public override IMatrixData ProcessData(IMatrixData[] inputData, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
Metadata mtd = new Metadata();
string name = string.Format("{0}{1}{2}", MetadataElement.MZTAB, MZTabConstants.MINUS,
MetadataProperty.MZTAB_VERSION);
StringParam stringParam = FindParam(param, name) as StringParam;
if (stringParam != null && !string.IsNullOrEmpty(stringParam.Value)){
mtd.MZTabVersion = stringParam.Value;
}
name = string.Format("{0}{1}{2}", MetadataElement.MZTAB, MZTabConstants.MINUS, MetadataProperty.MZTAB_MODE);
SingleChoiceParam single = FindParam(param, name) as SingleChoiceParam;
if (single != null && !string.IsNullOrEmpty(single.SelectedValue)){
MzTabMode mode;
if (Enum.TryParse(single.SelectedValue, true, out mode)){
mtd.MzTabMode = mode;
}
}
name = string.Format("{0}{1}{2}", MetadataElement.MZTAB, MZTabConstants.MINUS, MetadataProperty.MZTAB_TYPE);
single = FindParam(param, name) as SingleChoiceParam;
if (single != null && !string.IsNullOrEmpty(single.SelectedValue)){
MzTabType type;
if (Enum.TryParse(single.SelectedValue, true, out type)){
mtd.MzTabType = type;
}
}
name = string.Format("{0}{1}{2}", MetadataElement.MZTAB, MZTabConstants.MINUS, MetadataProperty.MZTAB_ID);
stringParam = FindParam(param, name) as StringParam;
if (stringParam != null && !string.IsNullOrEmpty(stringParam.Value)){
mtd.MZTabID = stringParam.Value;
}
stringParam = FindParam(param, MetadataElement.TITLE.Name) as StringParam;
if (stringParam != null && !string.IsNullOrEmpty(stringParam.Value)){
mtd.SetTitle(stringParam.Value);
}
stringParam = FindParam(param, MetadataElement.DESCRIPTION.Name) as StringParam;
if (stringParam != null && !string.IsNullOrEmpty(stringParam.Value)){
mtd.SetDescription(stringParam.Value);
}
SingleChoiceWithSubParams singleSub =
FindParam(param, MetadataElement.SAMPLE_PROCESSING.Name) as SingleChoiceWithSubParams;
if (singleSub != null){
SampleProcessingParam sub =
singleSub.SubParams[singleSub.Value].GetAllParameters().FirstOrDefault() as SampleProcessingParam;
if (sub != null){
if (sub.Value != null){
for (int j = 0; j < sub.Value.Length; j++){
mtd.SampleProcessingMap.Add(j + 1, sub.Value[j]);
}
}
}
}
singleSub = FindParam(param, MetadataElement.INSTRUMENT.Name) as SingleChoiceWithSubParams;
if (singleSub != null){
InstrumentParam sub =
singleSub.SubParams[singleSub.Value].GetAllParameters().FirstOrDefault() as InstrumentParam;
if (sub != null){
if (sub.Value != null){
for (int j = 0; j < sub.Value.Length; j++){
mtd.InstrumentMap.Add(j + 1, sub.Value[j]);
}
}
}
}
singleSub = FindParam(param, MetadataElement.SOFTWARE.Name) as SingleChoiceWithSubParams;
if (singleSub != null){
SoftwareParam sub =
singleSub.SubParams[singleSub.Value].GetAllParameters().FirstOrDefault() as SoftwareParam;
if (sub != null){
if (sub.Value != null){
for (int j = 0; j < sub.Value.Length; j++){
mtd.SoftwareMap.Add(j + 1, sub.Value[j]);
}
}
}
}
MultiChoiceParam multi = FindParam(param, MetadataElement.FALSE_DISCOVERY_RATE.Name) as MultiChoiceParam;
if (multi != null && multi.SelectedValues != null && multi.SelectedValues.Any()){
foreach (string sel in multi.SelectedValues){
string[] items = sel.Split('=');
if (items.Length != 2){
continue;
}
string key = items[0];
string value = items[1];
if (ContainsParameterKey(parameters.protein_fdr, key)){
key = "prot:global FDR";
} else if (ContainsParameterKey(parameters.psm_fdr, key)) {
key = "pep:global FDR";
} else if (ContainsParameterKey(parameters.site_fdr, key)) {
key = "site:global FDR";
}
Lib.Model.Param p = cv.GetParam(key, "MS", value);
if (p != null){
mtd.FalseDiscoveryRate.Add(p);
}
}
}
singleSub = FindParam(param, MetadataElement.PUBLICATION.Name) as SingleChoiceWithSubParams;
if (singleSub != null){
PublicationParam sub =
singleSub.SubParams[singleSub.Value].GetAllParameters().FirstOrDefault() as PublicationParam;
if (sub != null){
if (sub.Value != null){
for (int j = 0; j < sub.Value.Length; j++){
mtd.PublicationMap.Add(j + 1, sub.Value[j]);
}
}
}
}
singleSub = FindParam(param, MetadataElement.CONTACT.Name) as SingleChoiceWithSubParams;
if (singleSub != null){
ContactParam sub =
singleSub.SubParams[singleSub.Value].GetAllParameters().FirstOrDefault() as ContactParam;
if (sub != null){
if (sub.Value != null){
for (int j = 0; j < sub.Value.Length; j++){
mtd.ContactMap.Add(j + 1, sub.Value[j]);
}
}
}
}
singleSub = FindParam(param, MetadataElement.FIXED_MOD.Name) as SingleChoiceWithSubParams;
if (singleSub != null){
