public PrecursorTextId(SignedMz precursorMz, IonMobilityFilter ionMobilityFilter, Target target, ChromExtractor extractor) : this()
{
PrecursorMz = precursorMz;
IonMobility = ionMobilityFilter ?? IonMobilityFilter.EMPTY;
Target = target;
Extractor = extractor;
}
private static string GetExtractorName(ChromExtractor extractor)
{
switch (extractor)
{
case ChromExtractor.base_peak:
return("BasePeak"); // Not L10N
case ChromExtractor.summed:
return("Summed"); // Not L10N
default:
throw new InvalidDataException(Resources.ChromatogramExporter_GetExtractorName_Invalid_extractor_name_);
}
}
public ExtractedSpectrum(Target target,
Color peptideColor,
SignedMz precursorMz,
IonMobilityFilter ionMobility,
ChromExtractor chromExtractor,
int filterIndex,
SpectrumProductFilter[] productFilters,
float[] intensities,
float[] massErrors)
{
Target = target;
PeptideColor = peptideColor;
PrecursorMz = precursorMz;
IonMobility = ionMobility;
Extractor = chromExtractor;
FilterIndex = filterIndex;
ProductFilters = productFilters;
Intensities = intensities;
MassErrors = massErrors;
}
public ExtractedSpectrum(string textId,
Color peptideColor,
double precursorMz,
double ionMobilityValue,
double ionMobilityExtractionWidth,
ChromExtractor chromExtractor,
int filterIndex,
SpectrumProductFilter[] productFilters,
float[] intensities,
float[] massErrors)
{
TextId = textId;
PeptideColor = peptideColor;
PrecursorMz = precursorMz;
IonMobilityValue = ionMobilityValue;
IonMobilityExtractionWidth = ionMobilityExtractionWidth;
Extractor = chromExtractor;
FilterIndex = filterIndex;
ProductFilters = productFilters;
Intensities = intensities;
MassErrors = massErrors;
}
public ExtractedSpectrum(string textId,
Color peptideColor,
double precursorMz,
double ionMobilityValue,
double ionMobilityExtractionWidth,
ChromExtractor chromExtractor,
int filterIndex,
SpectrumProductFilter[] productFilters,
float[] intensities,
float[] massErrors)
{
TextId = textId;
PeptideColor = peptideColor;
PrecursorMz = precursorMz;
IonMobilityValue = ionMobilityValue;
IonMobilityExtractionWidth = ionMobilityExtractionWidth;
Extractor = chromExtractor;
FilterIndex = filterIndex;
ProductFilters = productFilters;
Intensities = intensities;
MassErrors = massErrors;
}
private static string GetExtractorName(ChromExtractor extractor)
{
switch (extractor)
{
case ChromExtractor.base_peak:
return "BasePeak"; // Not L10N
case ChromExtractor.summed:
return "Summed"; // Not L10N
default:
throw new InvalidDataException(Resources.ChromatogramExporter_GetExtractorName_Invalid_extractor_name_);
}
}
public PrecursorTextId(SignedMz precursorMz, string textId, ChromExtractor extractor) : this()
{
PrecursorMz = precursorMz;
TextId = textId;
Extractor = extractor;
}
private bool EnsureChromInfo(MeasuredResults results,
ChromatogramSet chromatograms,
TransitionGroupDocNode[] nodeGroups,
IdentityPath[] groupPaths,
ChromExtractor extractor,
out bool changedGroups,
out bool changedGroupIds)
{
if (UpdateGroups(nodeGroups, groupPaths, out changedGroups, out changedGroupIds) && _extractor == extractor)
return true;
_extractor = extractor;
bool success = false;
try
{
// Get chromatogram sets for all transition groups, recording unique
// file paths in the process.
var listArrayChromInfo = new List<ChromatogramGroupInfo[]>();
var listFiles = new List<MsDataFileUri>();
ChromatogramGroupInfo[] arrayAllIonsChromInfo;
if (!results.TryLoadAllIonsChromatogram(chromatograms, extractor, true,
out arrayAllIonsChromInfo))
{
return false;
}
else
{
listArrayChromInfo.Add(arrayAllIonsChromInfo);
foreach (var chromInfo in arrayAllIonsChromInfo)
{
var filePath = chromInfo.FilePath;
if (!listFiles.Contains(filePath))
listFiles.Add(filePath);
}
}
_hasMergedChromInfo = false;
_arrayChromInfo = new ChromatogramGroupInfo[listFiles.Count][];
for (int i = 0; i < _arrayChromInfo.Length; i++)
{
var arrayNew = new ChromatogramGroupInfo[listArrayChromInfo.Count];
for (int j = 0; j < arrayNew.Length; j++)
{
var arrayChromInfo = listArrayChromInfo[j];
if (arrayChromInfo == null)
continue;
foreach (var chromInfo in arrayChromInfo)
{
if (arrayNew[j] == null && Equals(listFiles[i], chromInfo.FilePath))
arrayNew[j] = chromInfo;
}
}
_arrayChromInfo[i] = arrayNew;
}
success = true;
}
finally
{
// Make sure the info array is set to null on failure.
if (!success)
_arrayChromInfo = null;
}
return true;
}
private void DisplayAllIonsSummary(IRegressionFunction timeRegressionFunction,
TransitionDocNode nodeTranSelected,
ChromatogramSet chromatograms,
ChromExtractor extractor,
ref double bestStartTime,
ref double bestEndTime)
{
if (ChromGroupInfos.Length == 0)
{
return;
}
var chromGroupInfo = ChromGroupInfos[0];
var info = chromGroupInfo.GetTransitionInfo(0, 0);
var fileId = chromatograms.FindFile(chromGroupInfo);
var nodeGroup = _nodeGroups != null ? _nodeGroups[0] : null;
if (nodeGroup == null)
nodeTranSelected = null;
TransitionChromInfo tranPeakInfo = null;
if (nodeGroup != null)
{
float maxPeakHeight = float.MinValue;
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
// Keep track of which chromatogram owns the tallest member of
// the peak on the document tree.
var transitionChromInfo = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, 0);
if (transitionChromInfo == null)
continue;
if (nodeTranSelected != null)
{
if (ReferenceEquals(nodeTran, nodeTranSelected))
tranPeakInfo = transitionChromInfo;
}
else if (transitionChromInfo.Height > maxPeakHeight)
{
maxPeakHeight = transitionChromInfo.Height;
tranPeakInfo = transitionChromInfo;
}
// Adjust best peak window used to zoom the graph to the best peak
AddBestPeakTimes(transitionChromInfo, ref bestStartTime, ref bestEndTime);
}
}
// Apply active transform
info.Transform(Transform);
int numPeaks = info.NumPeaks;
var annotationFlags = new bool[numPeaks];
for (int i = 0; i < numPeaks; i++)
{
// Exclude any peaks between the boundaries of the chosen peak.
annotationFlags[i] = !IntersectPeaks(info.GetPeak(i), tranPeakInfo);
}
var graphItem = new ChromGraphItem(nodeGroup,
nodeTranSelected,
info,
tranPeakInfo,
timeRegressionFunction,
annotationFlags,
null,
0,
true,
true,
0,
COLORS_GROUPS[(int)extractor],
FontSize,
LineWidth);
_graphHelper.AddChromatogram(new PaneKey(nodeGroup), graphItem);
}
public PrecursorTextId(SignedMz precursorMz, Target target, ChromExtractor extractor) : this()
{
PrecursorMz = precursorMz;
Target = target;
Extractor = extractor;
}