private float?GetValue(TransitionGroupChromInfo chromInfo)
{
if (chromInfo == null)
{
return(null);
}
return(chromInfo.MassError);
}
private TransitionGroupChromInfo GetTransitionGroupChromInfo(int chromIndex, int pepIndex)
{
TransitionGroupChromInfo result = null;
RunUI(() =>
{
var nodePep = SkylineWindow.DocumentUI.Peptides.ElementAt(pepIndex);
var nodeGroup = nodePep.TransitionGroups.First();
result = nodeGroup.ChromInfos.ToArray()[chromIndex];
});
return(result);
}
public static RetentionTimeValues?GetValues(TransitionGroupChromInfo transitionGroupChromInfo)
{
if (null == transitionGroupChromInfo ||
!transitionGroupChromInfo.RetentionTime.HasValue ||
!transitionGroupChromInfo.StartRetentionTime.HasValue ||
!transitionGroupChromInfo.EndRetentionTime.HasValue)
{
return(null);
}
return(new RetentionTimeValues(transitionGroupChromInfo.RetentionTime.Value,
transitionGroupChromInfo.StartRetentionTime.Value, transitionGroupChromInfo.EndRetentionTime.Value,
transitionGroupChromInfo.Fwhm));
}
private float?GetValue(TransitionGroupChromInfo chromInfo)
{
if (chromInfo == null)
{
return(null);
}
if (_ratioIndex == RATIO_INDEX_NONE)
{
return(chromInfo.Area);
}
var ratioValue = chromInfo.GetRatio(_ratioIndex);
return(ratioValue == null ? (float?)null : ratioValue.Ratio);
}
protected override FindMatch MatchTransitionGroup(TransitionGroupChromInfo transitionGroupChromInfo)
{
int truncatedCount = transitionGroupChromInfo.Truncated.GetValueOrDefault(0);
if (truncatedCount > 0)
{
if (truncatedCount == 1)
{
return new FindMatch(Resources.TruncatedPeakFinder_MatchTransitionGroup__1_truncated_peak);
}
return new FindMatch(string.Format(Resources.TruncatedPeakFinder_MatchTransitionGroup__0__truncated_peaks,
truncatedCount));
}
return null;
}
protected override FindMatch MatchTransitionGroup(TransitionGroupChromInfo transitionGroupChromInfo)
{
int truncatedCount = transitionGroupChromInfo.Truncated.GetValueOrDefault(0);
if (truncatedCount > 0)
{
if (truncatedCount == 1)
{
return(new FindMatch(Resources.TruncatedPeakFinder_MatchTransitionGroup__1_truncated_peak));
}
return(new FindMatch(string.Format(Resources.TruncatedPeakFinder_MatchTransitionGroup__0__truncated_peaks,
truncatedCount)));
}
return(null);
}
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));
}
}
public static double?GetArea(bool treatMissingAsZero, double?qValueCutoff, TransitionGroupDocNode transitionGroup,
TransitionDocNode transition, int replicateIndex, TransitionChromInfo chromInfo)
{
if (treatMissingAsZero && chromInfo.IsEmpty)
{
return(0);
}
if (chromInfo.IsEmpty || chromInfo.IsTruncated.GetValueOrDefault())
{
return(null);
}
if (qValueCutoff.HasValue)
{
TransitionGroupChromInfo transitionGroupChromInfo = FindTransitionGroupChromInfo(transitionGroup,
replicateIndex, chromInfo.FileId);
if (transitionGroupChromInfo != null && transitionGroupChromInfo.QValue > qValueCutoff.Value)
{
return(treatMissingAsZero ? 0 : default(double?));
}
}
return(chromInfo.Area);
}
protected override double?GetValue(TransitionGroupChromInfo chromInfo)
{
var retentionTimeValues = RetentionTimeValues.FromTransitionGroupChromInfo(chromInfo);
retentionTimeValues = ScaleRetentionTimeValues(chromInfo.FileId, retentionTimeValues);
if (retentionTimeValues == null)
{
return(null);
}
switch (RTValue)
{
case RTPeptideValue.Retention:
return(retentionTimeValues.RetentionTime);
case RTPeptideValue.FWHM:
return(retentionTimeValues.Fwhm);
case RTPeptideValue.FWB:
return(retentionTimeValues.Fwb);
}
return(null);
}
protected override double?GetValue(TransitionGroupChromInfo chromInfo)
{
return(chromInfo.Area);
}
protected override FindMatch MatchTransitionGroup(TransitionGroupChromInfo transitionGroupChromInfo)
{
return(transitionGroupChromInfo.IsUserSetManual
? new FindMatch(Resources.ManuallyIntegratedPeakFinder_DisplayName_Manually_integrated_peaks)
: null);
}
protected override FindMatch MatchTransitionGroup(TransitionGroupChromInfo transitionGroupChromInfo)
{
return transitionGroupChromInfo.IsUserSetManual
? new FindMatch(Resources.ManuallyIntegratedPeakFinder_DisplayName_Manually_integrated_peaks)
: null;
}
