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);
}
/**
* 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;
}
public object Clone()
{
Peptide peptide = new Peptide(base.factory, this.metadata);
peptide.Sequence = Sequence;
peptide.Accession = Accession;
peptide.Unique = Unique;
peptide.Database = Database;
peptide.DatabaseVersion = DatabaseVersion;
peptide.SearchEngine = SearchEngine;
peptide.BestSearchEngineScore = BestSearchEngineScore;
//TODO: peptide.setSearchEngineScore();
peptide.Reliability = Reliability;
peptide.Modifications = Modifications;
peptide.RetentionTime = RetentionTime;
peptide.RetentionTimeWindow = RetentionTimeWindow;
peptide.Charge = Charge;
peptide.MassToCharge = MassToCharge;
peptide.URI = URI;
peptide.SpectraRef = SpectraRef;
return peptide;
}
/**
* Add a Peptide record.
*
* @param peptide SHOULD NOT set null.
*/
public void addPeptide(Peptide peptide)
{
if (peptide == null){
throw new NullReferenceException("Peptide record is null!");
}
int position = peptides.Count == 0 ? 1 : peptides.Last().Key + 1;
peptides.Add(position, peptide);
}
/**
* Add a Peptide record.
*
* @param lineNumber SHOULD be positive integer
* @param peptide SHOULD NOT set null.
*
* @throws ArgumentException if there exists Peptide object for assigned lineNumber
*/
public void addPeptide(int lineNumber, Peptide peptide)
{
if (peptide == null){
throw new NullReferenceException("Peptide record is null!");
}
if (lineNumber <= 0){
throw new ArgumentException("Line number should be positive integer");
}
if (peptides.ContainsKey(lineNumber)){
throw new ArgumentException("There already exist peptide record in line number " + lineNumber);
}
peptides.Add(lineNumber, peptide);
}
