public PeakBoundsMatch(TransitionGroupChromInfo chromInfoTrue,
TransitionGroupChromInfo chromInfoPicked,
MatchKey key,
ChromatogramSet chromSet,
MsDataFileUri filePath,
TransitionGroupDocNode nodeGroup,
PeptideDocNode nodePep,
bool hasNoQValues,
bool hasNoScores,
bool apexPresent)
{
_chromatogramSet = chromSet;
ChromInfoTrue = chromInfoTrue;
ChromInfoPicked = chromInfoPicked;
Key = key;
FilePath = filePath;
NodeGroup = nodeGroup;
NodePep = nodePep;
// Read apex
if (apexPresent)
{
PickedApex = ParsePickedTimeAnnotation(ComparePeakBoundaries.APEX_ANNOTATION);
PickedStartBoundary = ParsePickedTimeAnnotation(ComparePeakBoundaries.START_TIME_ANNOTATION);
PickedEndBoundary = ParsePickedTimeAnnotation(ComparePeakBoundaries.END_TIME_ANNOTATION);
}
else
{
PickedApex = ChromInfoPicked.RetentionTime;
PickedStartBoundary = ChromInfoPicked.StartRetentionTime;
PickedEndBoundary = ChromInfoPicked.EndRetentionTime;
}
QValue = GetScoreValue(ChromInfoPicked, MProphetResultsHandler.AnnotationName, ci => ci.QValue);
if (QValue == null && !IsMissingPickedPeak && !hasNoQValues)
{
throw new IOException(string.Format(
Resources.PeakBoundsMatch_QValue_Unable_to_read_q_value_annotation_for_peptide__0__of_file__1_,
ModifiedSequence, FileName));
}
Score = GetScoreValue(ChromInfoPicked, MProphetResultsHandler.MAnnotationName, ci => ci.ZScore);
if (Score == null && !IsMissingPickedPeak && !hasNoScores)
{
throw new IOException(string.Format(
Resources.PeakBoundsMatch_PeakBoundsMatch_Unable_to_read_a_score_annotation_for_peptide__0__of_file__1_,
ModifiedSequence, FileName));
}
}
protected bool Equals(MatchKey other)
{
return(FileId == other.FileId && TransitionGroupId == other.TransitionGroupId);
}
public PeakBoundsMatch(TransitionGroupChromInfo chromInfoTrue,
TransitionGroupChromInfo chromInfoPicked,
MatchKey key,
MsDataFileUri filePath,
TransitionGroupDocNode nodeGroup,
bool hasNoQValues,
bool hasNoScores,
bool apexPresent)
{
ChromInfoTrue = chromInfoTrue;
ChromInfoPicked = chromInfoPicked;
Key = key;
FilePath = filePath;
NodeGroup = nodeGroup;
// Read apex
if (apexPresent)
{
string apexString = ChromInfoPicked.Annotations.GetAnnotation(ComparePeakBoundaries.APEX_ANNOTATION);
double apexDouble;
if (!double.TryParse(apexString, out apexDouble))
{
if (apexString == null || apexString.Equals(TextUtil.EXCEL_NA))
{
PickedApex = null;
}
else
{
throw new IOException(string.Format(Resources.PeakBoundsMatch_PeakBoundsMatch_Unable_to_read_apex_retention_time_value_for_peptide__0__of_file__1__, Sequence, FileName));
}
}
else
{
PickedApex = apexDouble;
}
}
else
{
PickedApex = ChromInfoPicked.RetentionTime;
}
string qValueString = ChromInfoPicked.Annotations.GetAnnotation(MProphetResultsHandler.AnnotationName);
double qValueDouble;
// qValue MUST be present unless the peak is null or ALL q Values are absent
if (!double.TryParse(qValueString, out qValueDouble))
{
if (!IsMissingPickedPeak && !hasNoQValues)
{
throw new IOException(string.Format(Resources.PeakBoundsMatch_QValue_Unable_to_read_q_value_annotation_for_peptide__0__of_file__1_, Sequence, FileName));
}
QValue = null;
}
else
{
QValue = qValueDouble;
}
// Same for score
string scoreString = ChromInfoPicked.Annotations.GetAnnotation(MProphetResultsHandler.MAnnotationName);
double scoreDouble;
if (!double.TryParse(scoreString, out scoreDouble))
{
if (!IsMissingPickedPeak && !hasNoScores)
{
throw new IOException(string.Format(Resources.PeakBoundsMatch_QValue_Unable_to_read_q_value_annotation_for_peptide__0__of_file__1_, Sequence, FileName));
}
Score = null;
}
else
{
