public bool AddSampleSpecies(int id, Param species)
{
Sample sample;
if (!_sampleMap.ContainsKey(id)){
sample = new Sample(id);
sample.AddSpecies(species);
_sampleMap.Add(id, sample);
return true;
}
sample = _sampleMap[id];
sample.AddSpecies(species);
return true;
}
protected void GetExperminetValues(IMatrixData summary, IMatrixData experimentalDesignTemplate,
IMatrixData experiment, IMatrixData spectraRef, ref List<MsRunImpl> msruns,
ref List<StudyVariable> studyvariables, ref List<Assay> assays,
ref List<Sample> samples, ref List<Instrument> instruments)
{
if (msruns == null) {
msruns = new List<MsRunImpl>();
}
if (studyvariables == null) {
studyvariables = new List<StudyVariable>();
}
if (assays == null) {
assays = new List<Assay>();
}
if (samples == null) {
samples = new List<Sample>();
}
if (instruments == null) {
instruments = new List<Instrument>();
}
#region parse experiment
if (experiment != null) {
int studyvarIndex = experiment.StringColumnNames.IndexOf(MetadataElement.STUDY_VARIABLE.Name);
int assayIndex = experiment.StringColumnNames.IndexOf(MetadataElement.ASSAY.Name);
int msrunIndex = experiment.StringColumnNames.IndexOf(MetadataElement.MS_RUN.Name);
int sampleIndex = experiment.StringColumnNames.IndexOf(MetadataElement.SAMPLE.Name);
Regex sampleRegex = new Regex(@"^([^\[]+) <([^;]*);([^;]*);([^;]*);([^;]*)>");
Regex runRegex = new Regex(@"^([^\[]+) <([^;]*);([^;]*);([^;]*);([^;]*)>");
Regex assayRegex = new Regex(@"^([^\[]+) <([^>]*)>");
for (int row = 0; row < experiment.RowCount; row++) {
string studyvariableDescription = experiment.StringColumns[studyvarIndex][row];
string assayReagent = experiment.StringColumns[assayIndex][row];
string msrunText = experiment.StringColumns[msrunIndex][row];
string sampleDescription = experiment.StringColumns[sampleIndex][row];
Lib.Model.Param specie = null;
Lib.Model.Param tissue = null;
Lib.Model.Param cellType = null;
Lib.Model.Param disease = null;
IList<Lib.Model.Param> mod = new List<Lib.Model.Param>();
if (sampleDescription != null && sampleRegex.IsMatch(sampleDescription)) {
var match = sampleRegex.Match(sampleDescription);
sampleDescription = match.Groups[1].Value;
string temp = match.Groups[2].Value;
if (!String.IsNullOrEmpty(temp)) {
specie = cv.GetParam(temp, "NEWT");
}
temp = match.Groups[3].Value;
if (!String.IsNullOrEmpty(temp)) {
tissue = cv.GetParam(temp, "BTO");
}
temp = match.Groups[4].Value;
if (!String.IsNullOrEmpty(temp)) {
cellType = cv.GetParam(temp, "CL");
}
temp = match.Groups[5].Value;
if (!String.IsNullOrEmpty(temp)) {
disease = cv.GetParam(temp, "DOID");
}
}
if (assayRegex != null && assayRegex.IsMatch(assayReagent)) {
var match = assayRegex.Match(assayReagent);
string temp = match.Groups[2].Value;
if (!String.IsNullOrEmpty(temp)) {
foreach (var t in temp.Split(';')) {
mod.Add(cv.GetParam(t, "PRIDE"));
}
}
assayReagent = match.Groups[1].Value;
}
string filename = null;
string path = null;
Lib.Model.Param format = null;
Lib.Model.Param idformat = null;
Lib.Model.Param fragementaion = null;
if (runRegex != null && runRegex.IsMatch(msrunText)) {
var match = runRegex.Match(msrunText);
filename = match.Groups[1].Value;
string temp = match.Groups[2].Value;
if (!String.IsNullOrEmpty(temp)) {
path = temp;
