public static void input(string terminatorSequence, int top, int minTTailSequenceLength, bool tailScoreAlgorithm, bool autoExtendTail, bool spacer, double HairpinscoreUpbounded, double ttailscoreUpbounded)
{
OverallManager.OverallManagerConstructor(terminatorSequence, top, minTTailSequenceLength, tailScoreAlgorithm, autoExtendTail, spacer, HairpinscoreUpbounded, ttailscoreUpbounded);
errorDisplay.errorDisplayConstructor();
if (OverallManager.errorState != 0)
{
Warn = true;
}
else
{
Warn = false;
}
Warning = errorDisplay.Warning;
Help = errorDisplay.Help;
if (Warn == false)
{
aTail = new string[top];
aTail = OverallManager.aTail;
stemloop = new string[top];
stemloop = OverallManager.stemloop;
tTail = new string[top];
tTail = OverallManager.tTail;
stemloopPosition = new int[top * 2];
stemloopPosition = Stemloop.tophairpinScorePosition;
structure = OverallManager.structure;
traceBackNumber = OverallManager.traceBackNumber;
terminatorEfficiency = OverallManager.terminatorEfficiency;
}
}
public static void input(string terminatorSequenceInput, int top, int minTTailSequenceLength, bool tailScoreAlgorithm, bool autoExtendTail, bool spacer, double HairpinscoreUpbounded, double ttailscoreUpbounded, bool forward, bool sbol, string path, string fileName)
{
Warning = null;
Help = null;
aTail = null;
stemloop = null;
spacerSequence = null;
tTail = null;
stemloopPosition = null;
ttailPosition = null;
traceBackNumber = null;
structure = null;
terminatorEfficiency = null;
hairpinscore = null;
ttailscore = null;
dscore = null;
OverallManager.OverallManagerConstructor(terminatorSequenceInput, top, minTTailSequenceLength, tailScoreAlgorithm, autoExtendTail, spacer, HairpinscoreUpbounded, ttailscoreUpbounded, forward, sbol, path, fileName);
terminatorSequence = OverallManager.terminatorSequence;
errorDisplay.errorDisplayConstructor();
if (OverallManager.errorState != 0)
{
Warn = true;
}
else
{
Warn = false;
}
Warning = errorDisplay.Warning;
Help = errorDisplay.Help;
if (Warn == false)
{
aTail = new string[top];
aTail = OverallManager.aTail;
stemloop = new string[top];
stemloop = OverallManager.stemloop;
spacerSequence = new string[top];
spacerSequence = OverallManager.spacerSequence;
tTail = new string[top];
tTail = OverallManager.tTail;
stemloopPosition = new int[top * 2];
stemloopPosition = OverallManager.stemloopPosition;
ttailPosition = new int[top];
ttailPosition = OverallManager.ttailPosition;
traceBackNumber = new int[top];
traceBackNumber = OverallManager.traceBackNumber;
structure = new int[top][, ];
for (int i = 0; i < top; i++)
{
structure[i] = new int[traceBackNumber[i], terminatorSequence.Length];
}
structure = OverallManager.structure;
ttailscore = new double[top];
ttailscore = OverallManager.ttailscore;
hairpinscore = new double[top];
hairpinscore = OverallManager.hairpinscore;
dscore = new double[top];
dscore = OverallManager.dscore;
terminatorEfficiency = new double[top];
terminatorEfficiency = OverallManager.terminatorEfficiency;
structure_string = new string[top][];
for (int i = 0; i < top; i++)
{
structure_string[i] = new string[traceBackNumber[i]];
for (int t = 0; t < traceBackNumber[i]; t++)
{
for (int j = 0; j < terminatorSequence.Length; j++)
{
structure_string[i][t] += structure[i][t, j].ToString();
}
}
}
}
}
