public static string GetHeader(IndexedElement element, CVParam param)
{
StringBuilder sb = new StringBuilder();
sb.Append(OPT).Append("_").Append(element == null ? GLOBAL : element.Reference);
sb.Append("_").Append(CV).Append(param.Accession).Append("_").Append(param.Name.Replace(" ", "_"));
return sb.ToString();
}
private void addPeptideValue()
{
MsRun msRun1 = new MsRun(1);
Assay assay1 = new Assay(1);
Assay assay2 = new Assay(2);
StudyVariable studyVariable1 = new StudyVariable(1);
MZTabColumnFactory factory = MZTabColumnFactory.GetInstance(Section.Peptide_Header);
factory.AddOptionalColumn(PeptideColumn.SEARCH_ENGINE_SCORE, msRun1);
factory.AddAbundanceOptionalColumn(assay1);
factory.AddAbundanceOptionalColumn(studyVariable1);
factory.AddAbundanceOptionalColumn(assay2);
factory.AddOptionalColumn(msRun1, "my_value", typeof (string));
CVParam param = new CVParam("MS", "MS:1002217", "decoy peptide", null);
factory.AddOptionalColumn(param, typeof (string));
Metadata metadata = new Metadata();
metadata.AddMsRunLocation(2, new Url("file://C:\\path\\to\\my\\file"));
Console.WriteLine(factory);
Peptide peptide = new Peptide(factory, metadata);
peptide.Sequence = "KVPQVSTPTLVEVSR";
peptide.Accession = "P02768";
peptide.SetUnique("0");
peptide.Database = "UniProtKB";
peptide.DatabaseVersion = "2011_11";
peptide.SetSearchEngine("[MS,MS:1001207,Mascot,]|[MS,MS:1001208,Sequest,]");
peptide.SetBestSearchEngineScore("[MS,MS:1001155,Sequest:xcorr,2]");
peptide.Reliability = Reliability.findReliability("3");
peptide.SetModifications(
"3[MS,MS:1001876, modification probability, 0.8]|4[MS,MS:1001876, modification probability, 0.2]-MOD:00412,8[MS,MS:1001876, modification probability, 0.3]-MOD:00412");
peptide.AddRetentionTime(10.2);
peptide.AddRetentionTimeWindow(1123.2);
peptide.AddRetentionTimeWindow(1145.3);
peptide.Charge = new Integer(2);
peptide.MassToCharge = 1234.4;
peptide.URI = new Uri("http://www.ebi.ac.uk/pride/link/to/peptide");
peptide.SetSpectraRef("ms_run[2]:index=7|ms_run[2]:index=9");
Console.WriteLine(peptide);
}
public bool addSearchEngineScore(MsRun msRun, CVParam param)
{
if (param == null){
return false;
}
SplitList<Param> paramList = getSearchEngineScore(msRun);
if (paramList == null){
paramList = new SplitList<Param>(MZTabConstants.BAR);
setSearchEngineScore(msRun, paramList);
}
paramList.Add(param);
return true;
}
public bool AddSearchEngineScore(MsRun msRun, CVParam param)
{
if (param == null){
return false;
}
SplitList<Param> searchparams = getSearchEngineScore(msRun);
if (searchparams == null){
searchparams = new SplitList<Param>(MZTabConstants.BAR);
SetSearchEngineScore(msRun, searchparams);
}
searchparams.Add(param);
return true;
}
private void addProteinValue()
{
MsRun msRun1 = new MsRun(1);
MsRun msRun2 = new MsRun(2);
Assay assay1 = new Assay(1);
Assay assay2 = new Assay(2);
StudyVariable studyVariable1 = new StudyVariable(1);
MZTabColumnFactory factory = MZTabColumnFactory.GetInstance(Section.Protein_Header);
factory.AddOptionalColumn(ProteinColumn.SEARCH_ENGINE_SCORE, msRun1);
factory.AddOptionalColumn(ProteinColumn.NUM_PSMS, msRun1);
factory.AddOptionalColumn(ProteinColumn.NUM_PEPTIDES_DISTINCT, msRun1);
factory.AddOptionalColumn(ProteinColumn.NUM_PEPTIDES_UNIQUE, msRun1);
factory.AddOptionalColumn(ProteinColumn.NUM_PSMS, msRun2);
factory.AddOptionalColumn(ProteinColumn.NUM_PEPTIDES_DISTINCT, msRun2);
factory.AddAbundanceOptionalColumn(assay1);
factory.AddAbundanceOptionalColumn(studyVariable1);
factory.AddAbundanceOptionalColumn(assay2);
factory.AddOptionalColumn(assay1, "my_value", typeof (string));
CVParam param = new CVParam("MS", "MS:1002217", "decoy peptide", null);
factory.AddOptionalColumn(param, typeof (string));
Console.WriteLine(factory);
Protein protein = new Protein(factory);
// set stable columns data.