}
temp = match.Groups[3].Value;
if (!String.IsNullOrEmpty(temp)) {
format = cv.GetParam(temp, "MS");
}
temp = match.Groups[4].Value;
if (!String.IsNullOrEmpty(temp)) {
idformat = cv.GetParam(temp, "MS");
}
temp = match.Groups[5].Value;
if (!String.IsNullOrEmpty(temp)) {
fragementaion = cv.GetParam(temp, "MS");
}
}
StudyVariable studyvariable;
if (!studyvariables.Any(x => x.Description.Equals(studyvariableDescription))) {
studyvariable = new StudyVariable(studyvariables.Count + 1) {
Description = studyvariableDescription
};
studyvariables.Add(studyvariable);
} else {
studyvariable = studyvariables.First(x => x.Description.Equals(studyvariableDescription));
}
Assay assay = new Assay(assays.Count + 1) {
QuantificationReagent = cv.GetParam(assayReagent, "PRIDE")
};
foreach (var m in mod) {
if (m == null) {
continue;
}
assay.addQuantificationMod(new AssayQuantificationMod(assay,
assay.QuantificationModMap.Count + 1) {
Param = m
});
}
assays.Add(assay);
MsRunImpl msrun;
if (!String.IsNullOrEmpty(filename) &&
!msruns.Any(x => x.Description != null && x.Description.Equals(filename))) {
msrun = new MsRunImpl(msruns.Count + 1) {
Format = format,
IdFormat = idformat,
FragmentationMethod = fragementaion
};
msruns.Add(msrun);
msrun.Location = new Url(String.IsNullOrEmpty(path) ? filename : Path.Combine(path, filename));
} else {
msrun = msruns.First(x => x.Description != null && x.Description.Equals(filename));
}
Sample sample;
if (!samples.Any(x => x.Description.Equals(sampleDescription))) {
sample = new Sample(samples.Count + 1) { Description = sampleDescription };
if (specie != null) {
sample.AddSpecies(specie);
}
if (tissue != null) {
sample.AddTissue(tissue);
}
if (cellType != null) {
sample.AddCellType(cellType);
}
if (disease != null) {
sample.AddDisease(disease);
}
samples.Add(sample);
} else {
sample = samples.First(x => x.Description.Equals(sampleDescription));
}
if (!studyvariable.AssayMap.ContainsKey(assay.Id)) {
studyvariable.AddAssay(assay);
}
if (!studyvariable.SampleMap.ContainsKey(sample.Id)) {
studyvariable.AddSample(sample);
}
assay.MsRun = msrun;
assay.Sample = sample;
}
}
#endregion
Dictionary<int, IList<string>> dictionary = new Dictionary<int, IList<string>>();
#region parse experimentalDesign
if (experimentalDesignTemplate != null) {
string[] rawfiles = null;
int index = Constants.GetKeywordIndex(experimentalDesign.rawfile,
experimentalDesignTemplate.StringColumnNames);
if (index != -1) {
rawfiles = experimentalDesignTemplate.StringColumns[index];
}
string[] experimentNames = null;
if (
(index =
Constants.GetKeywordIndex(experimentalDesign.variable,
experimentalDesignTemplate.StringColumnNames)) !=
-1) {
experimentNames = experimentalDesignTemplate.StringColumns[index];
} else if (
(index =
Constants.GetKeywordIndex(experimentalDesign.variable,
experimentalDesignTemplate.CategoryColumnNames)) != -1) {
experimentNames = MzTabMatrixUtils.ConvertToStringArray(experimentalDesignTemplate.GetCategoryColumnAt(index));
}
if (rawfiles != null && experimentNames != null) {
for (int i = 0; i < rawfiles.Length && i < experimentNames.Length; i++) {
string name = experimentNames[i];
StudyVariable variable = studyvariables.FirstOrDefault(x => x.Description.Equals(name));