ModificationParam sub =
singleSub.SubParams[singleSub.Value].GetAllParameters().FirstOrDefault() as ModificationParam;
if (sub != null){
if (sub.Value != null){
for (int j = 0; j < sub.Value.Length; j++){
mtd.FixedModMap.Add(j + 1, (FixedMod) sub.Value[j]);
}
}
}
}
singleSub = FindParam(param, MetadataElement.VARIABLE_MOD.Name) as SingleChoiceWithSubParams;
if (singleSub != null){
ModificationParam sub =
singleSub.SubParams[singleSub.Value].GetAllParameters().FirstOrDefault() as ModificationParam;
if (sub != null){
if (sub.Value != null){
for (int j = 0; j < sub.Value.Length; j++){
mtd.VariableModMap.Add(j + 1, (VariableMod) sub.Value[j]);
}
}
}
}
single = FindParam(param, MetadataElement.QUANTIFICATION_METHOD.Name) as SingleChoiceParam;
if (single != null && !string.IsNullOrEmpty(single.SelectedValue)){
Lib.Model.Param temp;
mtd.QuantificationMethod = Lib.Model.Param.TryParse(single.SelectedValue, out temp)
? temp
: cv.GetParam(single.SelectedValue, "MS");
}
name = string.Format("{0}{1}{2}", MetadataElement.PROTEIN, MZTabConstants.MINUS,
MetadataProperty.PROTEIN_QUANTIFICATION_UNIT);
single = FindParam(param, name) as SingleChoiceParam;
if (single != null && !string.IsNullOrEmpty(single.SelectedValue)){
Lib.Model.Param temp;
mtd.ProteinQuantificationUnit = Lib.Model.Param.TryParse(single.SelectedValue, out temp)
? temp
: cv.GetParam(single.SelectedValue, "PRIDE");
}
name = string.Format("{0}{1}{2}", MetadataElement.PEPTIDE, MZTabConstants.MINUS,
MetadataProperty.PROTEIN_QUANTIFICATION_UNIT);
single = FindParam(param, name) as SingleChoiceParam;
if (single != null && !string.IsNullOrEmpty(single.SelectedValue)){
Lib.Model.Param temp;
mtd.PeptideQuantificationUnit = Lib.Model.Param.TryParse(single.SelectedValue, out temp)
? temp
: cv.GetParam(single.SelectedValue, "PRIDE");
}
Regex regex = new Regex("[A-Z]{1}:/");
MsRunParam msrunParam = FindParam(param, MetadataElement.MS_RUN.Name) as MsRunParam;
if (msrunParam != null){
if (msrunParam.Value != null){
for (int j = 0; j < msrunParam.Value.Length; j++){
MsRunImpl runImpl = msrunParam.Value[j];
if (regex.IsMatch(runImpl.Location.Value)){
runImpl.Location = new Url("file:\\\\\\" + runImpl.Location.Value);
}
mtd.MsRunMap.Add(j + 1, runImpl);
}
}
}
SampleParam sampleParam = FindParam(param, MetadataElement.SAMPLE.Name) as SampleParam;
if (sampleParam != null){
if (sampleParam.Value != null){
for (int j = 0; j < sampleParam.Value.Length; j++){
mtd.SampleMap.Add(j + 1, sampleParam.Value[j]);
}
}
}
AssayParam assayParam = FindParam(param, MetadataElement.ASSAY.Name) as AssayParam;
if (assayParam != null){
if (assayParam.Value != null){
for (int j = 0; j < assayParam.Value.Length; j++){
mtd.AssayMap.Add(j + 1, assayParam.Value[j]);
}
}
}
StudyVariableParam studyVariableParam =
FindParam(param, MetadataElement.STUDY_VARIABLE.Name) as StudyVariableParam;
if (studyVariableParam != null){
if (studyVariableParam.Value != null){
for (int j = 0; j < studyVariableParam.Value.Length; j++){
mtd.StudyVariableMap.Add(j + 1, studyVariableParam.Value[j]);
}
}
}
multi = FindParam(param, MetadataElement.CV.Name) as MultiChoiceParam;
if (multi != null && multi.SelectedValues != null){
var headers = cv.Headers;
foreach (string value in multi.SelectedValues){
var temp = headers.FirstOrDefault(x => x.FullName.Equals(value));
if (temp == null){
continue;
}
int id = mtd.CvMap.Count + 1;
mtd.CvMap.Add(id,
new CV(id){
FullName = temp.FullName,
Label = temp.Label,
Url = temp.Url,
Version = temp.Version
});
}
}
string mtdString = mtd.ToString();
string[] lines = mtdString.Split(new[]{"\n"}, StringSplitOptions.RemoveEmptyEntries);
List<string> columnames = new List<string>{"MTH", "key", "value"};
List<string[]> columns = columnames.Select(columname => new string[lines.Length]).ToList();
for (int n = 0; n < lines.Length; n++){
string[] items = lines[n].Split(new[]{"\t", "\n", "\r"}, StringSplitOptions.None);
if (items.Length < 3){
continue;
}
columns[0][n] = items[0];
columns[1][n] = items[1];
columns[2][n] = items[2];
}
int nrows = lines.Length;
int ncols = columnames.Count;
IMatrixData data = (IMatrixData) inputData[0].CreateNewInstance(DataType.Matrix);
data.SetData(Matrix.MetadataSection, new List<string>(), new float[nrows,ncols], columnames, columns,
new List<string>(), new List<string[][]>(), new List<string>(), new List<double[]>(),
new List<string>(), new List<double[][]>(), new List<string>(), new List<string[][]>(),
new List<string>(), new List<double[]>());
return data;
}
