Beispiel #1
0
 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;
     }
 }
Beispiel #2
0
        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();
                        }
                    }
                }
            }
        }