private List<TableExporter.TableTreeNode> getSpectrumSourceGroupTree(DataFilter viewFilter, DataFilter dataFilter, ISession session)
{
var groupTreeHeaders = new List<string>
{
"'Group'",
"'Filtered Spectra'",
"'Distinct Peptides'",
"'Distinct Matches'",
"'Distinct Analyses'",
"'Distinct Charges'"
};
var sourceTreeHeaders = new List<string>
{
"'Source'",
"'Filtered Spectra'",
"'Distinct Peptides'",
"'Distinct Matches'",
"'Distinct Analyses'",
"'Distinct Charges'"
};
var groupNodes = new List<TableExporter.TableTreeNode>();
var groups = session.CreateQuery(SpectrumTableForm.AggregateRow.Selection + ", ssgl " +
dataFilter.GetFilteredQueryString(DataFilter.FromPeptideSpectrumMatch,
DataFilter.PeptideSpectrumMatchToProtein,
DataFilter.PeptideSpectrumMatchToSpectrumSourceGroupLink) +
"GROUP BY ssgl.Group.id")
.List<object[]>()
.Select(o => new SpectrumTableForm.SpectrumSourceGroupRow(o, viewFilter));
foreach (var group in groups)
{
var newNode = new TableExporter.TableTreeNode
{
Text = group.SpectrumSourceGroup.Name,
Headers = groupTreeHeaders,
Cells = new List<string>
{
"'" + group.SpectrumSourceGroup.Name + "'",
group.Spectra.ToString(),
group.DistinctPeptides.ToString(),
group.DistinctMatches.ToString(),
group.DistinctAnalyses.ToString(),
group.DistinctCharges.ToString()
}
};
var groupFilter = new DataFilter(viewFilter)
{
SpectrumSourceGroup = new List<SpectrumSourceGroup> { group.SpectrumSourceGroup }
};
var sources = session.CreateQuery(SpectrumTableForm.AggregateRow.Selection + ", s.Source " +
groupFilter.GetFilteredQueryString(DataFilter.FromPeptideSpectrumMatch,
DataFilter.PeptideSpectrumMatchToProtein,
DataFilter.PeptideSpectrumMatchToSpectrumSourceGroupLink) +
"GROUP BY s.Source.id")
.List<object[]>()
.Select(o => new SpectrumTableForm.SpectrumSourceRow(o, groupFilter));
SpectrumTableForm.SpectrumSourceGroupRow ssgr = group;
sources = from SpectrumTableForm.SpectrumSourceRow s in sources
where s.SpectrumSource.Group == ssgr.SpectrumSourceGroup
select s;
foreach (var source in sources)
{
var newSubNode = new TableExporter.TableTreeNode
{
Text = "source" + source.SpectrumSource.Id ?? string.Empty + ".html",
Headers = sourceTreeHeaders,
Cells = new List<string>
{
String.Format("'<a href=\"{0}.html\">{0}</a>'", source.SpectrumSource.Name),
source.Spectra.ToString(),
source.DistinctPeptides.ToString(),
source.DistinctMatches.ToString(),
source.DistinctAnalyses.ToString(),
source.DistinctCharges.ToString()
}
};
newNode.Nodes.Add(newSubNode);
}
groupNodes.Add(newNode);
}
return groupNodes;
}
private Dictionary<string, List<TableExporter.TableTreeNode>> getSourceContentsForHTML(DataFilter viewFilter, DataFilter dataFilter, ISession session)
{
const int decimalPlaces = 4;
var allContents = new Dictionary<string, List<TableExporter.TableTreeNode>>();
//get score info
//score gathering is one of the most time-intensive processes in item retreaval
//loading everything to memory if possible should speed things up significantly
//low speed system should stay in place in case memory cant handle the load
var rawScoreList = session.CreateSQLQuery("select name, id from PeptideSpectrumMatchScoreName").List<object[]>();
var scoreList = new List<string>();
var scoreNameToId = new Dictionary<string, string>();
foreach (var item in rawScoreList)
{
scoreList.Add(item[0].ToString());
if (!scoreNameToId.ContainsKey(item[0].ToString()))