if (variable == null) {
variable = new StudyVariable(studyvariables.Count + 1) { Description = name };
studyvariables.Add(variable);
}
string rawfile = rawfiles[i];
MsRunImpl runImpl = msruns.FirstOrDefault(x => x.Description.Equals(rawfile));
if (runImpl == null) {
runImpl = new MsRunImpl(msruns.Count + 1) {
Location = new Url(rawfile),
Format = cv.GetParam("MS:1000563", "MS"),
IdFormat = cv.GetParam("MS:1000768", "MS")
};
msruns.Add(runImpl);
}
if (rawfile != null) {
if (!dictionary.ContainsKey(variable.Id)) {
dictionary.Add(variable.Id, new List<string>());
}
dictionary[variable.Id].Add(rawfile);
}
}
} else {
Console.Out.WriteLine("Rawfiles " + rawfiles);
Console.Out.WriteLine("experimentNames " + experimentNames);
throw new Exception("Could not parse " + Matrix.ExperimentalDesign);
}
}
#endregion
#region add default samples from studyvariables
if (studyvariables != null && studyvariables.Count > 0) {
foreach (StudyVariable variable in studyvariables) {
string text = variable.Description;
Sample sample = samples.FirstOrDefault(x => text.Contains(x.Description));
if (sample == null) {
sample = new Sample(samples.Count + 1) { Description = text };
samples.Add(sample);
}
variable.AddSample(sample);
}
}
#endregion
#region parse summary
if (summary != null) {
int maxRow = msruns.Count;
string multi = "1";
string[] labels0 = null;
int index;
if ((index = Constants.GetKeywordIndex(Utils.summary.labels0, summary.StringColumnNames)) != -1) {
labels0 = summary.StringColumns[index];
multi = "1";
} else if ((index = Constants.GetKeywordIndex(Utils.summary.labels0, summary.CategoryColumnNames)) !=
-1) {
labels0 = MzTabMatrixUtils.ConvertToStringArray(summary.GetCategoryColumnAt(index));
multi = "1";
}
string[] labels1 = null;
if ((index = Constants.GetKeywordIndex(Utils.summary.labels1, summary.StringColumnNames)) != -1) {
labels1 = summary.StringColumns[index];
multi = "2";
} else if ((index = Constants.GetKeywordIndex(Utils.summary.labels1, summary.CategoryColumnNames)) !=
-1) {
labels1 = MzTabMatrixUtils.ConvertToStringArray(summary.GetCategoryColumnAt(index));
multi = "2";
}
string[] labels2 = null;
if ((index = Constants.GetKeywordIndex(Utils.summary.labels2, summary.StringColumnNames)) != -1) {
labels2 = summary.StringColumns[index];
multi = "3";
} else if ((index = Constants.GetKeywordIndex(Utils.summary.labels2, summary.CategoryColumnNames)) !=
-1) {
labels2 = MzTabMatrixUtils.ConvertToStringArray(summary.GetCategoryColumnAt(index));
multi = "3";
}
string[] multiplicity;
if ((index = Constants.GetKeywordIndex(Utils.summary.multiplicity, summary.StringColumnNames)) !=
-1) {
multiplicity = summary.StringColumns[index];
multiplicity = multiplicity.Where(x => !String.IsNullOrEmpty(x)).ToArray();
} else if (
(index =
Constants.GetKeywordIndex(Utils.summary.multiplicity, summary.CategoryColumnNames)) !=
-1) {
multiplicity = MzTabMatrixUtils.ConvertToStringArray(summary.GetCategoryColumnAt(index));
multiplicity = multiplicity.Where(x => !String.IsNullOrEmpty(x)).ToArray();
} else {
multiplicity = new string[maxRow];
for (int i = 0; i < multiplicity.Length; i++) {
multiplicity[i] = multi;
}
}
string[] labels;
switch (multi) {
case "1":
labels = null;
break;
case "2":
labels = new[] { "L", "H" };
