private void addGroupToolStripMenuItem_Click(object sender, EventArgs e)
{
var selNode = (tlvBranch)tlvGroupedFiles.GetModelObject(_clickedItem.Index);
_numberNewNodes++;
var ssg = new SpectrumSourceGroup();
ssg.Name = (string.Format("{0}/New Group({1})", selNode.Text, _numberNewNodes).Replace(@"//", @"/"));
var newNode = new tlvBranch
{
Text = Path.GetFileName(ssg.Name),
cms = cmRightClickGroupNode,
Parent = selNode,
Children = new List <tlvBranch>(),
Data = ssg
};
selNode.Children.Add(newNode);
OrganizeNode(selNode);
tlvGroupedFiles.RefreshObject(selNode);
if (selNode.Children.Count == 1)
{
tlvGroupedFiles.Expand(selNode);
}
tlvGroupedFiles.EditSubItem(tlvGroupedFiles.ModelToItem(newNode), 0);
}
public static void CreateTestData (NHibernate.ISession session, IList<SpectrumTuple> testPsmSummary)
{
var dbGroups = new Map<string, SpectrumSourceGroup>();
foreach (var ssg in session.Query<SpectrumSourceGroup>())
dbGroups[ssg.Name] = ssg;
var dbSources = new Map<long, SpectrumSource>();
foreach (var ss in session.Query<SpectrumSource>())
dbSources[ss.Id.Value] = ss;
var dbAnalyses = new Map<long, Analysis>();
foreach (var a in session.Query<Analysis>())
dbAnalyses[a.Id.Value] = a;
var dbPeptides = new Map<string, Peptide>();
foreach (var pep in session.Query<Peptide>())
dbPeptides[pep.Sequence] = pep;
var bulkInserter = new BulkInserter(session.Connection);
long lastPsmId = session.CreateQuery("SELECT MAX(Id) FROM PeptideSpectrumMatch").UniqueResult<long?>().GetValueOrDefault();
long lastModId = session.CreateQuery("SELECT MAX(Id) FROM Modification").UniqueResult<long?>().GetValueOrDefault();
long lastPmId = session.CreateQuery("SELECT MAX(Id) FROM PeptideModification").UniqueResult<long?>().GetValueOrDefault();
long lastGroupId = session.CreateQuery("SELECT MAX(Id) FROM SpectrumSourceGroup").UniqueResult<long?>().GetValueOrDefault();
long lastSourceId = session.CreateQuery("SELECT MAX(Id) FROM SpectrumSource").UniqueResult<long?>().GetValueOrDefault();
long lastSglId = session.CreateQuery("SELECT MAX(Id) FROM SpectrumSourceGroupLink").UniqueResult<long?>().GetValueOrDefault();
foreach (SpectrumTuple row in testPsmSummary)
{
string groupName = row.Group;
string sourceName = "Source " + row.Source;
string analysisId = "Engine " + row.Analysis;
string peptideTuples = row.PeptideTuples;
SpectrumSourceGroup group = dbGroups[groupName];
if (String.IsNullOrEmpty(group.Name))
{
group.Id = ++lastGroupId;
group.Name = groupName;
bulkInserter.Add(group);
}
SpectrumSource source = dbSources[row.Source];
if (String.IsNullOrEmpty(source.Name))
{
source.Id = ++lastSourceId;
source.Name = sourceName;
source.Group = group;
source.Spectra = new List<Spectrum>();
bulkInserter.Add(source);
// add a source group link for the source's immediate group
bulkInserter.Add(new SpectrumSourceGroupLink() { Id = ++lastSglId, Group = group, Source = source });
#region add source group links for all of the immediate group's parent groups
if (groupName != "/")
{
string parentGroupName = groupName.Substring(0, groupName.LastIndexOf("/"));
while (true)
{
if (String.IsNullOrEmpty(parentGroupName))
parentGroupName = "/";
// add the parent group if it doesn't exist yet
SpectrumSourceGroup parentGroup = session.UniqueResult<SpectrumSourceGroup>(o => o.Name == parentGroupName);