public static RetentionTimeValues? GetValues(TransitionGroupChromInfo transitionGroupChromInfo)
{
if (null == transitionGroupChromInfo ||
!transitionGroupChromInfo.RetentionTime.HasValue ||
!transitionGroupChromInfo.StartRetentionTime.HasValue ||
!transitionGroupChromInfo.EndRetentionTime.HasValue)
{
return null;
}
return new RetentionTimeValues(transitionGroupChromInfo.RetentionTime.Value,
transitionGroupChromInfo.StartRetentionTime.Value, transitionGroupChromInfo.EndRetentionTime.Value,
transitionGroupChromInfo.Fwhm);
}
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 override double? GetValue(TransitionGroupChromInfo chromInfo)
{
return chromInfo.Area;
}
public FinderChromFileKey(TransitionGroupChromInfo transitionGroupChromInfo)
{
ChromFileInfoId = transitionGroupChromInfo.FileId;
OptStep = transitionGroupChromInfo.OptimizationStep;
}
protected abstract double? GetValue(TransitionGroupChromInfo chromInfo);
public void ChangeChromInfo(EditDescription editDescription, TransitionGroupChromInfo newChromInfo)
{
var newDocNode = Precursor.DocNode.ChangeResults(GetResultFile().ChangeChromInfo(Precursor.DocNode.Results, newChromInfo));
Precursor.ChangeDocNode(editDescription, newDocNode);
}
private TransitionGroupChromInfoData(MeasuredResults measuredResults, int replicateIndex, ChromFileInfo chromFileInfo, TransitionGroupChromInfo transitionGroupChromInfo)
: base(measuredResults, replicateIndex, chromFileInfo, transitionGroupChromInfo)
{
}
// ReSharper restore UnusedParameter.Local
// ReSharper disable UnusedParameter.Local
public void AddChromInfo(TransitionGroupDocNode nodeGroup,
TransitionGroupChromInfo info)
{
if (info == null)
return;
Assume.IsTrue(FileId == null || ReferenceEquals(info.FileId, FileId));
var fileIdPrevious = FileId;
FileId = info.FileId;
FileOrder = Settings.MeasuredResults.Chromatograms[ResultsIndex].IndexOfId(FileId);
// First time through calculate the global standard area for this file
if (fileIdPrevious == null)
GlobalStandardArea = Settings.CalcGlobalStandardArea(ResultsIndex, FileId);
ResultsCount++;
PeakCountRatioTotal += info.PeakCountRatio;
if (info.RetentionTime.HasValue)
{
RetentionTimesMeasured++;
RetentionTimeTotal += info.RetentionTime.Value;
}
if (info.UserSet == UserSet.MATCHED)
IsSetMatching = true;
}
private float? GetPeakCenterTime(TransitionGroupChromInfo chromInfo)
{
if (!chromInfo.StartRetentionTime.HasValue || !chromInfo.EndRetentionTime.HasValue)
return null;
return (chromInfo.StartRetentionTime.Value + chromInfo.EndRetentionTime.Value) / 2;
}
public void ChangeChromInfo(EditDescription editDescription, TransitionGroupChromInfo newChromInfo)
{
var newDocNode = Precursor.DocNode.ChangeResults(GetResultFile().ChangeChromInfo(Precursor.DocNode.Results, newChromInfo));
Precursor.ChangeDocNode(editDescription, newDocNode);
}
protected override double? GetValue(TransitionGroupChromInfo chromInfo)
{
var retentionTimeValues = RetentionTimeValues.GetValues(chromInfo);
if (!retentionTimeValues.HasValue)
{
return null;
}
retentionTimeValues = ScaleRetentionTimeValues(chromInfo.FileId, retentionTimeValues.Value);
if (!retentionTimeValues.HasValue)
{
return null;
}
switch (RTValue)
{
case RTPeptideValue.Retention:
return retentionTimeValues.Value.RetentionTime;
case RTPeptideValue.FWHM:
return retentionTimeValues.Value.Fwhm;
case RTPeptideValue.FWB:
return retentionTimeValues.Value.Fwb;
}
return null;
}
protected abstract double?GetValue(TransitionGroupChromInfo chromInfo);
private float? GetValue(TransitionGroupChromInfo chromInfo)
{
if (chromInfo == null)
return null;
if (_ratioIndex == RATIO_INDEX_NONE)
return chromInfo.Area;
var ratioValue = chromInfo.GetRatio(_ratioIndex);
return ratioValue == null ? (float?)null : ratioValue.Ratio;
}
public FinderChromFileKey(TransitionGroupChromInfo transitionGroupChromInfo)
{
ChromFileInfoId = transitionGroupChromInfo.FileId;
OptStep = transitionGroupChromInfo.OptimizationStep;
}
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 abstract FindMatch MatchTransitionGroup(TransitionGroupChromInfo transitionGroupChromInfo);
protected abstract FindMatch MatchTransitionGroup(TransitionGroupChromInfo transitionGroupChromInfo);
