public void OutputResult(SequenceDesignContext context, object distillationResult, SortedList<DesignScoreResult, SequencesSaveState> best)
{
if (this.outputAsText)
{
string txtFileName = this.OutputText(context, distillationResult, best);
this.OutputScoringMatrices(txtFileName, context);
}
if (this.outputAsGraph)
{
this.OutputGraph(context, distillationResult);
}
}
//
//------------------------------------------------------------------------------
public AllocationStatistics(SequenceDesignContext context, bool fTracingEnabled)
{
this.fTracingEnabled = fTracingEnabled;
AddColumn(12, "iter", "N0", () => context.DesignIter);
AddColumn(9, "best", "", () => context.ScaleScoreFormatted(this.scoring.designScoreBest.Score));
AddColumn(9, "cur", "", () => context.ScaleScoreFormatted(this.scoring.designScoreCur.Score));
AddColumn(13, "mut'ns", "F2", "/iter", () => (double)this.cMutations / this.cScoringIter);
AddColumn(10, "overall", "F1", "/s", () => (this.cPrinted > cPrintedOmit) ? ((double)this.cTotalScoringIter / ((this.now-this.nowScoringTrialZero).TotalMilliseconds * 0.001)) : 0.0);
AddColumn(10, "iters", "F1", "/s", () => (double)this.cScoringIter / ((this.now - this.nowPrev).TotalMilliseconds * 0.001));
AddColumn(10, "legal", "F1", "/s", () => (double)(this.cLegalUp+this.cDown) / ((this.now - this.nowPrev).TotalMilliseconds * 0.001));
AddColumn(8, "temp", "F1", () => this.scoring.temperature);
AddColumn(6, "n", "D", () => this.scoring.designScoreStatistics.N);
// AddColumn(9, "mean", "F2", () => context.ScaleScore(scoring.designScoreDistribution.Mean));
// AddColumn(9, "stddev", "F2", () => context.ScaleScore(scoring.designcoreDistribution.StdDev));
AddColumn(8, "downs", "F1", "%", () => (double)this.cDown / this.cScoringIter * 100);
AddColumn(9, "legalup", "F1", "%", () => (double)this.cLegalUp / this.cScoringIter * 100);
AddColumn(9, "illegal", "F1", "%", () => (double)this.cIllegalUp / this.cScoringIter * 100);
AddColumn(8, "ups", "F1", "%", () => (double)this.cUp / this.cScoringIter * 100);
AddColumn(9, "abandon", "F1", "%", () => (double)this.cAbandon / this.cScoringIter * 100);
AddColumn(9, "hillexp", "g3", () => this.HillExpansion);
AddColumn(8, "cMutd", "F2", () => (double)this.cChangedStrandsSinceScored / this.cScoringAttempts);
AddColumn(5, "cTot", "D", () => this.cScoreable);
AddColumn(10, "remain", "", () =>
{
System.TimeSpan elapsed = this.now - this.nowIterZero;
if (context.DesignIter != 0 && elapsed.TotalMilliseconds > 0)
{
double itersPerSecond = context.DesignIter / (elapsed.TotalMilliseconds * 0.001);
long itersRemaining = context.Program.DesignIterMax - context.DesignIter;
return System.TimeSpan.FromSeconds(itersRemaining / itersPerSecond).ToString("dd':'hh':'mm");
}
else
return "unk";
});
if (fTracingEnabled)
{
this.fileWriter = context.Program.CreateWritableFile("-trace", out this.fileStream);
}
}
void OutputScoringMatrices(string txtFileName, SequenceDesignContext context)
// Output the current scoring matrices in a form that is easily importable into Mathematica.
