public UnknownFeatureIonInstanceSpectrumChartDataProvider(IEntityDataService entityDataService, IEnumerable <EntityItemData> entityItemData)
{
ArgumentHelper.AssertNotNull(entityItemData, "entityItemData");
m_entityDataService = entityDataService;
var entityReader = entityDataService.CreateEntityItemReader();
var compoundIonInstanceItem = entityReader.Read <UnknownFeatureIonInstanceItem>(entityItemData.First().GetEntityIds());
// make spectrum header
m_extraHeaderLine = String.Format(
"Ion: {0}, m/z: {1:F5}, Area: {2:F0}",
compoundIonInstanceItem.IonDescription,
compoundIonInstanceItem.Mass,
compoundIonInstanceItem.Area);
// set ion
m_unknownFeatureIonInstanceItems = new[] { compoundIonInstanceItem };
// get reader
entityReader = entityDataService.CreateEntityItemReader();
m_fileNames = entityReader.ReadAll <WorkflowInputFile>().ToDictionary(file => file.FileID, file => Path.GetFileNameWithoutExtension(file.FileName));
// load related chromatographic peak items
var peakItems = entityReader.ReadFlat <UnknownFeatureIonInstanceItem, ChromatogramPeakItem>(compoundIonInstanceItem).Item2;
m_chromatogramPeakItemsMap = new Dictionary <object[], IList <ChromatogramPeakItem> >(IdArrayComparer.Instance)
{
{ compoundIonInstanceItem.GetIDs(), peakItems }
};
// load related spectrum tree
SpectralTreeNodes = LoadSpectralTree();
}
public UnknownFeatureIonInstanceSpectrumChartDataProvider(IEntityDataService entityDataService, IEnumerable<EntityItemData> entityItemData)
{
ArgumentHelper.AssertNotNull(entityItemData, "entityItemData");
m_entityDataService = entityDataService;
var entityReader = entityDataService.CreateEntityItemReader();
var compoundIonInstanceItem = entityReader.Read<UnknownFeatureIonInstanceItem>(entityItemData.First().GetEntityIds());
// make spectrum header
m_extraHeaderLine = String.Format(
"Ion: {0}, m/z: {1:F5}, Area: {2:F0}",
compoundIonInstanceItem.IonDescription,
compoundIonInstanceItem.Mass,
compoundIonInstanceItem.Area);
// set ion
m_unknownFeatureIonInstanceItems = new[] { compoundIonInstanceItem };
// get reader
entityReader = entityDataService.CreateEntityItemReader();
m_fileNames = entityReader.ReadAll<WorkflowInputFile>().ToDictionary(file => file.FileID, file => Path.GetFileNameWithoutExtension(file.FileName));
// load related chromatographic peak items
var peakItems = entityReader.ReadFlat<UnknownFeatureIonInstanceItem, ChromatogramPeakItem>(compoundIonInstanceItem).Item2;
m_chromatogramPeakItemsMap = new Dictionary<object[], IList<ChromatogramPeakItem>>(IdArrayComparer.Instance) { { compoundIonInstanceItem.GetIDs(), peakItems } };
// load related spectrum tree
SpectralTreeNodes = LoadSpectralTree();
}
/// <summary>
/// Loads spectral tree for current compound.
/// </summary>
private IEnumerable <MassSpectrumItemTreeNode> LoadSpectralTree()
{
// get spectra for each ion
if ((m_unknownFeatureIonInstanceItems != null) && (m_unknownFeatureIonInstanceItems.Any()))
{
// check path
IList <string> shortestConnectingPath;
if (m_entityDataService.TryGetShortestConnection <UnknownFeatureIonInstanceItem, MassSpectrumItem>(out shortestConnectingPath))
{
// init container
var spectra = new List <MassSpectrumItem>();
// init reader
var readerSettings = FlatConnectedReaderSettings.Create(shortestConnectingPath);
var entityReader = m_entityDataService.CreateEntityItemReader();
// get spectra for each ion
foreach (var ionInstanceItem in m_unknownFeatureIonInstanceItems)
{
// get spectra
var connectedSpectra = entityReader.ReadFlat <UnknownFeatureIonInstanceItem, MassSpectrumItem>(
ionInstanceItem, readerSettingsT2: readerSettings);
// store spectra
if (connectedSpectra != null)
{
spectra.AddRange(connectedSpectra.Item2);
}
}
// use unique spectra only
var uniqueSpectra = spectra.GroupBy(g => g.Spectrum.Header.SpectrumID).Select(s => s.First()).ToList();
// build tree
return(MassSpectrumItemTreeNode.BuildSpectralTrees(uniqueSpectra));
}
}
return(Enumerable.Empty <MassSpectrumItemTreeNode>());
}
