protected virtual void InitData()
{
List <DocNode> docNodes = new List <DocNode>();
List <List <PointPairList> > pointPairLists = new List <List <PointPairList> >();
List <String> docNodeLabels = new List <string>();
// ReSharper disable CanBeReplacedWithTryCastAndCheckForNull
if (_docNode is TransitionDocNode)
{
var nodeTran = (TransitionDocNode)_docNode;
ReplicateGroups = GetReplicateGroups(GetReplicateIndices(nodeTran)).ToArray();
docNodes.Add(nodeTran);
pointPairLists.Add(GetPointPairLists(null, nodeTran, _displayType));
docNodeLabels.Add(ChromGraphItem.GetTitle(nodeTran));
}
else if (_docNode is TransitionGroupDocNode)
{
var nodeGroup = (TransitionGroupDocNode)_docNode;
ReplicateGroups = GetReplicateGroups(GetReplicateIndices(nodeGroup)).ToArray();
if (_displayType == DisplayTypeChrom.single || _displayType == DisplayTypeChrom.total)
{
docNodes.Add(nodeGroup);
pointPairLists.Add(GetPointPairLists(nodeGroup, _displayType));
docNodeLabels.Add(ChromGraphItem.GetTitle(nodeGroup));
}
else
{
foreach (TransitionDocNode nodeTran in GraphChromatogram.GetDisplayTransitions(nodeGroup, _displayType))
{
docNodes.Add(nodeTran);
pointPairLists.Add(GetPointPairLists(nodeGroup, nodeTran, _displayType));
docNodeLabels.Add(ChromGraphItem.GetTitle(nodeTran));
}
}
}
else if (_docNode is PeptideDocNode)
{
var nodePep = (PeptideDocNode)_docNode;
ReplicateGroups = GetReplicateGroups(GetReplicateIndices(nodePep)).ToArray();
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
if (!_paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
docNodes.Add(nodeGroup);
pointPairLists.Add(GetPointPairLists(nodeGroup, DisplayTypeChrom.total));
docNodeLabels.Add(ChromGraphItem.GetTitle(nodeGroup));
}
}
// ReSharper restore CanBeReplacedWithTryCastAndCheckForNull
PointPairLists = pointPairLists;
DocNodes = docNodes;
DocNodeLabels = docNodeLabels;
}
protected virtual List <LineInfo> GetPeptidePointPairLists(PeptideGroupDocNode peptideGroup, PeptideDocNode nodePep, bool multiplePeptides)
{
var pointPairLists = new List <LineInfo>();
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
if (!_paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
pointPairLists.Add(new LineInfo(nodeGroup, ChromGraphItem.GetTitle(nodeGroup), GetPointPairLists(nodePep, nodeGroup, DisplayTypeChrom.all)));
}
return(pointPairLists);
}
protected virtual void InitData()
{
List <DocNode> docNodes = new List <DocNode>();
List <IdentityPath> docNodePaths = new List <IdentityPath>();
List <List <PointPairList> > pointPairLists = new List <List <PointPairList> >();
List <String> docNodeLabels = new List <string>();
ReplicateGroups = new ReplicateGroup[0];
foreach (var docNodePath in _selectedDocNodePaths)
{
var nodeArray = _document.ToNodeArray(docNodePath);
var docNode = nodeArray.Last();
var replicateIndices = Enumerable.Range(0, _document.Settings.MeasuredResults.Chromatograms.Count);
// ReSharper disable CanBeReplacedWithTryCastAndCheckForNull
if (docNode is TransitionDocNode)
{
var nodeTran = (TransitionDocNode)docNode;
ReplicateGroups = GetReplicateGroups(replicateIndices).ToArray();
docNodes.Add(nodeTran);
docNodePaths.Add(docNodePath);
pointPairLists.Add(GetPointPairLists((PeptideDocNode)nodeArray[1], (TransitionGroupDocNode)nodeArray[2], nodeTran, _displayType));
docNodeLabels.Add(ChromGraphItem.GetTitle(nodeTran));
}
else if (docNode is TransitionGroupDocNode)
{
var nodeGroup = (TransitionGroupDocNode)docNode;
var peptideDocNode = (PeptideDocNode)nodeArray[1];
ReplicateGroups = GetReplicateGroups(replicateIndices).ToArray();
if (_displayType == DisplayTypeChrom.single || _displayType == DisplayTypeChrom.total)
{
docNodes.Add(nodeGroup);
docNodePaths.Add(docNodePath);
pointPairLists.Add(GetPointPairLists(peptideDocNode, nodeGroup, _displayType));
docNodeLabels.Add(ChromGraphItem.GetTitle(nodeGroup));
}
else
{
foreach (TransitionDocNode nodeTran in GraphChromatogram.GetDisplayTransitions(nodeGroup,
_displayType))
{
docNodes.Add(nodeTran);
docNodePaths.Add(new IdentityPath(docNodePath, nodeTran.Id));
pointPairLists.Add(GetPointPairLists(peptideDocNode, nodeGroup, nodeTran, _displayType));
docNodeLabels.Add(ChromGraphItem.GetTitle(nodeTran));
}
}
}
else if (docNode is PeptideDocNode)
{
var nodePep = (PeptideDocNode)docNode;
ReplicateGroups = GetReplicateGroups(replicateIndices).ToArray();
var isMultiSelect = _selectedDocNodePaths.Count > 1 ||
(_selectedDocNodePaths.Count == 1 && Program.MainWindow != null &&
Program.MainWindow.SelectedNode is PeptideGroupTreeNode);
foreach (var tuple in GetPeptidePointPairLists((PeptideGroupDocNode)nodeArray[0], nodePep, isMultiSelect))
{
docNodes.Add(tuple.Node);
docNodePaths.Add(docNodePath);
pointPairLists.Add(tuple.PointPairList);
docNodeLabels.Add(tuple.DisplaySeq);
}
}
}
// ReSharper restore CanBeReplacedWithTryCastAndCheckForNull
PointPairLists = pointPairLists;
DocNodes = docNodes;
_docNodePaths = ImmutableList.ValueOf(docNodePaths);
DocNodeLabels = docNodeLabels;
var oldGroupNames = ReplicateGroups.Select(g => g.GroupName).ToArray();
var uniqueGroupNames = oldGroupNames.Distinct().ToArray();
// Instert "All" groups and point pair lists in their correct positions
InsertAllGroupsAndPointPairLists(uniqueGroupNames, docNodes.Count);
// Collect all references to points that have a valid Y value
var references = CollectValidPointRefs(uniqueGroupNames, oldGroupNames, docNodes.Count);
// Merge groups if their replicate index is the same and each peptide only occurs in one of the files
MergeGroups(uniqueGroupNames, references);
// Remove groups that don't have any peptides in them
RemoveEmptyGroups(docNodes.Count);
}
public NotFoundChromGraphItem(TransitionGroupDocNode nodeGroup)
: base(string.Format(Resources.NotFoundChromGraphItem_NotFoundChromGraphItem__0__not_found, ChromGraphItem.GetTitle(nodeGroup)))
{
}
public FailedChromGraphItem(TransitionGroupDocNode nodeGroup, Exception x)
: base(string.Format(Resources.FailedChromGraphItem_FailedChromGraphItem__0__load_failed__1__, ChromGraphItem.GetTitle(nodeGroup), x.Message))
{
}