protein.Accession = "P12345";
protein.Description = "Aspartate aminotransferase, mitochondrial";
protein.SetTaxid("10116");
protein.Species = "Rattus norvegicus (Rat)";
protein.Database = "UniProtKB";
protein.DatabaseVersion = "2011_11";
protein.SetSearchEngine("[MS,MS:1001207,Mascot,]");
protein.AddSearchEngine("[MS,MS:1001208,Sequest,]");
protein.SetBestSearchEngineScore("[MS,MS:1001171,Mascot score,50]|[MS,MS:1001155,Sequest:xcorr,2]");
protein.Reliability = Reliability.High;
protein.SetAmbiguityMembers("P12347,P12348");
protein.SetModifications("3|4|8-MOD:00412, 3|4|8-MOD:00412");
protein.SetURI("http://www.ebi.ac.uk/pride/url/to/P12345");
protein.SetGOTerms("GO:0006457|GO:0005759|GO:0005886|GO:0004069");
protein.SetProteinCoverage("0.4");
Console.WriteLine(protein);
// set optional columns which have stable order.
protein.setSearchEngineScore(msRun1, "[MS,MS:1001171,Mascot score,50]|[MS,MS:1001155,Sequest:xcorr,2]");
protein.setNumPSMs(msRun1, 4);
protein.setNumPSMs(msRun2, 2);
protein.setNumPeptidesDistinct(msRun1, 3);
protein.setNumPeptidesUnique(msRun1, 2);
Console.WriteLine(protein);
// set abundance columns
protein.setAbundanceColumn(assay1, "0.4");
protein.setAbundanceColumn(assay2, "0.2");
protein.setAbundanceColumn(studyVariable1, "0.4");
protein.setAbundanceStdevColumn(studyVariable1, "0.3");
protein.setAbundanceStdErrorColumn(studyVariable1, "0.2");
Console.WriteLine(protein);
// set user defined optional columns
protein.setOptionColumn(assay1, "my_value", "My value about assay[1]");
protein.setOptionColumn(param, "TOM value");
Console.WriteLine(protein);
}
private void addSmallMoleculeValue()
{
MsRun msRun1 = new MsRun(1);
Assay assay1 = new Assay(1);
Assay assay2 = new Assay(2);
StudyVariable studyVariable1 = new StudyVariable(1);
MZTabColumnFactory factory = MZTabColumnFactory.GetInstance(Section.Small_Molecule);
factory.AddAbundanceOptionalColumn(assay1);
factory.AddAbundanceOptionalColumn(studyVariable1);
factory.AddAbundanceOptionalColumn(assay2);
factory.AddOptionalColumn(msRun1, "my_value", typeof (string));
CVParam param = new CVParam("MS", "MS:1002217", "decoy peptide", null);
factory.AddOptionalColumn(param, typeof (string));
Metadata metadata = new Metadata();
metadata.AddMsRunLocation(2, new Url("file://C:\\path\\to\\my\\file"));
Console.WriteLine(factory);
/*TODO: SmallMolecule sm = new SmallMolecule(factory, metadata);
sm.setIdentifier("CID:00027395");
sm.setChemicalFormula("C17H20N4O2");
sm.setSmiles("C1=CC=C(C=C1)CCNC(=O)CCNNC(=O)C2=CC=NC=C2");
sm.setInchiKey("QXBMEGUKVLFJAM-UHFFFAOYSA-N");
sm.setDescription("N-(2-phenylethyl)-3-[2-(pyridine-4-carbonyl)hydrazinyl]propanamide");
sm.setExpMassToCharge("1234.4");
sm.setCalcMassToCharge("1234.5");
sm.setCharge("2");
sm.setRetentionTime("10.2|11.5");
sm.setTaxid("10116");
sm.setSpecies("Rattus norvegicus (Rat)");
sm.setDatabase("UniProtKB");
sm.setDatabaseVersion("2011_11");
sm.setReliability("2");
sm.setURI("http://www.ebi.ac.uk/pride/link/to/identification");
sm.setSpectraRef("ms_run[2]:index=7|ms_run[2]:index=9");
sm.setSearchEngine("[MS, MS:1001477, SpectraST,]");
sm.setBestSearchEngineScore("[MS, MS:1001419, SpectraST:discriminant score F, 0.7]");
sm.setModifications("CHEMMOD:+Na-H");
Console.WriteLine(sm);*/
}
private void addPSMValue()
{