scoreNameToId.Add(item[0].ToString(), item[1].ToString());
}
var scoresCaptured = true;
var scoreCache = new Dictionary<string, Dictionary<string, string>>();
try
{
var allScores = session.CreateSQLQuery("Select PsmID, ScoreNameId, CAST(Value AS TEXT) from PeptideSpectrumMatchScore").List();
foreach (var row in allScores)
{
var rowContents = (object[])row;
if (!scoreCache.ContainsKey(rowContents[0].ToString()))
scoreCache.Add(rowContents[0].ToString(), new Dictionary<string, string>());
if (!scoreCache[rowContents[0].ToString()].ContainsKey(rowContents[1].ToString()))
scoreCache[rowContents[0].ToString()].Add(rowContents[1].ToString(), rowContents[2].ToString());
}
}
catch (Exception e)
{
scoresCaptured = false;
var errorMessage =
"[SpectrumTableForm] Error when precaching data. " +
"Results may be processed slower than expected - " +
Environment.NewLine + e.Message;
if (InvokeRequired)
Invoke(new Action(() => MessageBox.Show(errorMessage)));
else
MessageBox.Show(errorMessage);
}
var sourceTreeHeaders = new List<string>
{
"'Spectrum'",
"'Distinct Peptides'",
"'Distinct Analyses'",
"'Distinct Charges'",
"'Precursor M/Z'"
};
var psmHeaders = new List<string>()
{
"'Rank'",
"'Charge'",
"'Observed Mass'",
"'Monoisotopic Mass'",
"'Mass Error'",
"'Q Value'",
"'Sequence'"
};
psmHeaders.AddRange(scoreList.Select(item => string.Format("'{0}'", item)));
//get source info
var sources = session.QueryOver<SpectrumSource>().List();
foreach (var source in sources)
{
var exportTable = new List<TableExporter.TableTreeNode>();
var sourceFilter = new DataFilter(dataFilter) { SpectrumSource = new List<SpectrumSource> { source } };
var grouping = new List<Grouping<GroupBy>> { new Grouping<GroupBy>(true) { Mode = GroupBy.Spectrum } };
var spectraRows = SpectrumTableForm.getSpectrumRows(session, grouping, sourceFilter);
foreach (SpectrumTableForm.SpectrumRow spectra in spectraRows)
{
var key = spectra.Spectrum.NativeID;
try
{
key = pwiz.CLI.msdata.id.abbreviate(key);
}
catch
{
}
var newBranch = new TableExporter.TableTreeNode
{
Text = key,
Headers = sourceTreeHeaders,
Cells = new List<string>
{
"'" + key + "'",
spectra.DistinctPeptides.ToString(),
spectra.DistinctAnalyses.ToString(),
spectra.DistinctCharges.ToString(),
Math.Round(spectra.Spectrum.PrecursorMZ,decimalPlaces).ToString()
}
};
foreach (var match in spectra.Spectrum.Matches)
{
var observedMass = match.Spectrum.PrecursorMZ * match.Charge -
match.Charge * pwiz.CLI.chemistry.Proton.Mass;
var matchNode = new TableExporter.TableTreeNode { Text = match.Rank.ToString(), Headers = psmHeaders };
var cells = new List<string>
{
"'" + match.Rank + "'",
match.Charge.ToString(),
Math.Round(observedMass,decimalPlaces).ToString(),
Math.Round(match.ObservedNeutralMass,decimalPlaces).ToString(),
Math.Round(match.MonoisotopicMassError,decimalPlaces).ToString(),
Math.Round(match.QValue,decimalPlaces).ToString(),
"'" + match.Peptide.Sequence + "'"
};
foreach (var score in scoreList)
{
if (scoresCaptured)
{
var scoreValue = scoreCache[match.Id.ToString()][scoreNameToId[score]];
cells.Add(Math.Round(double.Parse(scoreValue), decimalPlaces).ToString());
}
else
{
try
{
cells.Add(Math.Round(match.Scores[score.Trim("'".ToCharArray())], decimalPlaces).ToString());
}
catch
{
cells.Add(string.Empty);
}
}
}
matchNode.Cells = cells;
newBranch.Nodes.Add(matchNode);
}
exportTable.Add(newBranch);
}
allContents.Add(source.Name, exportTable);
}
return allContents;
}
