private void ExportImport(ResultsTestDocumentContainer docContainer, string resultsPath)
{
var optRegression = docContainer.Document.Settings.TransitionSettings.Prediction.CollisionEnergy;
int optSteps = optRegression.StepCount * 2 + 1;
int optSteps1 = optSteps - 1; // First precursor is below 10 volts CE for 1 step
int optSteps2 = optSteps - 3; // Second precursor is below 10 volts CE for 3 steps
// First export
var exporter = new AbiMassListExporter(docContainer.Document)
{
OptimizeType = ExportOptimize.CE,
OptimizeStepCount = optRegression.StepCount,
OptimizeStepSize = optRegression.StepSize
};
string tranListPath = Path.ChangeExtension(docContainer.DocumentFilePath, TextUtil.EXT_CSV);
exporter.Export(tranListPath);
// Make sure line count matches expectations for steps below 10 volts CE
Assert.AreEqual(5 * optSteps1 + 5 * optSteps2, File.ReadAllLines(tranListPath).Length);
// Then import
var resultsUri = new MsDataFilePath(resultsPath);
var chromSet = new ChromatogramSet("Optimize", new[] { resultsUri }, Annotations.EMPTY, optRegression);
var measuredResults = new MeasuredResults(new[] { chromSet });
docContainer.ChangeMeasuredResults(measuredResults, 2, optSteps1 + optSteps2, 5 * optSteps1 + 5 * optSteps2);
// Check expected optimization data with missing values for steps below 10 volts CE
int expectedMissingSteps = optSteps - optSteps1;
foreach (var nodeGroup in docContainer.Document.MoleculeTransitionGroups)
{
foreach (var nodeTran in nodeGroup.Transitions)
{
Assert.IsTrue(nodeTran.HasResults, "No results for transition Mz: {0}", nodeTran.Mz);
Assert.IsNotNull(nodeTran.Results[0]);
Assert.AreEqual(optSteps, nodeTran.Results[0].Count);
for (int i = 0; i < optSteps; i++)
{
if (i < expectedMissingSteps)
{
Assert.IsTrue(nodeTran.Results[0][i].IsEmpty);
}
else
{
Assert.IsFalse(nodeTran.Results[0][i].IsEmpty);
}
}
}
expectedMissingSteps = optSteps - optSteps2;
}
}
protected override void WriteTransition(TextWriter writer,
XmlFastaSequence sequence,
XmlPeptide peptide,
XmlTransition transition)
{
char separator = TextUtil.GetCsvSeparator(_cultureInfo);
writer.Write(transition.PrecursorMz.ToString(_cultureInfo));
writer.Write(separator);
writer.Write(transition.ProductMz.ToString(_cultureInfo));
writer.Write(separator);
if (MethodType == ExportMethodType.Standard)
{
writer.Write(Math.Round(DwellTime, 2).ToString(_cultureInfo));
}
else
{
if (!peptide.PredictedRetentionTime.HasValue)
{
throw new InvalidOperationException(Resources.XmlThermoMassListExporter_WriteTransition_Attempt_to_write_scheduling_parameters_failed);
}
writer.Write(peptide.PredictedRetentionTime.Value.ToString(_cultureInfo));
}
writer.Write(separator);
// Write special ID for ABI software
var fastaSequence = new FastaSequence(sequence.Name, sequence.Description, null, peptide.Sequence);
var newPeptide = new Peptide(fastaSequence, peptide.Sequence, 0, peptide.Sequence.Length, peptide.MissedCleavages);
var nodePep = new PeptideDocNode(newPeptide);
string modifiedPepSequence = AbiMassListExporter.GetSequenceWithModsString(nodePep, _document.Settings); // Not L10N;
string extPeptideId = string.Format("{0}.{1}.{2}.{3}", // Not L10N
sequence.Name,
modifiedPepSequence,
GetTransitionName(transition),
"light"); // Not L10N : file format
writer.WriteDsvField(extPeptideId, separator);
writer.Write(separator);
writer.Write(Math.Round(transition.DeclusteringPotential ?? 0, 1).ToString(_cultureInfo));
writer.Write(separator);
writer.Write(Math.Round(transition.CollisionEnergy, 1).ToString(_cultureInfo));
writer.WriteLine();
}
protected override DataObject GetNodeData()
{
FastaSequence fastaSeq = DocNode.Id as FastaSequence;
if (fastaSeq == null)
{
return(base.GetNodeData());
}
DataObject data = new DataObject();
string fastaText = fastaSeq.FastaFileText;
// If protein has been renamed in the UI
if (!Equals(DocNode.Name, fastaSeq.Name))
{
int oldNameLen = (fastaSeq.Name != null ? fastaSeq.Name.Length : 0);
fastaText = @">" + DocNode.Name + fastaText.Substring(oldNameLen + 1);
}
data.SetData(DataFormats.Text, fastaText);
var sb = new StringBuilder();
sb.Append(@"<b>").Append(DocNode.Name).Append(@"</b> ");
sb.Append(@"<i>");
if (string.IsNullOrEmpty(DocNode.Description)) // CONSIDER bspratt - a more complete set of data here, maybe - accession etc
{
sb.AppendLine(@"<br/>");
}
else
{