Assay assay1 = new Assay(1);
MZTabColumnFactory factory = MZTabColumnFactory.GetInstance(Section.PSM_Header);
factory.AddOptionalColumn(assay1, "my_value", typeof (string));
CVParam param = new CVParam("MS", "MS:1002217", "decoy peptide", null);
factory.AddOptionalColumn(param, typeof (string));
Metadata metadata = new Metadata();
metadata.AddMsRunLocation(2, new Url("file://C:\\path\\to\\my\\file"));
Console.WriteLine(factory);
PSM psm = new PSM(factory, metadata);
psm.Sequence = "KVPQVSTPTLVEVSR";
psm.SetPSM_ID("1");
psm.Accession = "P02768";
psm.Unique = MZBoolean.False;
psm.Database = "UniProtKB";
psm.DatabaseVersion = "2011_11";
psm.setSearchEngine("[MS,MS:1001207,Mascot,]|[MS,MS:1001208,Sequest,]");
psm.setSearchEngineScore("[MS,MS:1001155,Sequest:xcorr,2]");
psm.setReliability("3");
psm.setModifications("CHEMMOD:+159.93");
psm.AddRetentionTime(10.2);
psm.Charge = new Integer(2);
psm.SetExpMassToCharge("1234.4");
psm.SetCalcMassToCharge("123.4");
psm.SetUri("http://www.ebi.ac.uk/pride/link/to/peptide");
psm.SetSpectraRef("ms_run[2]:index=7|ms_run[2]:index=9");
psm.Pre = "K";
psm.Post = "D";
psm.Start = "45";
psm.End = "57";
Console.WriteLine(psm);
}
public void AddPosition(int id, CVParam param)
{
_positionMap.Add(id, param);
}
/**
* Add {@link CVParamOptionColumn} followed by ms_run into {@link #optionalColumnMapping} and {@link #columnMapping}.
* The header like: opt_ms_run[1]_cv_{accession}_{parameter name}
*
* @param msRun SHOULD NOT empty.
* @param param SHOULD NOT empty.
* @param columnType SHOULD NOT empty.
*/
public string AddOptionalColumn(MsRun msRun, CVParam param, Type columnType)
{
MZTabColumn column = new CVParamOptionColumn(msRun, param, columnType,
ParseColumnOrder(columnMapping.Last().Key));
return AddOptionColumn(column);
}
/**
* Add {@link CVParamOptionColumn} followed by study variable into {@link #optionalColumnMapping} and {@link #columnMapping}.
* The header like: opt_study_variable[1]_cv_{accession}_{parameter name}
*
* @param studyVariable SHOULD NOT empty.
* @param param SHOULD NOT empty.
* @param columnType SHOULD NOT empty.
*/
public string AddOptionalColumn(StudyVariable studyVariable, CVParam param, Type columnType)
{
MZTabColumn column = new CVParamOptionColumn(studyVariable, param, columnType,
ParseColumnOrder(columnMapping.Last().Key));
return AddOptionColumn(column);
}
/**
* Some {@link CVParamOptionColumn}, their data type have defined. Currently, we provide two {@link CVParam}
* which defined in the mzTab specification. One is "emPAI value" (MS:1001905), data type is Double;
* another is "decoy peptide" (MS:1002217), the data type is Boolean (0/1). Besides them, "opt_" start optional
* column data type is string.
*
* @see #checkOptColumnName(string)
*/
private Type getDataType(CVParam param)
{
Type dataType;
if (param == null){
dataType = typeof (string);
}
else if (param.Accession.Equals("MS:1001905")){
dataType = typeof (double);
}
else if (param.Accession.Equals("MS:1002217")){
dataType = typeof (MZBoolean);
}
else{
dataType = typeof (string);
}
return dataType;
}
public CVParamOptionColumn(IndexedElement element, CVParam param, System.Type columnType, int offset)
: base(element, CV + param.Accession + "_" + param.Name.Replace(" ", "_"), columnType, offset)
{
this.param = param;
}
