public static void OverallManagerConstructor(string terminatorSequenceInput, int top, int minTTailSequenceLength, bool tailScoreAlgorithm, bool autoExtendTail, bool spacer, double HairpinscoreUpbounded, double ttailscoreUpbounded, bool forward, bool sbol, string path, string fileName)
{
terminatorSequence = "";
terminatorSequence = getTerminatorSequence(forward, sbol, terminatorSequenceInput, path, fileName);
errorState = 0;
recrusionTrackArray = new int[top][];
structure = new int[top][, ];
traceBackNumber = new int[top];
terminatorEfficiency = new double[top];
aTail = new string[top];
stemloop = new string[top];
spacerSequence = new string[top];
tTail = new string[top];
ttailscore = new double[top];
hairpinscore = new double[top];
dscore = new double[top];
stemloopPosition = new int[top * 2];
ttailPosition = new int[top];
foreach (char A in terminatorSequence)
{
if (A != ' ' & A != 'u' & A != 'c' & A != 'g' & A != 't' & A != 'a' & A != 'U' & A != 'C' & A != 'G' & A != 'T' & A != 'A')
{
errorState = 6; break;
}
}
if (errorState != 6)
{
if (terminatorSequence.Length >= 150)
{
errorState = 4;
}
else if (terminatorSequence.Length <= 11)
{
errorState = 5;
}
else
{
protentialTTail.protentialTtailCalculation(terminatorSequence, minTTailSequenceLength);
if (protentialTTail.getNoTTailWarning() == true)
{
errorState = 1;
}
else
{
calculationCore.terminatorSequence = terminatorSequence;
calculationCore.calculationCoreConstructor();
Stemloop.stemloopConstructor(terminatorSequence, spacer, top, HairpinscoreUpbounded);
if ((Stemloop.getArraySizeWarning() == false) && (Stemloop.getStemLoopMinSizeWarning() == false))
{
stemloopPosition = Stemloop.tophairpinScorePosition;
ttailPosition = Stemloop.topttailPosition;
for (int i = 0; i <= top - 1; i++)
{
calculationCore.traceBack(Stemloop.tophairpinScorePosition[2 * i], Stemloop.tophairpinScorePosition[2 * i + 1]);
recrusionTrackArray[i] = new int[calculationCore.recrusionTrackNumber * terminatorSequence.Length];
structure[i] = new int[calculationCore.recrusionTrackNumber, terminatorSequence.Length];
for (int j = 0; j <= calculationCore.recrusionTrackNumber * terminatorSequence.Length - 1; j++)
{
recrusionTrackArray[i][j] = calculationCore.recrusionTrack[j];
}
for (int t = 0; t <= calculationCore.recrusionTrackNumber; t++)
{
for (int j = 0; j <= calculationCore.recrusionTrackNumber * terminatorSequence.Length - 1; j++)
{
if ((j <= (t + 1) * terminatorSequence.Length - 1) && (j >= t * terminatorSequence.Length))
{
structure[i][t, j - t * terminatorSequence.Length] = recrusionTrackArray[i][j];
}
}
}
tTailScore.tTailScoreCal.tTailScoreConstructor(terminatorSequence.Substring(ttailPosition[i]), minTTailSequenceLength, tailScoreAlgorithm, autoExtendTail);
aTail[i] = terminatorSequence.Substring(0, stemloopPosition[2 * i]);
stemloop[i] = terminatorSequence.Substring(stemloopPosition[2 * i], stemloopPosition[2 * i + 1] - stemloopPosition[2 * i] + 1);
spacerSequence[i] = terminatorSequence.Substring(stemloopPosition[2 * i + 1] + 1, ttailPosition[i] - stemloopPosition[2 * i + 1] - 1);
tTail[i] = terminatorSequence.Substring(ttailPosition[i]);
ttailscore[i] = tTailScore.tTailScoreCal.getTailScore();