foreach (string desc in Descriptions)
{
sb.Append(desc).AppendLine(@"<br/>");
}
}
sb.Append(@"</i>");
using (var peptides = GetChoices(true).GetEnumerator())
{
HashSet <DocNode> peptidesChosen = new HashSet <DocNode>(Chosen);
PeptideDocNode nodePep = (PeptideDocNode)(peptides.MoveNext() ? peptides.Current : null);
bool chosen = (nodePep != null && peptidesChosen.Contains(nodePep));
bool inPeptide = false;
string aa = fastaSeq.Sequence;
for (int i = 0; i < aa.Length; i++)
{
if (nodePep != null)
{
while (nodePep != null && i >= nodePep.Peptide.End)
{
nodePep = (PeptideDocNode)(peptides.MoveNext() ? peptides.Current : null);
if (nodePep != null)
{
bool chosenNew = peptidesChosen.Contains(nodePep);
// Need a new font tag, if the chosen state is changing
if (chosenNew != chosen)
{
sb.Append(@"</font>");
inPeptide = false;
}
chosen = chosenNew;
}
}
if (nodePep != null && i >= nodePep.Peptide.Begin)
{
if (!inPeptide)
{
sb.Append(chosen
// ReSharper disable LocalizableElement
? "<font style=\"font-weight: bold; color: blue\">"
: "<font style=\"font-weight: bold\">");
// ReSharper restore LocalizableElement
inPeptide = true;
}
}
else if (inPeptide)
{
sb.Append(@"</font>");
inPeptide = false;
}
}
sb.Append(aa[i]);
}
if (inPeptide)
{
sb.Append(@"</font>");
}
}
data.SetData(DataFormats.Html, HtmlFragment.ClipBoardText(sb.ToString()));
var transitionListExporter = new AbiMassListExporter(Document, DocNode);
transitionListExporter.Export(null);
data.SetData(DataFormats.CommaSeparatedValue,
transitionListExporter.MemoryOutput[AbstractMassListExporter.MEMORY_KEY_ROOT].ToString());
return(data);
}
private static string GetTransitionName(XmlTransition transition)
{
return(AbiMassListExporter.GetTransitionName(Adduct.FromChargeProtonated(transition.PrecursorCharge),
transition.FragmentType.ToString().ToLower() + transition.FragmentOrdinal,
Adduct.FromChargeProtonated(transition.ProductCharge)));
}
protected override DataObject GetNodeData()
{
FastaSequence fastaSeq = DocNode.Id as FastaSequence;
if (fastaSeq == null)
return base.GetNodeData();
DataObject data = new DataObject();
string fastaText = fastaSeq.FastaFileText;
// If protein has been renamed in the UI
if (!Equals(DocNode.Name, fastaSeq.Name))
{
int oldNameLen = (fastaSeq.Name != null ? fastaSeq.Name.Length : 0);
fastaText = ">" + DocNode.Name + fastaText.Substring(oldNameLen + 1); // Not L10N
}
data.SetData(DataFormats.Text, fastaText);
var sb = new StringBuilder();
sb.Append("<b>").Append(DocNode.Name).Append("</b> "); // Not L10N
sb.Append("<i>"); // Not L10N
if (string.IsNullOrEmpty(DocNode.Description)) // CONSIDER bspratt - a more complete set of data here, maybe - accession etc
sb.AppendLine("<br/>"); // Not L10N
else
{
foreach (string desc in Descriptions)
sb.Append(desc).AppendLine("<br/>"); // Not L10N
}
sb.Append("</i>"); // Not L10N
IEnumerator<DocNode> peptides = GetChoices(true).GetEnumerator();
HashSet<DocNode> peptidesChosen = new HashSet<DocNode>(Chosen);
PeptideDocNode nodePep = (PeptideDocNode)(peptides.MoveNext() ? peptides.Current : null);
bool chosen = (nodePep != null && peptidesChosen.Contains(nodePep));
bool inPeptide = false;
string aa = fastaSeq.Sequence;
for (int i = 0; i < aa.Length; i++)
{
if (nodePep != null)
{
while (nodePep != null && i >= nodePep.Peptide.End)
{
nodePep = (PeptideDocNode)(peptides.MoveNext() ? peptides.Current : null);
if (nodePep != null)
{
bool chosenNew = peptidesChosen.Contains(nodePep);
// Need a new font tag, if the chosen state is changing
if (chosenNew != chosen)
{
sb.Append("</font>"); // Not L10N
inPeptide = false;
}
chosen = chosenNew;
}
}
if (nodePep != null && i >= nodePep.Peptide.Begin)
{
if (!inPeptide)
{
sb.Append(chosen
? "<font style=\"font-weight: bold; color: blue\">" // Not L10N
: "<font style=\"font-weight: bold\">"); // Not L10N
inPeptide = true;
}
}
else if (inPeptide)
{
sb.Append("</font>"); // Not L10N
inPeptide = false;
}
}
sb.Append(aa[i]);
}
if (inPeptide)
sb.Append("</font>"); // Not L10N
data.SetData(DataFormats.Html, HtmlFragment.ClipBoardText(sb.ToString()));
var transitionListExporter = new AbiMassListExporter(Document, DocNode);
transitionListExporter.Export(null);
data.SetData(DataFormats.CommaSeparatedValue,
transitionListExporter.MemoryOutput[AbstractMassListExporter.MEMORY_KEY_ROOT].ToString());
return data;
}
