public static SrmDocument ApplyPeak(SrmDocument doc, PeptideTreeNode nodePepTree, TransitionGroupDocNode nodeTranGroup,
int resultsIndex, int? resultsFile, bool subsequent, ILongWaitBroker longWaitBroker)
{
nodeTranGroup = nodeTranGroup ?? PickTransitionGroup(doc, nodePepTree, resultsIndex);
PeakMatchData referenceTarget;
PeakMatchData[] referenceMatchData;
DateTime? runTime;
GetReferenceData(doc, nodePepTree.DocNode, nodeTranGroup, resultsIndex, resultsFile, out referenceTarget, out referenceMatchData, out runTime);
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
for (int i = 0; i < chromatograms.Count; i++)
{
var chromSet = chromatograms[i];
for (int j = 0; j < chromSet.MSDataFileInfos.Count; j++)
{
var fileInfo = chromSet.MSDataFileInfos[j];
if ((i == resultsIndex && (!resultsFile.HasValue || resultsFile.Value == j)) ||
(subsequent && runTime != null && fileInfo.RunStartTime < runTime))
{
continue;
}
var bestMatch = GetPeakMatch(doc, chromSet, fileInfo, nodeTranGroup, referenceTarget, referenceMatchData);
if (bestMatch != null)
doc = bestMatch.ChangePeak(doc, nodePepTree, nodeTranGroup, chromSet.Name, fileInfo.FilePath);
}
longWaitBroker.SetProgressCheckCancel(i + 1, chromatograms.Count);
}
return doc;
}
public static PeptideTreeNode CreateInstance(SequenceTree tree, DocNode nodeDoc)
{
Debug.Assert(nodeDoc is PeptideDocNode);
var nodeTree = new PeptideTreeNode(tree, (PeptideDocNode)nodeDoc);
if (tree.ExpandPeptides)
{
nodeTree.Expand();
}
return(nodeTree);
}
public override Size RenderTip(Graphics g, Size sizeMax, bool draw)
{
var sizeInitial = base.RenderTip(g, sizeMax, draw);
if (ShowAnnotationTipOnly)
{
return(sizeInitial);
}
g.TranslateTransform(0, sizeInitial.Height);
FastaSequence fastaSeq = DocNode.Id as FastaSequence;
var tableDetails = new TableDesc();
using (RenderTools rt = new RenderTools())
{
SizeF sizeX80 = g.MeasureString(X80, rt.FontNormal);
float widthLine = sizeX80.Width;
float heightLine = sizeX80.Height;
float heightMax = sizeMax.Height;
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Name, DocNode.Name, rt);
// If current name isn't the original, show that.
if (DocNode.PeptideGroup.Name != null && !Equals(DocNode.Name, DocNode.PeptideGroup.Name))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Original_Name, DocNode.OriginalName, rt);
}
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.Accession))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Accession, DocNode.ProteinMetadata.Accession, rt);
}
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.PreferredName))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Preferred_Name, DocNode.ProteinMetadata.PreferredName, rt);
}
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.Gene))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Gene, DocNode.ProteinMetadata.Gene, rt);
}
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.Species))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Species, DocNode.ProteinMetadata.Species, rt);
}
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.DisplaySearchHistory()))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Searched, DocNode.ProteinMetadata.DisplaySearchHistory(), rt);
}
if (!String.IsNullOrEmpty(DocNode.ProteinMetadata.Description))
{
tableDetails.AddDetailRowLineWrap(g, Resources.PeptideGroupTreeNode_RenderTip_Description, DocNode.ProteinMetadata.Description, rt);
}
if (DocNode.PeptideGroup.Description != null && !Equals(DocNode.Description, DocNode.PeptideGroup.Description))
{
tableDetails.AddDetailRow(Resources.PeptideGroupTreeNode_RenderTip_Original_Description, DocNode.OriginalDescription, rt);
}
SizeF sizeDetails = tableDetails.CalcDimensions(g);
sizeDetails.Height += TableDesc.TABLE_SPACING; // Spacing between details and fragments
float heightTotal = sizeDetails.Height;
widthLine = Math.Max(widthLine, sizeDetails.Width);
if (draw)
{
tableDetails.Draw(g);
}
if (fastaSeq != null)
{
IList <DocNode> peptidesChoices = GetChoices(true).ToArray();
HashSet <DocNode> peptidesChosen = new HashSet <DocNode>(Chosen);
// Make sure all chosen peptides get listed
HashSet <DocNode> setChoices = new HashSet <DocNode>(peptidesChoices);
setChoices.UnionWith(peptidesChosen);
var arrayChoices = setChoices.ToArray();
Array.Sort(arrayChoices, (choice1, choice2) =>
PeptideFromChoice(choice1).Order - PeptideFromChoice(choice2).Order);
peptidesChoices = arrayChoices;
// Get the selected peptide, if there is one
PeptideTreeNode nodePepTree = SequenceTree.GetNodeOfType <PeptideTreeNode>();
Peptide peptideSelected = (nodePepTree != null ? nodePepTree.DocNode.Peptide : null);
int i = 0;
string aa = fastaSeq.Sequence;
const bool peptideList = false;
while (i < aa.Length)
{
// If this is not the last possible line, just render it.