Score = scoreDouble;
}
}
public void GenerateComparison(SrmDocument docOriginal, IProgressMonitor progressMonitor)
{
DocOriginal = docOriginal;
_docCompare = docOriginal;
if (IsModel)
{
var handler = new MProphetResultsHandler(DocOriginal, PeakScoringModel)
{
AddAnnotation = true,
AddMAnnotation = true
};
handler.ScoreFeatures(progressMonitor);
_docCompare = handler.ChangePeaks(progressMonitor);
}
else
{
// Add in the necessary annotation definitions so that ImportPeakBoundaries can read them
_docCompare = AddAnnotationIfMissing(_docCompare, MProphetResultsHandler.AnnotationName);
_docCompare = AddAnnotationIfMissing(_docCompare, MProphetResultsHandler.MAnnotationName);
_docCompare = AddAnnotationIfMissing(_docCompare, APEX_ANNOTATION);
// But strip the values of these annotations if there were any
var annotationNamesToStrip = new List <string>
{
MProphetResultsHandler.AnnotationName,
MProphetResultsHandler.MAnnotationName,
APEX_ANNOTATION
};
var annotationNamesToKeep = _docCompare.Settings.DataSettings.AnnotationDefs
.Where(def => !annotationNamesToStrip.Contains(def.Name))
.Select(def => def.Name).ToList();
_docCompare = (SrmDocument)_docCompare.StripAnnotationValues(annotationNamesToKeep);
Importer = new PeakBoundaryImporter(_docCompare);
long lineCount = Helpers.CountLinesInFile(FilePath);
// Peek at the file to see if it has a column called "Apex"
using (var reader = new StreamReader(FilePath))
{
var line = reader.ReadLine();
var fieldNames = PeakBoundaryImporter.FIELD_NAMES.ToList();
fieldNames.Add(new [] { APEX_ANNOTATION });
int fieldsTotal;
int[] fieldIndices;
var separator = PeakBoundaryImporter.DetermineCorrectSeparator(line, fieldNames,
PeakBoundaryImporter.REQUIRED_NO_CHROM, out fieldIndices, out fieldsTotal);
ApexPresent = separator != null && fieldIndices.Last() != -1;
}
_docCompare = Importer.Import(FilePath, progressMonitor, lineCount, true, !ApexPresent);
}
var matches = new List <PeakBoundsMatch>();
var truePeptides = DocOriginal.Molecules.ToList();
var pickedPeptides = _docCompare.Molecules.ToList();
int nTruePeptides = truePeptides.Count;
var chromatogramSets = DocOriginal.Settings.MeasuredResults.Chromatograms;
for (int i = 0; i < chromatogramSets.Count; i++)
{
var set = chromatogramSets[i];
for (int j = 0; j < nTruePeptides; j++)
{
var truePeptide = truePeptides[j];
var pickedPeptide = pickedPeptides[j];
// We don't care about peak picking performance for decoys
if (truePeptide.IsDecoy)
{
continue;
}
// We don't care about peak picking performance for standard peptides
if (truePeptide.GlobalStandardType != null)
{
continue;
}
var trueGroups = truePeptide.TransitionGroups.ToList();
var pickedGroups = pickedPeptide.TransitionGroups.ToList();
for (int k = 0; k < trueGroups.Count; k++)
{
var trueGroup = trueGroups[k];
var pickedGroup = pickedGroups[k];
var trueResults = trueGroup.Results[i];
var pickedResults = pickedGroup.Results[i];
if (trueResults == null)
{
continue;
}
int nChromInfos = trueResults.Count;
for (int m = 0; m < nChromInfos; m++)
{
var trueInfo = trueResults[m];
var pickedInfo = pickedResults[m];
var fileInfo = set.GetFileInfo(trueInfo.FileId);
var filePath = fileInfo.FilePath;
var key = new MatchKey(trueGroup.Id.GlobalIndex, trueInfo.FileId.GlobalIndex);
matches.Add(new PeakBoundsMatch(trueInfo, pickedInfo, key, filePath, trueGroup,
HasNoQValues, HasNoScores, ApexPresent));
}
}
}
}
Matches = matches;
// Detect if the apex time is in seconds, and if so adjust it to minutes
if (ApexPresent)
{
double maxTime = matches.Where(match => match.PickedApex.HasValue)