if (parentGroup == null)
{
parentGroup = new SpectrumSourceGroup() { Id = ++lastGroupId, Name = parentGroupName };
bulkInserter.Add(parentGroup);
}
bulkInserter.Add(new SpectrumSourceGroupLink() { Id = ++lastSglId, Group = parentGroup, Source = source });
if (parentGroupName == "/")
break;
parentGroupName = parentGroupName.Substring(0, parentGroupName.LastIndexOf("/"));
}
}
#endregion
}
Spectrum spectrum = source.Spectra.SingleOrDefault(o => o.Source.Id == source.Id &&
o.Index == row.Spectrum - 1);
if (spectrum == null)
{
spectrum = new Spectrum()
{
Id = source.Id * 10000 + row.Spectrum,
Index = row.Spectrum - 1,
NativeID = "scan=" + row.Spectrum,
Source = source,
PrecursorMZ = 42
};
source.Spectra.Add(spectrum);
bulkInserter.Add(spectrum);
}
Analysis analysis = dbAnalyses[row.Analysis];
if (String.IsNullOrEmpty(analysis.Name))
{
analysis.Id = dbAnalyses.Max(o => o.Value.Id).GetValueOrDefault() + 1;
analysis.Name = analysisId + " 1.0";
analysis.Software = new AnalysisSoftware() {Name = analysisId, Version = "1.0"};
analysis.StartTime = DateTime.Today.AddHours(row.Analysis);
analysis.Type = AnalysisType.DatabaseSearch;
analysis.Parameters = new SortedSet<AnalysisParameter>()
{
new AnalysisParameter()
{
Id = analysis.Id * 10000,
Analysis = analysis,
Name = "Parameter 1",
Value = "Value 1"
}
};
bulkInserter.Add(analysis);
}
// make sure peptides are sorted by their score divider (which will determine rank)
var peptideList = new SortedList<int, List<PeptideTuple>>();
foreach (string tuple in peptideTuples.Split(" ".ToCharArray(), StringSplitOptions.RemoveEmptyEntries))
{
var peptideTuple = new PeptideTuple()
{
Sequence = tuple.Split('@', '/')[0],
Charge = Convert.ToInt32(tuple.Split('@', '/')[1]),
ScoreDivider = Convert.ToInt32(tuple.Split('@', '/')[2])
};
if (!peptideList.ContainsKey(peptideTuple.ScoreDivider))
peptideList[peptideTuple.ScoreDivider] = new List<PeptideTuple>();
peptideList[peptideTuple.ScoreDivider].Add(peptideTuple);
}
int rank = 1;
int lastDivider = 1;
foreach (var peptideTupleList in peptideList.Values)
foreach (var peptideTuple in peptideTupleList)
{
using (PwizPeptide pwizPeptide = new PwizPeptide(peptideTuple.Sequence, ModParsing.ModificationParsing_Auto, ModDelimiter.ModificationDelimiter_Brackets))
{
Peptide peptide = dbPeptides[pwizPeptide.sequence];
if (String.IsNullOrEmpty(peptide.Sequence))
{
peptide = new TestPeptide(pwizPeptide.sequence);
peptide.Id = dbPeptides.Max(o => o.Value.Id).GetValueOrDefault() + 1;
peptide.MonoisotopicMass = pwizPeptide.monoisotopicMass(false);
peptide.MolecularWeight = pwizPeptide.molecularWeight(false);
dbPeptides[pwizPeptide.sequence] = peptide;
bulkInserter.Add(peptide);
createTestPeptideInstances(session, bulkInserter, peptide);
}
double neutralPrecursorMass = (spectrum.PrecursorMZ*peptideTuple.Charge) - (peptideTuple.Charge*Proton.Mass);
var psm = new PeptideSpectrumMatch()
{
Id = ++lastPsmId,
Peptide = peptide,
Spectrum = spectrum,
Analysis = analysis,
ObservedNeutralMass = neutralPrecursorMass,
MonoisotopicMassError = neutralPrecursorMass - pwizPeptide.monoisotopicMass(),
MolecularWeightError = neutralPrecursorMass - pwizPeptide.molecularWeight(),
Charge = peptideTuple.Charge,
Rank = (peptideTuple.ScoreDivider == lastDivider ? rank : ++rank),
QValue = (rank == 1 ? row.QValue : PeptideSpectrumMatch.DefaultQValue),
