//-----------------------------------------------------------------------------------
// Construction
//-----------------------------------------------------------------------------------
public EnumeratedSequenceAllocator(EnumeratedNucleotideSequence seq, NadirAST nodeDefinition, SequenceDesigner designer)
// We require that all our domains have the same enumerated sequence, but that
// doesn't mean that they all share the same id (why?). (eh?)
{
Trace.Assert(seq != null);
this.enumeratedSequence = seq;
this.nodeSequenceDefinition = nodeDefinition;
this.designer = designer;
//
if (this.enumeratedSequence.Length != 0)
{
if (this.HasLength && this.Length != this.enumeratedSequence.Length)
throw new InconsistentLengthException(this.Length);
}
//
AddAllocationPattern(this.enumeratedSequence.UndecoratedPattern);
//
// We always verify both the normal and the complement form, as that's
// easier than reliably keeping track of which of those two forms is
// actually used in an actual strand. We wish we could be more careful about
// that, because if we could keep track, it'd be a big perf improvement.
//
this.normalVerifier = new EnumeratedSequenceVerifier(this, false, designer);
this.complementaryVerifier = new EnumeratedSequenceVerifier(this, true, designer);
}
public void PrintFinalOutput(SequenceDesigner designer, NadirContext context)
{
FixDomainNames(this.resultToOutput);
if (designer != null)
OutputResult(designer.Context, this.resultToOutput, designer.Context.Scoring.BestScores);
else
OutputResult(new SequenceDesignContext(context), this.resultToOutput, new SortedList<DesignScoreResult, SequencesSaveState>());
}
public Mutator(SequenceDesigner designer, AllocationStatistics stats)
{
this.designer = designer;
this.stats = stats;
this.sweepInProgress = false;
bool isInosineUsed = designer.mutableAllocators.Select(alloc => alloc.AllowsAnyMutableInosine).Aggregate((before, cur) => before || cur);
this.iNtMax = isInosineUsed ? rgchNucleotides.Length : rgchNucleotides.Length - 1;
this.allowUpHill = false;
ResetSweep();
}
public void PrintInterimOuput(SequenceDesigner designer)
{
FixDomainNames(this.distillationResult);
OutputResult(designer.Context, this.distillationResult, designer.Context.Scoring.BestScores);
}
//-----------------------------------------------------------------------------------
// Ctor
//-----------------------------------------------------------------------------------
public Verifier(SequenceDesigner designer)
{
this.Designer = designer;
}
// public override string DisplayName { get { return this.Domains[0].DisplayName; } }
//
//-----------------------------------------------------------------------------------
// Construction
//-----------------------------------------------------------------------------------
public EnumeratedSequenceVerifier(EnumeratedSequenceAllocator allocator, bool isComplemented, SequenceDesigner designer) : base(designer)
{
this.EnumeratedSequence = allocator.EnumeratedSequence;
this.EnumeratedSequenceAllocator = allocator;
this.IsComplemented = isComplemented;
}
//-----------------------------------------------------------------------------------
// Construction
//-----------------------------------------------------------------------------------
public StrandVerifier(Strand strand, SequenceDesigner designer) : base(designer)
{
this.strand = strand;
}
