/// <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);
}
/// <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();
}