// We choose a simple JSON format
{
string jsonFileName = Path.GetFileNameWithoutExtension(txtFileName) + ".scores.json";
FileStream fs = new FileStream(jsonFileName, FileMode.Create, FileAccess.Write, FileShare.Read);
if (context.Designer != null)
{
using (StreamWriter writer = new StreamWriter(fs))
{
writer.WriteLine("{");
int strandCount = context.Designer.StrandVerifiers.Count;
for (int i = 0; i < strandCount; i++)
{
writer.WriteLine($"\t\"s{i}\" : \"{context.Designer.StrandVerifiers[i].Strand.Sequence.Nucleotides}\",");
writer.WriteLine($"\t\"m{i}\" : \"{MutabiltiesString(context.Designer.StrandVerifiers[i].Strand.Sequence.Mutabilities)}\",");
}
writer.WriteLine("\t\"scores\" : [");
writer.Flush();
fs.Flush();
SafeFileHandle handle = fs.SafeFileHandle;
context.Designer.PrintScoresMatrix(handle);
fs.Position = fs.Length;
writer.WriteLine("\t]");
writer.WriteLine("}");
}
}
}
void OutputGraph(SequenceDesignContext context, object result)
{
// Render the result
//
RenderingContext ctx = new RenderingContext(result);
ctx.Compose();
ctx.EmitSchematic();
}
void OutputStrands(int resultNumber, SequenceDesignContext context, PrettyPrintContext pp, List<Strand> strands, long iteration)
{
List<string> prints = strands.ConvertAll<string>(s => pp.Cloned().PrettyPrint(BuiltIns.orient(s, Strand.Direction.FiveToThree)));
//
pp.NewLine();
string strStrandsCaption = context.Designer==null
? $"#{resultNumber}: Strands:"
: $"#{resultNumber}: Strands: score={context.ScaleScoreFormatted(context.Scoring.designScoreCur.Score)} iter={iteration:N0}";
string strStrandsUnderline = new string('-', strStrandsCaption.Length);
pp.AppendLine(strStrandsCaption);
pp.AppendLine(strStrandsUnderline);
pp.Indent();
//
AutoWidthTable formatter = new AutoWidthTable();
List<string> formats = new List<string>();
formatter.AddColumn(strands, s => s.DisplayName); formats.Add("{0}");
formatter.AddColumn(strands, s => s.Length); formats.Add(" len={0}");
if (context.Designer !=null)
{
formatter.AddColumn(strands, s => context.ScaleScoreFormatted(s.DesignScore)); formats.Add(" score={0}");
formatter.AddColumn(strands, s => true
? String.Format("{1}{0:F1}", (s.MeltInfo as IMeltInfo).TempCelsiusCur, (s.MeltInfo.hasGoal ? ":" : "="))
: "=n/a");
formats.Add(" Tm{0}");
}
formatter.AddColumn(prints, p => p); formats.Add(" {0}");
// formatter.AddColumn(strands, s => s.ChunckedNucleotidesWithDecorations); formats.Add(" {0}");
formatter.FormatTo(pp, formats.ToArray());
//
if (context.Designer != null)
{
pp.NewLine();
formatter = new AutoWidthTable();
formats = new List<string>();
formatter.AddColumn(strands, s => $"{s.DisplayName}.seed="); formats.Add("{0}");
formatter.AddColumn(strands, s => $"\"{s.ChunckedNucleotidesWithDecorations}\";"); formats.Add("{0}");
formatter.FormatTo(pp, formats.ToArray());
}
//
pp.Outdent();
}
void OutputDomains(SequenceDesignContext context, PrettyPrintContext pp, Model m)
{
List<Domain> domains = new List<Domain>();
domains.AddRange(m.AllDomains().Distinct<Domain>(new ChemicalEqualitor<Domain>()).Where<Domain>(d => (d.Length > 0)));
domains.Sort((x,y) => x.FullDisplayName.CompareTo(y.FullDisplayName));
//
pp.NewLine();
string strDomainsCaption = context.Designer==null ? "Domains" : "Domains (nucleotides as in #1 below)";
string strDoaminsUnderline = new string('-', strDomainsCaption.Length);
pp.AppendLine(strDomainsCaption);
pp.AppendLine(strDoaminsUnderline);
pp.Indent();
//
AutoWidthTable formatter = new AutoWidthTable();
List<string> formats = new List<string>();
formatter.AddColumn(domains, d => d.FullDisplayName); formats.Add("{0}");
formatter.AddColumn(domains, d => d.Id); formats.Add(" id={0}");
formatter.AddColumn(domains, d => d.Length); formats.Add(" len={0}");
if (context.Designer != null)
{
formatter.AddColumn(domains, d =>
{
double tm = ThermodynamicsData.ComputeThermodynamics(context.Designer.ExperimentalConfiguration, d.Nucleotides, 0).MeltTempCelsius;
return tm > 0 ? $"{tm:F1}" : "n/a";
});
formats.Add(" Tm={0}");
}
formatter.AddColumn(domains, d => d.ChunkedNucleotides); formats.Add(" {0}");
formatter.FormatTo(pp, formats.ToArray());
//
pp.Outdent();
}
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 void Print(SequenceDesignContext context, Scoring scoring)
{
if (!this.fTracingEnabled) return;
this.context = context;
this.scoring = scoring;
this.now = System.DateTime.Now;
if (context.Program.Verbose || context.Program.DesignVerbose)
{
if (context.DesignIter % context.Program.DesignVerboseColumnHeadersCount == 0)
{
this.WriteLine(this.columnHeaders);
}
StringBuilder line = new StringBuilder();
for (int i = 0; i < this.columnValues.Count; i++)
{
object value = this.columnValues[i]();
string formatted = String.Format(this.columnFormats[i], value);
line.Append(formatted);
}
this.WriteLine(line.ToString());
}
else
{
MiscUtil.Trace($"{scoring.designScoreBest:F1} ");
}
this.cPrinted++;
if (this.cPrinted == cPrintedOmit)
{
this.cTotalScoringIter = 0;
this.nowScoringTrialZero = System.DateTime.Now;
}
this.nowPrev = this.now;
}