/// <summary>
/// Compute overlap's hairpin melting temperature.
/// </summary>
/// <returns>Hairpin melting temperature.</returns>
private double GetHairpinTemperature()
{
double T = 0.0;
String upper = this.Sequence.ToString().ToUpper();
Thermodynamics.thal_results results = new Thermodynamics.thal_results();
Thermodynamics.p3_thal_args args = this.Settings.ThalHairpinSettings;
Thermodynamics.p3_thal(upper, upper, ref args, ref results);
T = results.temp;
return T;
}
/// <summary>
/// Compute overlap's duplex melting temperature.
/// </summary>
/// <returns>Duplex melting temperature.</returns>
public double GetDuplexTemperature(Overlap twin)
{
double T = 0.0;
String upper = this.Sequence.ToString().ToUpper();
String upperTwin = twin.Sequence.ToString().ToUpper();
Thermodynamics.thal_results results = new Thermodynamics.thal_results();
Thermodynamics.p3_thal_args args = this.Settings.ThalSettings;
Thermodynamics.p3_thal(upper, upperTwin, ref args, ref results);
T = results.temp;
return T;
}
/// <summary>
/// Construct initialization.
/// </summary>
/// <param name="fragList">Fragment list.</param>
/// <param name="maxOverlapLen">Minimum overlap length.</param>
private void Init(ObservableCollection<Fragment> fragList, DesignerSettings settings)
{
this.Overlaps = new List<Overlap>();
this.Settings = settings;
Thermodynamics.thal_results results = new Thermodynamics.thal_results();
Thermodynamics.p3_get_thermodynamic_values(Settings.TmThalParamPath, ref results);
String message = new String(results.msg);
message = message.Trim('\0');
if (!String.IsNullOrEmpty(message))
{
throw new TmThalParamException(message);
}
//forward
String seq_5 = "";
String seq_3 = "";
String name = "";
List<MiscFeature> featList = new List<MiscFeature>();
int pairIndex;
int len_5;
int len_3;
for (int i = 0; i < fragList.Count; i++)
{
name += fragList[i].Name;
seq_3 = fragList[i].GetString();
len_5 = Math.Min(settings.MaxLen_5, seq_5.Length);
len_3 = Math.Min(settings.MaxLen_3, seq_3.Length);
String overhang_5 = seq_5.Substring(seq_5.Length - len_5, len_5);
String geneSpecific_3 = seq_3.Substring(0, len_3);
String loc = (seq_5.Length + 1).ToString() + ".." + (seq_5.Length + seq_3.Length).ToString();
MiscFeature gene = new MiscFeature(loc);
gene.StandardName = fragList[i].Name;
featList.Add(gene);
seq_5 += seq_3;
if (i == 0)
{
pairIndex = fragList.Count;
Overlaps.Add(new Overlap(Designer.VectorLabel + fragList[i].Name + "-fwd", new Sequence(Alphabets.AmbiguousDNA, geneSpecific_3), settings.TmThalSettings, pairIndex));
}
else
{
pairIndex = 2 * fragList.Count - i;
Overlaps.Add(new Overlap(fragList[i].Name + "-fwd", new Sequence(Alphabets.AmbiguousDNA, overhang_5), new Sequence(Alphabets.AmbiguousDNA, geneSpecific_3), settings.TmThalSettings, pairIndex));
}
}
this.Sequence = new Sequence(Alphabets.AmbiguousDNA, seq_5);
//meta
GenBankMetadata meta = new GenBankMetadata();
meta.Locus = new GenBankLocusInfo();
meta.Locus.MoleculeType = MoleculeType.DNA;
meta.Locus.Name = name;
meta.Locus.Date = System.DateTime.Now;
meta.Locus.SequenceLength = seq_5.Length;
meta.Comments.Add("designed with mufasa");
meta.Definition = "synthetic construct";
meta.Features = new SequenceFeatures();
meta.Features.All.AddRange(featList);
this.Sequence.Metadata.Add("GenBank", meta);
//reverse
fragList.Add(new Fragment(fragList[0]));
fragList.RemoveAt(0);
seq_5 = "";
seq_3 = "";
for (int i = fragList.Count - 1; i >= 0; i--)
{
seq_5 = fragList[i].GetReverseComplementString();
len_5 = Math.Min(settings.MaxLen_5, seq_3.Length);
len_3 = Math.Min(settings.MaxLen_3, seq_5.Length);
String overhang_5 = seq_3.Substring(seq_3.Length - len_5, len_5);
String geneSpecific_3 = seq_5.Substring(0, len_3);
seq_3 += seq_5;
if (i == fragList.Count - 1)
{
pairIndex = 0;
Overlaps.Add(new Overlap(Designer.VectorLabel + fragList[i].Name + "-rev", new Sequence(Alphabets.AmbiguousDNA, geneSpecific_3), settings.TmThalSettings, pairIndex));
}
else
{
pairIndex = i + 1;
Overlaps.Add(new Overlap(fragList[i].Name + "-rev", new Sequence(Alphabets.AmbiguousDNA, overhang_5), new Sequence(Alphabets.AmbiguousDNA, geneSpecific_3), settings.TmThalSettings, pairIndex));
}
}
for (int i = 0; i < fragList.Count; i++)
{
//Duplex melting temperatures
Overlaps[i].HeterodimerMeltingTemperature = Overlaps[i].GetDuplexTemperature(Overlaps[Overlaps[i].PairIndex]);
}
}