break;
case "3":
labels = new[] { "L", "H", "M" };
break;
default:
labels = null;
break;
}
if (labels != null) {
List<StudyVariable> list = new List<StudyVariable>();
Dictionary<int, IList<string>> dict = new Dictionary<int, IList<string>>();
foreach (StudyVariable studyVariable in studyvariables){
foreach (var variable in SILAC(studyVariable, labels)) {
IList<string> rawfile = null;
if (dictionary.ContainsKey(variable.Id)) {
rawfile = dictionary[variable.Id];
}
StudyVariable tmp = new StudyVariable(list.Count + 1){Description = variable.Description};
tmp.AddAllAssays(variable.AssayMap.Values.ToList());
tmp.AddAllSamples(variable.SampleMap.Values.ToList());
list.Add(tmp);
if (rawfile != null) {
if (!dict.ContainsKey(tmp.Id)) {
dict.Add(tmp.Id, rawfile);
}
}
}
}
studyvariables = list;
dictionary = dict;
}
string[] rawfiles = null;
if ((index = Constants.GetKeywordIndex(Utils.summary.rawfile, summary.StringColumnNames)) != -1) {
rawfiles = summary.StringColumns[index];
rawfiles = rawfiles.Where(x => !String.IsNullOrEmpty(x)).ToArray();
} else if ((index = Constants.GetKeywordIndex(Utils.summary.rawfile, summary.CategoryColumnNames)) !=
-1) {
rawfiles = MzTabMatrixUtils.ConvertToStringArray(summary.GetCategoryColumnAt(index));
rawfiles = rawfiles.Where(x => !String.IsNullOrEmpty(x)).ToArray();
}
string[] orbitrapInstruments = new[] { "LTQ Orbitrap", "LTQ Orbitrap XL", "LTQ Orbitrap Velos", "LTQ Orbitrap Elite", "Q Exactive" };
string[] instrument = null;
if ((index = Constants.GetKeywordIndex(Utils.summary.instrument, summary.StringColumnNames)) != -1) {
instrument = summary.StringColumns[index];
instrument = instrument.Where(x => !String.IsNullOrEmpty(x)).ToArray();
} else if ((index = Constants.GetKeywordIndex(Utils.summary.instrument, summary.CategoryColumnNames)) !=
-1) {
instrument = MzTabMatrixUtils.ConvertToStringArray(summary.GetCategoryColumnAt(index));
instrument = instrument.Where(x => !String.IsNullOrEmpty(x)).ToArray();
}
if (rawfiles != null) {
for (int i = 0; i < rawfiles.Length; i++) {
int id = assays.Count + 1;
string rawfile = rawfiles[i];
if (!dictionary.Values.Any(x => x.Contains(rawfile))) {
continue;
}
IList<StudyVariable> temp = new List<StudyVariable>();
foreach (var v in dictionary.Where(x => x.Value.Contains(rawfile))) {
temp.Add(studyvariables.FirstOrDefault(x => x.Id == v.Key));
}
StudyVariable variable1 = null;
StudyVariable variable2 = null;
StudyVariable variable3 = null;
if (temp != null) {
if (temp.Any()) {
variable1 = temp[0];
}
if (temp.Count() > 1) {
variable2 = temp[1];
}
if (temp.Count() > 2) {
variable3 = temp[2];
}
}
if (multiplicity[i].Equals("1")) {
#region Add assay for label free
Assay assay = new Assay(id) {
QuantificationReagent = cv.GetParam("Unlabeled sample", "PRIDE"),
MsRun = msruns[i]
};
if (variable1 != null) {
assay.Sample = variable1.SampleMap.Values.FirstOrDefault();
variable1.AddAssay(assay);
}
assays.Add(assay);
#endregion
} else if (multiplicity[i].Equals("2")) {
#region Add assays for Double SILAC labeling
Assay assay = new Assay(id) {
QuantificationReagent = cv.GetParam("SILAC light", "PRIDE"),
MsRun = msruns[i]
};
IList<AssayQuantificationMod> mods = MzTabMatrixUtils.GetQuantificationMod(labels0, i, assay);