if (heightTotal + heightLine * 2 <= heightMax)
{
i = RenderAALine(aa, peptideList, i, false, draw,
peptidesChoices, peptidesChosen, peptideSelected,
g, rt, heightTotal, widthLine);
heightTotal += heightLine;
}
// If not drawing, then this is the last possible line, and
// it will have content.
else if (!draw)
{
heightTotal += heightLine;
break;
}
// Otherwise, measure first, and then re-render, with an elipsis
// if the full sequence cannot be shown.
else
{
RenderAALine(aa, peptideList, i, false, false,
peptidesChoices, peptidesChosen, peptideSelected,
g, rt, heightTotal, widthLine);
RenderAALine(aa, peptideList, i, i < aa.Length, true,
peptidesChoices, peptidesChosen, peptideSelected,
g, rt, heightTotal, widthLine);
heightTotal += heightLine;
break;
}
}
}
return(TipSize(Math.Max(widthLine, sizeInitial.Width), heightTotal + sizeInitial.Height));
}
}
public Size RenderTip(Graphics g, Size sizeMax, bool draw)
{
return(PeptideTreeNode.RenderTip(_nodePep, null,
_settings, g, sizeMax, draw));
}
public override Image GetPickPeakImage(DocNode child)
{
return(PeptideTreeNode.GetPeakImage((PeptideDocNode)child, SequenceTree));
}
public override bool DrawPickLabel(DocNode child, Graphics g, Rectangle bounds, ModFontHolder fonts, Color foreColor, Color backColor)
{
PeptideTreeNode.DrawPeptideText((PeptideDocNode)child, DocSettings, null,
g, bounds, fonts, foreColor, backColor);
return(true);
}
public static PeptideTreeNode CreateInstance(SequenceTree tree, DocNode nodeDoc)
{
Debug.Assert(nodeDoc is PeptideDocNode);
var nodeTree = new PeptideTreeNode(tree, (PeptideDocNode)nodeDoc);
if (tree.ExpandPeptides)
nodeTree.Expand();
return nodeTree;
}
private static TransitionGroupDocNode PickTransitionGroup(SrmDocument doc, PeptideTreeNode nodePepTree, int resultsIndex)
{
// Determine which transition group to use
var nodeTranGroups = nodePepTree.DocNode.TransitionGroups.ToArray();
if (!nodeTranGroups.Any())
return null;
if (nodeTranGroups.Count() == 1)
return nodeTranGroups.First();
var standards = doc.Settings.PeptideSettings.Modifications.InternalStandardTypes;
var standardList = nodeTranGroups.Where(tranGroup => standards.Contains(tranGroup.TransitionGroup.LabelType)).ToArray();
if (standardList.Count() == 1)
return standardList.First();
if (standardList.Count() > 1)
nodeTranGroups = standardList;
// Still not sure, pick the one with the most peak area
TransitionGroupDocNode best = null;
float mzMatchTolerance = (float) doc.Settings.TransitionSettings.Instrument.MzMatchTolerance;
float highestAreaSum = 0;
foreach (var tranGroup in nodeTranGroups)
{
ChromatogramSet chromSet = doc.Settings.MeasuredResults.Chromatograms[resultsIndex];
ChromatogramGroupInfo[] chromGroupInfos;
if (!doc.Settings.MeasuredResults.TryLoadChromatogram(chromSet, nodePepTree.DocNode, tranGroup, mzMatchTolerance, false, out chromGroupInfos))
continue;
float areaSum = chromGroupInfos.Where(info => info != null && info.TransitionPointSets != null)
.Sum(chromGroupInfo => chromGroupInfo.TransitionPointSets.Sum(chromInfo => chromInfo.Peaks.Sum(peak => peak.Area)));
if (areaSum > highestAreaSum)
{
best = tranGroup;
highestAreaSum = areaSum;
}
}
return best;
}
