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;
}
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();
}
int test = 0; // if non-zero, is internal test to run
void Usage()
{
PrettyPrintContext pp = new PrettyPrintContext();
this.OutputBannerAndCopyright(pp);
pp.NewLine();
pp.AppendLine($"usage: nadir [options] input.nadir");
pp.Indent();
pp.AppendLine($"[-f] inputFile input file(s) to read from (multiple input files are allowed)");
pp.AppendLine($"-distill globalItem process definition globalItem into its parts; defaults to first in first file");
pp.AppendLine($"-nodistill force no distillation");
pp.AppendLine($"-design [designerName] design nucleotides using indicated designer; default to first designer, or trivial designer if none");
pp.AppendLine($"-nodesign do not design nucleotide sequences");
pp.AppendLine($"-nice run a background scheduling priority");
pp.Outdent();
pp.AppendLine("");
pp.AppendLine($"nucleotide sequence design options");
pp.Indent();
pp.AppendLine($"-keepBest nnnn report this many of the best nucleic acid assignments we fine (default: {designKeepBestCountDefault:N0})");
pp.AppendLine($"-seed nnnn set the seed of the random number generator (default: random seed)");
pp.AppendLine($"-designRate rate mean mutation rate per iteration (default: {designMutationsPerIterationDefault})");
pp.AppendLine($"-designSweep iter sweep for SNP improvements every # of iterations (default: {designIterMutSweepDefault:N0})");
pp.AppendLine($"-designMin iter run sequence designer at least this # of iterations (default: {designIterMinDefault})");
pp.AppendLine($"-designMax iter run sequence designer at most this # of iterations (default: {designIterMaxDefault:N0})");
pp.AppendLine($"-designGoal score run sequence designer until this score level reached (default: {designGoalDefault})");
pp.AppendLine($"-designTemp t initial temperature for annealling (default: {designTempDefault})");
pp.AppendLine($"-[no]designTrace iter print tracing every # of iterations (default: {designIterTraceDefault})");
pp.Outdent();
if (this.showHiddenUsage)
{
pp.AppendLine("felony options");
pp.Indent();
pp.AppendLine("-felony");
pp.AppendLine("-fasta file");
pp.AppendLine("-forward primer");
pp.AppendLine("-reverse primer");
pp.AppendLine("-amplicon index length");
pp.Outdent();
pp.AppendLine("output options");
pp.Indent();
pp.AppendLine("-out text show output in human-readable text to stdout (default)");
pp.Indent();
pp.AppendLine("-[no]verbose show verbose details in text output");
pp.AppendLine("-debug show debugging-related details in text output");
pp.AppendLine("-nt show nucleotides instead of domains in text output");
pp.AppendLine("-debugTrace tracing to debug output");
pp.AppendLine("-consoleTrace tracing to console output");
pp.AppendLine("-dumpParse trace the parse trees");
pp.AppendLine("-dumpTrees trace the parse trees");
pp.Outdent();
pp.AppendLine("-out graph show a graphical representation of the output");
pp.Outdent();
pp.AppendLine("rare options");
pp.Indent();
pp.AppendLine("-designBad pessimize rather than optimize interactions while designing");
pp.AppendLine("-domconn show domain connections in output");
pp.Outdent();
}
System.Console.Error.Write(pp.PrettyPrintedOutputString());
Environment.Exit(-1);
}
