/**
* Translate the data line to a {@link MZTabRecord}.
*
* NOTICE: Normally, we suggest user do convert operation after validate successfully.
*
* @see #parse(int, string, uk.ac.ebi.pride.jmztab.utils.errors.MZTabErrorList)
*/
protected MZTabRecord getRecord(Section section, string line)
{
MZTabRecord record = null;
if (section.Equals(Section.Protein)){
record = new Protein(factory);
}
else if (section.Equals(Section.Peptide)){
record = new Peptide(factory, metadata);
}
else if (section.Equals(Section.PSM)){
record = new PSM(factory, metadata);
}
else if (section.Equals(Section.Small_Molecule)){
record = new SmallMolecule(factory, metadata);
}
int offset = loadStableData(record, line);
if (offset == _items.Length - 1){
return record;
}
loadOptionalData(record, offset);
return record;
}
/**
* Add a Protein record.
*
* @param protein SHOULD NOT set null.
*/
public void addProtein(Protein protein)
{
if (protein == null){
throw new NullReferenceException("Protein record is null!");
}
int lineNumber = proteins.Count == 0 ? 1 : proteins.Last().Key + 1;
proteins.Add(lineNumber, protein);
}
/**
* Add a Protein record.
*
* @param lineNumber SHOULD be positive integer
* @param protein SHOULD NOT set null.
*
* @throws ArgumentException if there exists Protein object for assigned lineNumber
*/
public void addProtein(int lineNumber, Protein protein)
{
if (protein == null){
throw new NullReferenceException("Protein record is null!");
}
if (lineNumber <= 0){
throw new ArgumentException("Line number should be positive integer");
}
if (proteins.ContainsKey(lineNumber)){
throw new ArgumentException("There already exist protein record in line number " + lineNumber);
}
proteins.Add(lineNumber, protein);
}
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);
}