if (mods != null) {
foreach (var m in mods) {
assay.addQuantificationMod(m);
}
}
if (variable1 != null) {
assay.Sample = variable1.SampleMap.Values.FirstOrDefault();
variable1.AddAssay(assay);
}
assays.Add(assay);
assay = new Assay(id + 1) {
QuantificationReagent = cv.GetParam("SILAC heavy", "PRIDE"),
MsRun = msruns[i]
};
mods = MzTabMatrixUtils.GetQuantificationMod(labels1, i, assay);
if (mods != null) {
foreach (var m in mods) {
assay.addQuantificationMod(m);
}
}
if (variable2 != null) {
assay.Sample = variable2.SampleMap.Values.FirstOrDefault();
variable2.AddAssay(assay);
}
assays.Add(assay);
#endregion
} else if (multiplicity[i].Equals("3")) {
#region Add assays for Triple SILAC labeling
Assay assay = new Assay(id) {
QuantificationReagent = cv.GetParam("SILAC light", "PRIDE"),
MsRun = msruns[i]
};
IList<AssayQuantificationMod> mods = MzTabMatrixUtils.GetQuantificationMod(labels0, i, assay);
if (mods != null) {
foreach (var m in mods) {
assay.addQuantificationMod(m);
}
}
if (variable1 != null) {
assay.Sample = variable1.SampleMap.Values.FirstOrDefault();
variable1.AddAssay(assay);
}
assays.Add(assay);
assay = new Assay(id + 1) {
QuantificationReagent = cv.GetParam("SILAC medium", "PRIDE"),
MsRun = msruns[i]
};
mods = MzTabMatrixUtils.GetQuantificationMod(labels1, i, assay);
if (mods != null) {
foreach (var m in mods) {
assay.addQuantificationMod(m);
}
}
if (variable2 != null) {
assay.Sample = variable2.SampleMap.Values.FirstOrDefault();
variable2.AddAssay(assay);
}
assays.Add(assay);
assay = new Assay(id + 2) {
QuantificationReagent = cv.GetParam("SILAC heavy", "PRIDE"),
MsRun = msruns[i]
};
mods = MzTabMatrixUtils.GetQuantificationMod(labels2, i, assay);
if (mods != null) {
foreach (var m in mods) {
assay.addQuantificationMod(m);
}
}
if (variable3 != null) {
assay.Sample = variable3.SampleMap.Values.FirstOrDefault();
variable3.AddAssay(assay);
}
assays.Add(assay);
#endregion
}
if (instrument != null && !String.IsNullOrEmpty(instrument[i])) {
var tmp = new Instrument(instruments.Count + 1) { Name = cv.GetParam(instrument[i], "MS") };
if (orbitrapInstruments.Contains(instrument[i])) {
tmp.Source = cv.GetParam("electrospray ionization", "MS");
tmp.Analyzer = cv.GetParam("orbitrap", "MS");
}
instruments.Add(tmp);
}
}
}
}
#endregion
#region parse search
Lib.Model.Param run_idFormat = cv.GetParam("MS:1000774", "MS");
Lib.Model.Param run_format = cv.GetParam("Andromeda Peak list file", "MS");
if (spectraRef != null && Constants.GetKeywordName(Utils.spectraRef.location, spectraRef.StringColumnNames) != null) {
int colindex = Constants.GetKeywordIndex(Utils.spectraRef.location, spectraRef.StringColumnNames);
string[] values =
ArrayUtils.UniqueValues(spectraRef.StringColumns[colindex]);
for (int i = 0; i < values.Length; i++) {
Lib.Model.Param frag = null;
if (values[i].Contains("CID")) {
frag = cv.GetParam("MS:1000133", "MS");
} else if (values[i].Contains("HCD")) {
frag = cv.GetParam("MS:1000422", "MS");
}
msruns.Add(new MsRunImpl(msruns.Count + 1) {
IdFormat = run_idFormat,
Format = run_format,
FragmentationMethod = frag,
Location = new Url(values[i])
});
}
} else {
msruns.Add(new MsRunImpl(msruns.Count + 1) {
IdFormat = run_idFormat,
Format = run_format
});
}
#endregion
}