};
if (row.Score != null)
psm.Scores = new Dictionary<string, double>()
{
{"score1", (double) row.Score/peptideTuple.ScoreDivider},
{"score2", 1/((double) row.Score/peptideTuple.ScoreDivider)}
};
bulkInserter.Add(psm);
lastDivider = peptideTuple.ScoreDivider;
// add PeptideModifications and Modifications
foreach (KeyValuePair<int, ModList> itr in pwizPeptide.modifications())
{
foreach (PwizMod pwizMod in itr.Value)
{
Modification mod = session.UniqueResult<Modification>(o => o.Formula == pwizMod.formula());
if (mod == null)
{
mod = new Modification()
{
Id = ++lastModId,
Formula = pwizMod.formula(),
MonoMassDelta = pwizMod.monoisotopicDeltaMass(),
AvgMassDelta = pwizMod.averageDeltaMass(),
Name = pwizMod.formula()
};
bulkInserter.Add(mod);
}
bulkInserter.Add(new PeptideModification()
{
Id = ++lastPmId,
PeptideSpectrumMatch = psm,
Modification = mod,
Offset = itr.Key == ModMap.NTerminus() ? int.MinValue
: itr.Key == ModMap.CTerminus() ? int.MaxValue
: itr.Key
});
}
}
}
}
}
bulkInserter.Execute();
bulkInserter.Reset("");
}
private List<SpectrumSourceGroup> applyAssemblyText(ISession session, string filepath)
{
var spectrumSources = session.Query<SpectrumSource>().ToList();
var sourcesByGroup = new Map<string, List<SpectrumSource>>();
var alreadyGroupedSources = new Set<string>();
var sourceGroups = new List<SpectrumSourceGroup>();
// open the assembly.txt file
using (var assembleTxtFile = File.OpenText(filepath))
{
string line;
while ((line = assembleTxtFile.ReadLine()) != null)
{
if (line.Length == 0)
continue;
try
{
Regex groupFilemaskPair = new Regex("((\"(.+)\")|(\\S+))\\s+((\"(.+)\")|(\\S+))");
Match lineMatch = groupFilemaskPair.Match(line);
string group = lineMatch.Groups[3].ToString() + lineMatch.Groups[4].ToString();
string filemask = lineMatch.Groups[7].ToString() + lineMatch.Groups[8].ToString();
// for wildcards, use old style behavior
if (filemask.IndexOfAny("*?".ToCharArray()) > -1)
{
if (!Path.IsPathRooted(filemask))
filemask = Path.Combine(Path.GetDirectoryName(filepath), filemask);
if (!sourcesByGroup.Contains(group))
sourcesByGroup[group] = new List<SpectrumSource>();
if (!Directory.Exists(Path.GetDirectoryName(filemask)))
continue;
var files = Directory.GetFiles(Path.GetDirectoryName(filemask), Path.GetFileName(filemask));
var sourceNames = files.Select(o => Path.GetFileNameWithoutExtension(o));
foreach (string sourceName in sourceNames)
{
var spectrumSource = spectrumSources.SingleOrDefault(o => o.Name == sourceName);
if (spectrumSource == null)
continue;
var insertResult = alreadyGroupedSources.Insert(sourceName);
if (insertResult.WasInserted)
sourcesByGroup[group].Add(spectrumSource);
}
}
else
{
// otherwise, match directly to source names
string sourceName = Path.GetFileNameWithoutExtension(filemask);
var spectrumSource = spectrumSources.SingleOrDefault(o => o.Name == sourceName);
if (spectrumSource == null)
continue;
var insertResult = alreadyGroupedSources.Insert(sourceName);
if (insertResult.WasInserted)
sourcesByGroup[group].Add(spectrumSource);
}
}
catch (Exception ex)
{
Program.HandleException(new Exception("Error reading assembly text from \"" + filepath + "\": " + ex.Message, ex));
}
}
}
// remove existing groups
RemoveGroupNode(_rootNode, false);