.Select(match => match.PickedApex.Value).Max();
if (maxTime > PeakBoundaryImporter.GetMaxRt(DocOriginal))
{
foreach (var match in matches.Where(match => match.PickedApex.HasValue))
{
match.PickedApex = match.PickedApex / 60;
}
}
}
}
public void GenerateComparison(SrmDocument docOriginal, IProgressMonitor progressMonitor)
{
DocOriginal = docOriginal;
_docCompare = docOriginal;
if (IsModel)
{
var handler = new MProphetResultsHandler(DocOriginal, PeakScoringModel);
handler.ScoreFeatures(progressMonitor, true);
_docCompare = handler.ChangePeaks(progressMonitor);
}
else
{
// Add in the necessary annotation definitions so that ImportPeakBoundaries can read them
var annotationNamesToStrip = new List <string>
{
MProphetResultsHandler.AnnotationName,
MProphetResultsHandler.MAnnotationName,
APEX_ANNOTATION,
START_TIME_ANNOTATION,
END_TIME_ANNOTATION
};
foreach (var annotationName in annotationNamesToStrip)
{
_docCompare = AddAnnotationIfMissing(_docCompare, annotationName);
}
// But strip the values of these annotations if there were any
var annotationNamesToKeep = _docCompare.Settings.DataSettings.AnnotationDefs
.Where(def => !annotationNamesToStrip.Contains(def.Name))
.Select(def => def.Name).ToList();
_docCompare = (SrmDocument)_docCompare.StripAnnotationValues(annotationNamesToKeep);
Importer = new PeakBoundaryImporter(_docCompare);
long lineCount = Helpers.CountLinesInFile(FilePath);
// Peek at the file to see if it has a column called "Apex"
using (var reader = new StreamReader(FilePath))
{
var line = reader.ReadLine();
var fieldNames = PeakBoundaryImporter.FIELD_NAMES.ToList();
int fieldsTotal;
int[] fieldIndices;
var separator = PeakBoundaryImporter.DetermineCorrectSeparator(line, fieldNames,
PeakBoundaryImporter.REQUIRED_NO_CHROM, out fieldIndices, out fieldsTotal);
ApexPresent = separator != null && fieldIndices[(int)PeakBoundaryImporter.Field.apex_time] != -1;
}
_docCompare = Importer.Import(FilePath, progressMonitor, lineCount, true, !ApexPresent);
if (progressMonitor.IsCanceled)
{
return;
}
}
var matches = new List <PeakBoundsMatch>();
var truePeptides = DocOriginal.Molecules.ToList();
var pickedPeptides = _docCompare.Molecules.ToList();
int nTruePeptides = truePeptides.Count;
var chromatogramSets = DocOriginal.Settings.MeasuredResults.Chromatograms;
for (int i = 0; i < chromatogramSets.Count; i++)
{
var chromSet = chromatogramSets[i];
var set = chromatogramSets[i];
for (int j = 0; j < nTruePeptides; j++)
{
var truePeptide = truePeptides[j];
var pickedPeptide = pickedPeptides[j];
// We don't care about peak picking performance for decoys
if (truePeptide.IsDecoy)
{
continue;
}
// We don't care about peak picking performance for standard peptides
if (truePeptide.GlobalStandardType != null)
{
continue;
}
var trueGroups = truePeptide.TransitionGroups.ToList();
var pickedGroups = pickedPeptide.TransitionGroups.ToList();
for (int k = 0; k < trueGroups.Count; k++)
{
var trueGroup = trueGroups[k];
var pickedGroup = pickedGroups[k];
var trueResults = trueGroup.Results[i];
var pickedResults = pickedGroup.Results[i];
if (trueResults.IsEmpty)
{
continue;
}
int nChromInfos = trueResults.Count;
for (int m = 0; m < nChromInfos; m++)
{
var trueInfo = trueResults[m];
var pickedInfo = pickedResults[m];
// For TRIC testing at the moment
// double? qvaluePicked = PeakBoundsMatch.GetScoreValue(pickedInfo,
// MProphetResultsHandler.AnnotationName, ci => pickedInfo.QValue);
// if (qvaluePicked.HasValue && qvaluePicked.Value > 0.01)
// continue;
var fileInfo = set.GetFileInfo(trueInfo.FileId);
