public void PrettyPrint(PrettyPrintContext context)
{
if (this.children==null || this.ChildCount == 0)
{
context.Append('(');
context.Append(this.ToStringCore());
context.Append(')');
}
else
{
if (!this.IsNil)
{
context.Append('(');
context.Append(this.ToStringCore());
}
//
if (this.ChildCount == 1)
{
if (!this.IsNil) context.Append(' ');
this.GetNadirChild(0).PrettyPrint(context);
}
else
{
if (!this.IsNil) context.Indent();
//
foreach (NadirAST child in this.NadirChildren)
{
context.NewLine();
child.PrettyPrint(context);
}
//
if (!this.IsNil) context.Outdent();
}
//
if (!this.IsNil)
{
context.Append(')');
}
}
}
public override string ErrorMessage()
{
PrettyPrintContext pp = new PrettyPrintContext();
pp.Append(Format("annealing {1} produces {0} molecular configurations:", configs.Count, annealingFlavor)); // REVIEW: AppendFormat should work, but uses differnt pp context inside, which is wrong
pp.NewLine();
pp.Append(Format("input:"));
pp.Indent(); pp.NewLine();
pp.Append(Format("{0}", annealed));
pp.Outdent(); pp.NewLine();
pp.Append(Format("output:"));
pp.Indent();
int i = 0;
foreach (MoleculeMultiSet config in configs)
{
pp.NewLine();
pp.Append(Format("{0}:", i));
pp.Indent();
pp.Append(config);
pp.Outdent();
i++;
}
pp.Outdent();
return pp.PrettyPrintedOutputString();
}
string OutputText(SequenceDesignContext context, object result, SortedList<DesignScoreResult, SequencesSaveState> best)
{
string fileName = null;
PrettyPrintContext pp = new PrettyPrintContext();
//
DateTime now = DateTime.Now;
//
if (this.nadirFiles.Count > 0)
{
StreamWriter writer = CreateWritableFile("");
fileName = (writer.BaseStream as FileStream)?.Name;
pp.LogToFile(writer);
}
//
pp.NewLine();
this.OutputBannerAndCopyright(pp);
//
pp.Append("Parameters: ");
pp.Append(this.args.Interleave(" "));
pp.NewLine();
//
pp.AppendLine("Start: {0}, {1}", this.StartTime.ToLongDateString(), this.StartTime.ToLongTimeString());
pp.AppendLine("Now: {0}, {1}", now.ToLongDateString(), now.ToLongTimeString());
pp.AppendLine("Elapsed time: {0}", FormatElapsed(now - this.StartTime));
pp.AppendLine("Iterations: {0:N0}", context.DesignIter);
pp.AppendLine("Random Seed: {0}", MiscUtil.RandSeed);
//
List<Strand> strands = new List<Strand>();
if (result is Model)
{
strands = new List<Strand>((result as Model).ChemicallyUniqueStrands());
strands.Sort();
pp.AppendLine("Nucleotides: {0,6:N0} unique nucleotide bases", context.IndependentNucleotideCount);
pp.AppendLine(" {0,6:N0} of those are mutable", context.MutableNucleotideCount);
pp.AppendLine("Strands: {0,6:N0} unique strands", strands.Count);
pp.AppendLine(" {0,6:N0} bases total length", context.TotalNucleotideCount);
if (context.Designer != null)
{
pp.AppendLine("Tm Calculation Parameters:");
pp.AppendLine(" {0,6:F2} mM monovalent salt concentration", context.Designer.MonovalentConcentration * 1000);
pp.AppendLine(" {0,6:F2} mM divalent salt concentration", context.Designer.DivalentConcentration * 1000);
pp.AppendLine(" {0,6:F2} uM oligo concentration", context.Designer.OligoConcentration * 1000000);
pp.AppendLine("Scoring Complexity: {0,6:F3}", context.Designer.ScoringComplexity());
}
}
pp.NewLine();
//
string title = "Result of Distillation Computation";
pp.AppendLine(title);
pp.AppendLine(new string('-', title.Length));
pp.NewLine();
pp.Indent();
//
// Note: this Append here will cause all the domain ids to disambiguate.
// We want to keep the same disambiguation through the rest of the output here.
//
pp.What = PrettyPrintContext.WHAT.DOMAINS;
pp.AppendLine(result);
//
if (this.fOutputNucleotides)
{
pp.NewLine();
pp.What = PrettyPrintContext.WHAT.NUCLEOTIDES;
pp.AppendLine(result);
}
pp.Outdent();
pp.What = PrettyPrintContext.WhatDefault;
//
if (result is Model)
{
Model m = result as Model;
OutputDomains(context, pp, m);
if (best==null || best.Count == 0)
{
OutputStrands(1, context, pp, strands, context.DesignIter);
}
else
{
int i=1;
foreach (KeyValuePair<DesignScoreResult,SequencesSaveState> pair in best)
{
pair.Value.RestoreAndRescore();
// scores should be as they originally were, but scoring uses parallelization, which introduces some small numerical uncertainty
Trace.Assert(DesignScoreResult.ApproximatelyEquals(pair.Key, pair.Value.SavedDesignScore));
OutputStrands(i++, context, pp, strands, pair.Value.Iteration);
}
}
}
//
if (this.nadirFileContents.Length > 0)
{
pp.InhibitConsole();
pp.Append(this.nadirFileContents.ToString());
pp.DisinhibitConsole();
}
//
MiscUtil.TraceLine(pp.PrettyPrintedOutputString());
pp.CloseLogFile();
return fileName;
}