
Debug.Log("Critical Failure");
MainManager.getInstance().CalculationsComplete(false);
return(false);
}
return(true);
}