var filePath = fileInfo.FilePath;
var key = new MatchKey(trueGroup.Id.GlobalIndex, trueInfo.FileId.GlobalIndex);
matches.Add(new PeakBoundsMatch(trueInfo, pickedInfo, key, chromSet, filePath,
trueGroup, truePeptide, HasNoQValues, HasNoScores, ApexPresent));
}
}
}
}
Matches = matches;
// Detect if the apex time is in seconds, and if so adjust it to minutes
if (ApexPresent)
{
// ReSharper disable PossibleMultipleEnumeration
var matchesWithApex = matches.Where(match => match.PickedApex.HasValue).ToArray();
double maxTime = 0;
if (matchesWithApex.Length > 0)
{
maxTime = matchesWithApex.Select(match => match.PickedApex.Value).Max();
}
if (maxTime > PeakBoundaryImporter.GetMaxRt(DocOriginal))
{
foreach (var match in matchesWithApex)
{
// If the end is greater than the Apex, then it must also be in seconds (otherwise minutes)
if (match.PickedEndBoundary.HasValue && match.PickedEndBoundary > match.PickedApex)
{
match.PickedEndBoundary = match.PickedEndBoundary / 60;
}
match.PickedApex = match.PickedApex / 60;
// If the start is now greater than the apex, then it must also be in seconds (otherwise minutes)
if (match.PickedStartBoundary.HasValue && match.PickedStartBoundary > match.PickedApex)
{
match.PickedStartBoundary = match.PickedStartBoundary / 60;
}
}
}
// ReSharper restore PossibleMultipleEnumeration
}
}
public PeakBoundsMatch(TransitionGroupChromInfo chromInfoTrue,
TransitionGroupChromInfo chromInfoPicked,
MatchKey key,
MsDataFileUri filePath,
TransitionGroupDocNode nodeGroup,
bool hasNoQValues,
bool hasNoScores,
bool apexPresent)
{
ChromInfoTrue = chromInfoTrue;
ChromInfoPicked = chromInfoPicked;
Key = key;
FilePath = filePath;
NodeGroup = nodeGroup;
// Read apex
if (apexPresent)
{
string apexString = ChromInfoPicked.Annotations.GetAnnotation(ComparePeakBoundaries.APEX_ANNOTATION);
double apexDouble;
if (!double.TryParse(apexString, out apexDouble))
{
if (apexString == null || apexString.Equals(TextUtil.EXCEL_NA))
{
PickedApex = null;
}
else
{
throw new IOException(string.Format(Resources.PeakBoundsMatch_PeakBoundsMatch_Unable_to_read_apex_retention_time_value_for_peptide__0__of_file__1__, Sequence, FileName));
}
}
else
{
PickedApex = apexDouble;
}
}
else
{
PickedApex = ChromInfoPicked.RetentionTime;
}
string qValueString = ChromInfoPicked.Annotations.GetAnnotation(MProphetResultsHandler.AnnotationName);
double qValueDouble;
// qValue MUST be present unless the peak is null or ALL q Values are absent
if (!double.TryParse(qValueString, out qValueDouble))
{
if (!IsMissingPickedPeak && !hasNoQValues)
{
throw new IOException(string.Format(Resources.PeakBoundsMatch_QValue_Unable_to_read_q_value_annotation_for_peptide__0__of_file__1_, Sequence, FileName));
}
QValue = null;
}
else
{
QValue = qValueDouble;
}
// Same for score
string scoreString = ChromInfoPicked.Annotations.GetAnnotation(MProphetResultsHandler.MAnnotationName);
double scoreDouble;
if (!double.TryParse(scoreString, out scoreDouble))
{
if (!IsMissingPickedPeak && !hasNoScores)
{
throw new IOException(string.Format(Resources.PeakBoundsMatch_QValue_Unable_to_read_q_value_annotation_for_peptide__0__of_file__1_, Sequence, FileName));
}
Score = null;
}
else
{
Score = scoreDouble;
}
}
protected bool Equals(MatchKey other)
{
return FileId == other.FileId && TransitionGroupId == other.TransitionGroupId;
}
public void GenerateComparison(SrmDocument docOriginal, IProgressMonitor progressMonitor)
{
DocOriginal = docOriginal;
_docCompare = docOriginal;
if (IsModel)
{
var handler = new MProphetResultsHandler(DocOriginal, PeakScoringModel)
