/// <summary>
/// Overlap copying constructor.
/// </summary>
/// <param name="overlap">Overlap.</param>
public Overlap(Overlap overlap)
: this(overlap.Name, overlap.Seq_5, overlap.Seq_3, overlap.Settings, overlap.PairIndex)
{ }
/// <summary>
/// Converts the chromosome to its corresponding overlap list.
/// </summary>
/// <param name="templates">List of overlap templates.</param>
/// <returns>List of overlaps represented by this chromosome.</returns>
public List<Overlap> ToOverlaps(List<Overlap> templates)
{
Overlaps.Clear();
for (int i = 0; i < templates.Count; i++)
{
Overlap temp;
Sequence seq_3 = (Sequence)templates[i].Seq_3.GetSubSequence(0, this.Lengths_3[i]);
if (templates[i].Seq_5.Count > 0)
{
Sequence seq_5 = (Sequence)templates[i].Seq_5.GetSubSequence(templates[i].Seq_5.Count - this.Lengths_5[i], this.Lengths_5[i]);
temp = new Overlap(templates[i].Name, seq_5, seq_3, templates[i].Settings, templates[i].PairIndex);
}
else
{
temp = new Overlap(templates[i].Name, seq_3, templates[i].Settings, templates[i].PairIndex);
}
Overlaps.Add(temp);
}
return Overlaps;
}
/// <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>
/// Overlap naive-greedy temperature optimization.
/// </summary>
/// <param name="o"></param>
/// <param name="args"></param>
public void SemiNaiveOptimizeOverlaps(object o, DoWorkEventArgs args)
{
stop = false;
this.b = o as BackgroundWorker;
const byte end_3 = 255;
const byte end_5 = 255;
int progress = 0;
for (int i = 0; i < this.Construct.Overlaps.Count; i++)
{
byte item_3 = 0;
byte item_5 = 0;
bool done_3 = false;
bool done_5 = false;
bool tmTooHigh = true;
double diff = this.Construct.Overlaps[i].MeltingTemperature - this.Construct.Settings.TargetTm;
double _bestDiff = diff;
Overlap _best = new Overlap(this.Construct.Overlaps[i]);
do
{
if ((item_5 != end_5))
{
item_5 = this.Construct.Overlaps[i].Dequeue(this.Construct.Settings.MinLen_5);
diff = this.Construct.Overlaps[i].MeltingTemperature - this.Construct.Settings.TargetTm;
tmTooHigh = (this.Construct.Overlaps[i].MeltingTemperature > this.Construct.Settings.TargetTm);
if (Math.Abs(_bestDiff) > Math.Abs(diff))
{
//check if hairpin is acceptable
if (this.Construct.Overlaps[i].IsAcceptable(this.Construct.Settings.MaxTh, this.Construct.Settings.MaxTd, false))
{
//if found a better solution, copy it, and do not stop
_bestDiff = diff;
_best = new Overlap(this.Construct.Overlaps[i]);
done_5 = false;
}
}
else
{
//if passed the threshold, done
if (!tmTooHigh)
{
done_5 = true;
}
}
}
else
{
done_5 = true;
}
if ((item_3 != end_3))
{
item_3 = this.Construct.Overlaps[i].Pop(this.Construct.Settings.MinLen_3);
diff = this.Construct.Overlaps[i].MeltingTemperature - this.Construct.Settings.TargetTm;
tmTooHigh = (this.Construct.Overlaps[i].MeltingTemperature > this.Construct.Settings.TargetTm);
if (Math.Abs(_bestDiff) > Math.Abs(diff))
{
//check if hairpin is acceptable
if (this.Construct.Overlaps[i].IsAcceptable(this.Construct.Settings.MaxTh, this.Construct.Settings.MaxTd, false))
{
//if found a better solution, copy it, and do not stop
_bestDiff = diff;
_best = new Overlap(this.Construct.Overlaps[i]);
done_3 = false;
}
}
else
{
//if passed the threshold, done
if (!tmTooHigh)
{
done_3 = true;
}
}
}
else
{
done_3 = true;
}
if (!this.IgnorePreoptimizationExceptions && item_3 == end_3 && item_5 == end_5 && !this.Construct.Overlaps[i].IsAcceptable(this.Construct.Settings.MaxTh, this.Construct.Settings.MaxTd, true))
{
/*
* If you are running under the Visual Studio debugger, the debugger will break
* at the point in the DoWork event handler where the unhandled exception was raised.
* - Mark Cranness, Mar 9 '11 @ StackOverflow
*
* Solution: run without debugging. I want that exception here, for now.
*/
throw new AssemblyException(this.Construct.Overlaps[i].ToString());
}
} while (!stop && (!done_5 || !done_3));
this.Construct.Overlaps[i] = _best;
progress = (int)(100.0 * (double)i / (double)(this.Construct.Overlaps.Count - 1));
b.ReportProgress(progress);
}
stop = false;
this.Construct.Evaluate();
if (!this.IgnorePreoptimizationExceptions && Double.IsPositiveInfinity(this.Construct.Score.NormalizedScore))
{
//if failed to achieve an acceptable construct
throw new AssemblyException("Heteroduplex melting temperature too high. ");
}
}