sourceGroups.Add(new SpectrumSourceGroup { Name = "/" });
// build new group hierarchy
foreach (var itr in sourcesByGroup)
{
if (itr.Value.IsNullOrEmpty())
continue;
var ssg = new SpectrumSourceGroup { Name = itr.Key };
if (!alreadyGroupedSources.Contains(ssg.Name))
sourceGroups.Add(ssg);
// decompose group path into segments, e.g. /foo/bar/ -> {foo, bar}
IEnumerable<string> segments = ssg.Name.Split("/".ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
segments = segments.Take(segments.Count() - 1); // ignore the last segment
var parentNode = _rootNode;
foreach(string segment in segments)
{
var segmentNode = parentNode.Children.FirstOrDefault(o => o.Text == segment);
if (segmentNode == null)
{
var segmentGroup = new SpectrumSourceGroup { Name = (parentNode.Text + "/").Replace("//", "/") + segment };
if (!alreadyGroupedSources.Contains(segmentGroup.Name))
sourceGroups.Add(segmentGroup);
segmentNode = new tlvBranch
{
Text = segment,
cms = cmRightClickGroupNode,
Parent = parentNode,
Children = new List<tlvBranch>(),
Data = segmentGroup
};
parentNode.Children.Add(segmentNode);
}
parentNode = segmentNode;
}
// parentNode is now the immediate parent of the current group
var groupNode = new tlvBranch
{
Text = Path.GetFileName(ssg.Name),
cms = cmRightClickGroupNode,
Parent = parentNode,
Children = new List<tlvBranch>(),
Data = ssg
};
foreach (var source in itr.Value)
{
var sourceNode = new tlvBranch
{
Text = Path.GetFileName(source.Name),
Parent = groupNode,
Data = source,
cms = cmRightClickFileNode
};
groupNode.Children.Add(sourceNode);
lvNonGroupedFiles.Items.RemoveByKey(sourceNode.Text);
}
parentNode.Children.Add(groupNode);
}
tlvGroupedFiles.RefreshObject(_rootNode);
tlvGroupedFiles.ExpandAll();
return sourceGroups.ToList();
}
private void addGroupToolStripMenuItem_Click(object sender, EventArgs e)
{
var selNode = (tlvBranch)tlvGroupedFiles.GetModelObject(_clickedItem.Index);
_numberNewNodes++;
var ssg = new SpectrumSourceGroup();
ssg.Name = (string.Format("{0}/New Group({1})", selNode.Text, _numberNewNodes).Replace(@"//",@"/"));
var newNode = new tlvBranch
{
Text = Path.GetFileName(ssg.Name),
cms = cmRightClickGroupNode,
Parent = selNode,
Children = new List<tlvBranch>(),
Data = ssg
};
selNode.Children.Add(newNode);
OrganizeNode(selNode);
tlvGroupedFiles.RefreshObject(selNode);
if (selNode.Children.Count == 1)
tlvGroupedFiles.Expand(selNode);
tlvGroupedFiles.EditSubItem(tlvGroupedFiles.ModelToItem(newNode),0);
}
private List <SpectrumSourceGroup> applyAssemblyText(ISession session, string filepath)
{
var spectrumSources = session.Query <SpectrumSource>().ToList();
var sourcesByGroup = new Map <string, List <SpectrumSource> >();
var alreadyGroupedSources = new Set <string>();
var sourceGroups = new List <SpectrumSourceGroup>();
// open the assembly.txt file
using (var assembleTxtFile = File.OpenText(filepath))
{
string line;
while ((line = assembleTxtFile.ReadLine()) != null)
{
if (line.Length == 0)
{
continue;
}
try
{
Regex groupFilemaskPair = new Regex("((\"(.+)\")|(\\S+))\\s+((\"(.+)\")|(\\S+))");
Match lineMatch = groupFilemaskPair.Match(line);
string group = lineMatch.Groups[3].ToString() + lineMatch.Groups[4].ToString();
string filemask = lineMatch.Groups[7].ToString() + lineMatch.Groups[8].ToString();
group = group.TrimEnd(' ', '/');
// for wildcards, use old style behavior