{
AddAnnotation = true,
AddMAnnotation = true
};
handler.ScoreFeatures(progressMonitor);
_docCompare = handler.ChangePeaks(progressMonitor);
}
else
{
// Add in the necessary annotation definitions so that ImportPeakBoundaries can read them
_docCompare = AddAnnotationIfMissing(_docCompare, MProphetResultsHandler.AnnotationName);
_docCompare = AddAnnotationIfMissing(_docCompare, MProphetResultsHandler.MAnnotationName);
_docCompare = AddAnnotationIfMissing(_docCompare, APEX_ANNOTATION);
// But strip the values of these annotations if there were any
var annotationNamesToStrip = new List<string>
{
MProphetResultsHandler.AnnotationName,
MProphetResultsHandler.MAnnotationName,
APEX_ANNOTATION
};
var annotationNamesToKeep = _docCompare.Settings.DataSettings.AnnotationDefs
.Where(def => !annotationNamesToStrip.Contains(def.Name))
.Select(def => def.Name).ToList();
_docCompare = (SrmDocument)_docCompare.StripAnnotationValues(annotationNamesToKeep);
Importer = new PeakBoundaryImporter(_docCompare);
long lineCount = Helpers.CountLinesInFile(FilePath);
// Peek at the file to see if it has a column called "Apex"
using (var reader = new StreamReader(FilePath))
{
var line = reader.ReadLine();
var fieldNames = PeakBoundaryImporter.FIELD_NAMES.ToList();
fieldNames.Add(new [] {APEX_ANNOTATION});
int fieldsTotal;
int[] fieldIndices;
var separator = PeakBoundaryImporter.DetermineCorrectSeparator(line, fieldNames,
PeakBoundaryImporter.REQUIRED_NO_CHROM, out fieldIndices, out fieldsTotal);
ApexPresent = separator != null && fieldIndices.Last() != -1;
}
_docCompare = Importer.Import(FilePath, progressMonitor, lineCount, true, !ApexPresent);
}
var matches = new List<PeakBoundsMatch>();
var truePeptides = DocOriginal.Molecules.ToList();
var pickedPeptides = _docCompare.Molecules.ToList();
int nTruePeptides = truePeptides.Count;
var chromatogramSets = DocOriginal.Settings.MeasuredResults.Chromatograms;
for (int i = 0; i < chromatogramSets.Count; i++)
{
var set = chromatogramSets[i];
for (int j = 0; j < nTruePeptides; j++)
{
var truePeptide = truePeptides[j];
var pickedPeptide = pickedPeptides[j];
// We don't care about peak picking performance for decoys
if (truePeptide.IsDecoy)
continue;
// We don't care about peak picking performance for standard peptides
if (truePeptide.GlobalStandardType != null)
continue;
var trueGroups = truePeptide.TransitionGroups.ToList();
var pickedGroups = pickedPeptide.TransitionGroups.ToList();
for (int k = 0; k < trueGroups.Count; k++)
{
var trueGroup = trueGroups[k];
var pickedGroup = pickedGroups[k];
var trueResults = trueGroup.Results[i];
var pickedResults = pickedGroup.Results[i];
if (trueResults == null)
continue;
int nChromInfos = trueResults.Count;
for (int m = 0; m < nChromInfos; m++)
{
var trueInfo = trueResults[m];
var pickedInfo = pickedResults[m];
var fileInfo = set.GetFileInfo(trueInfo.FileId);
var filePath = fileInfo.FilePath;
var key = new MatchKey(trueGroup.Id.GlobalIndex, trueInfo.FileId.GlobalIndex);
matches.Add(new PeakBoundsMatch(trueInfo, pickedInfo, key, filePath, trueGroup,
HasNoQValues, HasNoScores, ApexPresent));
}
}
}
}
Matches = matches;
// Detect if the apex time is in seconds, and if so adjust it to minutes
if (ApexPresent)
{
double maxTime = matches.Where(match => match.PickedApex.HasValue)
.Select(match => match.PickedApex.Value).Max();
if (maxTime > PeakBoundaryImporter.GetMaxRt(DocOriginal))
{
foreach (var match in matches.Where(match => match.PickedApex.HasValue))
{
match.PickedApex = match.PickedApex / 60;
}
}
}
}