public TransitionChromInfo(ChromFileInfoId fileId, int optimizationStep, float?massError,
float retentionTime, float startRetentionTime, float endRetentionTime,
float area, float backgroundArea, float height,
float fwhm, bool fwhmDegenerate, bool?truncated,
PeakIdentification identified, IList <float?> ratios,
Annotations annotations, UserSet userSet)
: base(fileId)
{
OptimizationStep = optimizationStep;
MassError = massError;
RetentionTime = retentionTime;
StartRetentionTime = startRetentionTime;
EndRetentionTime = endRetentionTime;
Area = area;
BackgroundArea = backgroundArea;
Height = height;
Fwhm = fwhm;
// Crawdad can set FWHM to NaN. Need to protect against that here.
if (float.IsNaN(fwhm))
{
Fwhm = 0;
}
IsFwhmDegenerate = fwhmDegenerate;
IsTruncated = truncated;
Identified = identified;
Ratios = ratios;
Annotations = annotations;
UserSet = userSet;
}
public TransitionGroupChromInfo(ChromFileInfoId fileId,
int optimizationStep,
float peakCountRatio,
float?retentionTime,
float?startTime,
float?endTime,
float?fwhm,
float?area,
float?areaMs1,
float?areaFragment,
float?backgroundArea,
float?backgroundAreaMs1,
float?backgroundAreaFragment,
float?height,
IList <RatioValue> ratios,
float?massError,
int?truncated,
PeakIdentification identified,
float?libraryDotProduct,
float?isotopeDotProduct,
Annotations annotations,
UserSet userSet)
: base(fileId)
{
OptimizationStep = optimizationStep;
PeakCountRatio = peakCountRatio;
RetentionTime = retentionTime;
StartRetentionTime = startTime;
EndRetentionTime = endTime;
Fwhm = fwhm;
Area = area;
AreaMs1 = areaMs1;
AreaFragment = areaFragment;
BackgroundArea = backgroundArea;
BackgroundAreaMs1 = backgroundAreaMs1;
BackgroundAreaFragment = backgroundAreaFragment;
Height = height;
Ratios = ratios;
MassError = massError;
Truncated = truncated;
Identified = identified;
LibraryDotProduct = libraryDotProduct;
IsotopeDotProduct = isotopeDotProduct;
Annotations = annotations;
UserSet = userSet;
}
public ChangedPeakBoundsEventArgs(IdentityPath groupPath,
Transition transition,
string nameSet,
MsDataFileUri filePath,
ScaledRetentionTime startTime,
ScaledRetentionTime endTime,
PeakIdentification identified,
PeakBoundsChangeType changeType)
: base(groupPath, nameSet, filePath)
{
Transition = transition;
StartTime = startTime;
EndTime = endTime;
Identified = identified;
ChangeType = changeType;
}
private void DoFileImportTests(SrmDocument docResults,
string importFile,
int[] chargeList,
double?[] minTime,
double?[] maxTime,
PeakIdentification[] identified,
double?[] peakAreas,
string[] peptides,
int fileId,
string[] precursorMzs = null,
string annotationName = null)
{
SrmDocument docNew = ImportFileToDoc(docResults, importFile);
int i = 0;
// Check peptide nodes are correct
foreach (PeptideDocNode peptideNode in docNew.Peptides)
{
Assert.AreEqual(peptideNode.Peptide.Sequence, peptides[i]);
++i;
}
int j = 0;
foreach (TransitionGroupDocNode groupNode in docNew.PeptideTransitionGroups)
{
var groupChromInfo = groupNode.ChromInfos.ToList()[fileId];
// Make sure charge on each transition group is correct
Assert.AreEqual(groupNode.TransitionGroup.PrecursorCharge, chargeList[j]);
// Make sure imported retention time boundaries, including nulls, are correct
Assert.IsTrue(ApproxEqualNullable(groupChromInfo.StartRetentionTime, minTime[j], RT_TOLERANCE));
Assert.IsTrue(ApproxEqualNullable(groupChromInfo.EndRetentionTime, maxTime[j], RT_TOLERANCE));
// Check that peak areas are updated correctly
double peakArea = peakAreas[j] ?? 0;
Assert.IsTrue(ApproxEqualNullable(groupChromInfo.Area, peakAreas[j], RT_TOLERANCE*peakArea));
// Check that identified values are preserved/updated appropriately
Assert.IsTrue(groupChromInfo.Identified == identified[j],
string.Format("No identification match for {0} ({1})", groupNode.TransitionGroup.Peptide, j));
var annotations = groupChromInfo.Annotations;
if (precursorMzs != null)
{
Assert.AreEqual(annotations.ListAnnotations().Length, 1);
Assert.AreEqual(annotations.GetAnnotation(annote), precursorMzs[j]);
}
else
Assert.AreEqual(annotations.ListAnnotations().Length, 0);
++j;
}
}
