public static ThermodynamicsResult ComputeThermodynamics(INucleotideSequence seq, ExperimentalConfiguration config) // const
{
return ThermodynamicsData.ComputeThermodynamics(config, seq.Nucleotides, Strand.IsFivePrimePhosphorylated(seq)?1:0);
}
//------------------------------------------------------------------
// INamedSequence
public abstract string GetDecoratedName(string coreName, PrettyPrintContext context, INucleotideSequence root, NAMED_SEQUENCE_DECORATOR caller, out NAMED_SEQUENCE_DECORATOR callee);
public void UpdateThermodynamics(ExperimentalConfiguration config, INucleotideSequence sequence)
{
if (config != this.Configuration || sequence.Nucleotides != this.Nucleotides)
{
this.Nucleotides = sequence.Nucleotides;
this.Configuration = config;
this.Thermodynamics = ComputeThermodynamics(sequence, config);
}
}
//--------------------------------------------------------------------------
// INamedSequence
public override string GetDecoratedName(string coreName, PrettyPrintContext ppContext, INucleotideSequence root, NAMED_SEQUENCE_DECORATOR caller, out NAMED_SEQUENCE_DECORATOR callee)
{
return this.GetDecoratedNameDoubleHelper(coreName, ppContext, root, caller, out callee, "{0}'", NAMED_SEQUENCE_DECORATOR.COMPLEMENT);
}
//--------------------------------------------------------------------------
// Construction
public ExtractedSequence(DistillationContext context, SymbolTable symtab, INucleotideSequence target, int intFirst, int cnt) : base(context, symtab, target)
{
this.id = EnumeratedNucleotideSequence.NewId();
//
StringExtractor.Confine(0, target.Length, ref intFirst, ref cnt); // note, though: target's length can change
this.stringExtractor = new StringExtractor(intFirst, cnt);
//
this.isOurDecoration = dec =>
{
if (dec.Ich >= this.stringExtractor.IchFirst && dec.Ich < this.stringExtractor.IchMax)
return true;
if (this.stringExtractor.IchFirst == 0 && dec.Ich < 0)
return true;
if (this.stringExtractor.IchMax >= this.target.Length && dec.Ich == this.target.Length)
return true;
return false;
};
}
//--------------------------------------------------------------------------
// Construction
ComplementedSequence(DistillationContext context, SymbolTable symtab, INucleotideSequence target) : base(context, symtab, target)
{
}
public static INucleotideSequence Create(DistillationContext context, SymbolTable symtab, INucleotideSequence target)
{
return new ComplementedSequence(context, symtab, target);
}
public static INucleotideSequence Create(IReverseSequenceIdContainer idmgr, DistillationContext context, SymbolTable symtab, INucleotideSequence target)
{
return new ReversedSequence(idmgr, context, symtab, target);
}
//--------------------------------------------------------------------------
// INamedSequence
public override string GetDecoratedName(string coreName, PrettyPrintContext context, INucleotideSequence root, NAMED_SEQUENCE_DECORATOR caller, out NAMED_SEQUENCE_DECORATOR callee)
{
return this.GetDecoratedNameDoubleHelper(coreName, context, root, caller, out callee, "reversed({0})", NAMED_SEQUENCE_DECORATOR.REVERSE);
}
//--------------------------------------------------------------------------
// Construction
ReversedSequence(IReverseSequenceIdContainer idmgr, DistillationContext context, SymbolTable symtab, INucleotideSequence target) : base(context, symtab, target)
{
this.id = idmgr.IdForReversedTarget(target.Id);
}
protected string GetDecoratedNameDoubleHelper(string coreName, PrettyPrintContext context, INucleotideSequence root, NAMED_SEQUENCE_DECORATOR caller, out NAMED_SEQUENCE_DECORATOR callee,
string format,
NAMED_SEQUENCE_DECORATOR usFlavor
)
// Shared code for reversing and complementing
{
callee = usFlavor;
//
if (this == root)
return context.FormatDisplayName(coreName, this.Id);
//
if (this.target is INamedSequence)
{
INamedSequence decorator = this.target as INamedSequence;
NAMED_SEQUENCE_DECORATOR decoratorFlavor;
if (caller == usFlavor)
{
// us and caller are of same flavor: just forward on to the target so that the two cancel
return decorator.GetDecoratedName(coreName, context, root, NAMED_SEQUENCE_DECORATOR.NONE, out decoratorFlavor);
}
else
{
// get from target
string his = (this.target as INamedSequence).GetDecoratedName(coreName, context, root, usFlavor, out decoratorFlavor);
//
if (decoratorFlavor==usFlavor)
return his;
else
return string.Format(format, his);
}
}
return string.Format(format, context.FormatDisplayName(coreName, this.Id));
}
//--------------------------------------------------------------------------
// INamedSequence
public override string GetDecoratedName(string coreName, PrettyPrintContext context, INucleotideSequence root, NAMED_SEQUENCE_DECORATOR caller, out NAMED_SEQUENCE_DECORATOR callee)
// Default implementation that just stops at us if we're the root and forwards on to target if not
{
callee = NAMED_SEQUENCE_DECORATOR.NONE;
//
if (this == root)
return context.FormatDisplayName(coreName, this.Id);
//
if (this.target is INamedSequence)
{
INamedSequence decorator = this.target as INamedSequence;
NAMED_SEQUENCE_DECORATOR decoratorFlavor;
return decorator.GetDecoratedName(coreName, context, root, NAMED_SEQUENCE_DECORATOR.NONE, out decoratorFlavor);
}
//
return context.FormatDisplayName(coreName, this.Id);
}
//--------------------------------------------------------------------------
// Construction
public ComputedSequence(DistillationContext context, SymbolTable symtab, INucleotideSequence target) : base(context, symtab)
{
this.target = target;
}
//--------------------------------------------------------------------------
// INamedSequence
public override string GetDecoratedName(string coreName, PrettyPrintContext context, INucleotideSequence root, NAMED_SEQUENCE_DECORATOR caller, out NAMED_SEQUENCE_DECORATOR callee)
{
callee = NAMED_SEQUENCE_DECORATOR.NONE;
return context.FormatDisplayName(coreName, this.Id);
}