hairpinscore[i] = Stemloop.tophairpinScore[i];
traceBackNumber[i] = calculationCore.recrusionTrackNumber;
terminatorEfficiency[i] = Efficiency.terminatorEfficiencyCal(ttailscore[i], hairpinscore[i], stemloopPosition[2 * i + 1] - stemloopPosition[2 * i] + 1);
dscore[i] = Efficiency.dscore;
}
}
else
{
if (Stemloop.getArraySizeWarning() == true)
{
errorState = 2;
}
if (Stemloop.getStemLoopMinSizeWarning() == true)
{
errorState = 3;
}
}
}
}
}
}
public static void OverallManagerConstructor(string terminatorSequence, int top, int minTTailSequenceLength, bool tailScoreAlgorithm, bool autoExtendTail, bool spacer, double HairpinscoreUpbounded, double ttailscoreUpbounded)
{
protentialTTail.protentialTtailCalculation(terminatorSequence);
if (protentialTTail.getNoTTailWarning() == true)
{
errorState = 1;
}
else
{
calculationCore.terminatorSequence = terminatorSequence;
calculationCore.calculationCoreConstructor();
Stemloop.stemloopConstructor(terminatorSequence, spacer, top, HairpinscoreUpbounded);
recrusionTrackArray = new int[top][];
structure = new int[top][, ];
traceBackNumber = new int[top];
terminatorEfficiency = new double[top];
aTail = new string[top];
stemloop = new string[top];
tTail = new string[top];
if ((Stemloop.getArraySizeWarning() == false) && (Stemloop.getStemLoopMinSizeWarning() == false))
{
for (int i = 0; i <= top - 1; i++)
{
calculationCore.traceBack(Stemloop.tophairpinScorePosition[2 * i], Stemloop.tophairpinScorePosition[2 * i + 1]);
recrusionTrackArray[i] = new int[calculationCore.recrusionTrackNumber * terminatorSequence.Length];
structure[i] = new int[calculationCore.recrusionTrackNumber, terminatorSequence.Length];
for (int j = 0; j <= calculationCore.recrusionTrackNumber * terminatorSequence.Length - 1; j++)
{
recrusionTrackArray[i][j] = calculationCore.recrusionTrack[j];
}
for (int t = 0; t <= calculationCore.recrusionTrackNumber; t++)
{
for (int j = 0; j <= calculationCore.recrusionTrackNumber * terminatorSequence.Length - 1; j++)
{
if ((j <= (t + 1) * terminatorSequence.Length - 1) && (j >= t * terminatorSequence.Length))
{
structure[i][t, j - t * terminatorSequence.Length] = recrusionTrackArray[i][j];
}
}
}
tTailScore.tTailScoreConstructor(terminatorSequence.Substring(Stemloop.tophairpinScorePosition[2 * i + 1] + 1), minTTailSequenceLength, tailScoreAlgorithm, autoExtendTail);
ttailscore = tTailScore.getTailScore();
traceBackNumber[i] = calculationCore.recrusionTrackNumber;
terminatorEfficiency[i] = Efficiency.terminatorEfficiencyCal(ttailscore, Stemloop.tophairpinScore[i], Stemloop.tophairpinScorePosition[2 * i + 1] - Stemloop.tophairpinScorePosition[2 * i]);
aTail[i] = terminatorSequence.Substring(0, Stemloop.tophairpinScorePosition[2 * i]);
stemloop[i] = terminatorSequence.Substring(Stemloop.tophairpinScorePosition[2 * i], Stemloop.tophairpinScorePosition[2 * i + 1] - Stemloop.tophairpinScorePosition[2 * i] + 1);
tTail[i] = terminatorSequence.Substring(Stemloop.tophairpinScorePosition[2 * i + 1] + 1);
}
}
else
{
if (Stemloop.getArraySizeWarning() == true)
{
errorState = 2;
}
if (Stemloop.getStemLoopMinSizeWarning() == true)
{
errorState = 3;
}
}
}
}
