Beispiel #1
0
 /// <summary>
 /// Overlap constructor.
 /// </summary>
 /// <param name="name">Overlap name.</param>
 /// <param name="overhang_5">Overhang sequence.</param>
 /// <param name="geneSpecific_3">Gene specific sequence.</param>
 public Overlap(String name, ISequence overhang_5, ISequence geneSpecific_3, TmThalSettings settings, int pairIndex = -1)
 {
     this.PairIndex = pairIndex;
     this.Settings = settings;
     this.Name = name;
     this.TemplateSeq_3 = new Sequence(Alphabets.AmbiguousDNA, geneSpecific_3.ToString().ToUpper());
     this.TemplateSeq_5 = new Sequence(Alphabets.AmbiguousDNA, overhang_5.ToString().ToLower());
     this.Seq_3 = this.TemplateSeq_3;
     this.Seq_5 = this.TemplateSeq_5;
     this.Sequence = new Sequence(Alphabets.AmbiguousDNA, this.Seq_5.ToString() + this.Seq_3.ToString());
     this.TempInit();
     this.meltingTemperature = GetMeltingTemperature();
     this.hairpinMeltingTemperature = GetHairpinTemperature();
     this.homodimerMeltingTemperature = GetDuplexTemperature(this);
 }
Beispiel #2
0
 /// <summary>
 /// Overlap constructor.
 /// </summary>
 /// <param name="name">Overlap name.</param>
 /// <param name="primer">Primer sequence.</param>
 public Overlap(String name, ISequence primer, TmThalSettings settings, int pairIndex = -1)
     : this(name, new Sequence(Alphabets.AmbiguousDNA, ""), primer, settings, pairIndex) { }
 /// <summary>
 /// Designer settings constructor.
 /// </summary>
 public DesignerSettings()
 {
     this.TmThalParamPath = ".\\tmthal_config\\";
     this.MinLen_3 = 18;
     this.MaxLen_3 = 25;
     this.MinLen_5 = 20;
     this.MaxLen_5 = 30;
     this.TargetTm = 65.0;
     this.MaxTh = 70.0;
     this.MaxTd= 70.0;
     this.ReactionVolume = 50.0;
     this.UseNaive = false;
     this.TmThalSettings = new TmThalSettings();
     this.LeaSettings = new LeaSettings();
 }