if (filemask.IndexOfAny("*?".ToCharArray()) > -1)
{
if (!Path.IsPathRooted(filemask))
{
filemask = Path.Combine(Path.GetDirectoryName(filepath), filemask);
}
if (!sourcesByGroup.Contains(group))
{
sourcesByGroup[group] = new List <SpectrumSource>();
}
if (!Directory.Exists(Path.GetDirectoryName(filemask)))
{
continue;
}
var files = Directory.GetFiles(Path.GetDirectoryName(filemask), Path.GetFileName(filemask));
var sourceNames = files.Select(o => Path.GetFileNameWithoutExtension(o));
foreach (string sourceName in sourceNames)
{
var spectrumSource = spectrumSources.SingleOrDefault(o => o.Name == sourceName);
if (spectrumSource == null)
{
continue;
}
var insertResult = alreadyGroupedSources.Insert(sourceName);
if (insertResult.WasInserted)
{
sourcesByGroup[group].Add(spectrumSource);
}
}
}
else
{
// otherwise, match directly to source names
string sourceName = Path.GetFileNameWithoutExtension(filemask);
var spectrumSource = spectrumSources.SingleOrDefault(o => o.Name == sourceName);
if (spectrumSource == null)
{
continue;
}
var insertResult = alreadyGroupedSources.Insert(sourceName);
if (insertResult.WasInserted)
{
sourcesByGroup[group].Add(spectrumSource);
}
}
}
catch (Exception ex)
{
Program.HandleException(new Exception("Error reading assembly text from \"" + filepath + "\": " + ex.Message, ex));
}
}
}
// remove existing groups
RemoveGroupNode(_rootNode, false);
sourceGroups.Add(new SpectrumSourceGroup {
Name = "/"
});
// build new group hierarchy
foreach (var itr in sourcesByGroup)
{
if (itr.Value.IsNullOrEmpty())
{
continue;
}
var ssg = new SpectrumSourceGroup {
Name = itr.Key
};
if (!alreadyGroupedSources.Contains(ssg.Name))
{
sourceGroups.Add(ssg);
}
// decompose group path into segments, e.g. /foo/bar/ -> {foo, bar}
IEnumerable <string> segments = ssg.Name.Split("/".ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
segments = segments.Take(segments.Count() - 1); // ignore the last segment
var parentNode = _rootNode;
foreach (string segment in segments)
{
var segmentNode = parentNode.Children.FirstOrDefault(o => o.Text == segment);
if (segmentNode == null)
{
var segmentGroup = new SpectrumSourceGroup {
Name = (parentNode.Text + "/").Replace("//", "/") + segment
};
if (!alreadyGroupedSources.Contains(segmentGroup.Name))
{
sourceGroups.Add(segmentGroup);
}
segmentNode = new tlvBranch
{
Text = segment,
cms = cmRightClickGroupNode,
Parent = parentNode,
Children = new List <tlvBranch>(),
Data = segmentGroup
};
parentNode.Children.Add(segmentNode);
}
parentNode = segmentNode;
}
// parentNode is now the immediate parent of the current group
var groupNode = new tlvBranch
{
Text = Path.GetFileName(ssg.Name),
cms = cmRightClickGroupNode,
Parent = parentNode,
Children = new List <tlvBranch>(),
Data = ssg
};
foreach (var source in itr.Value)
{
var sourceNode = new tlvBranch
{
Text = Path.GetFileName(source.Name),
Parent = groupNode,
Data = source,
cms = cmRightClickFileNode
};
groupNode.Children.Add(sourceNode);
lvNonGroupedFiles.Items.RemoveByKey(sourceNode.Text);
}
parentNode.Children.Add(groupNode);
}
tlvGroupedFiles.RefreshObject(_rootNode);
tlvGroupedFiles.ExpandAll();
return(sourceGroups.ToList());
}
public void Add (SpectrumSourceGroup ssg)
{
insertRow(Table.SpectrumSourceGroup, new object[] {ssg.Id, ssg.Name});
}