/**
* 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()
{
PSM psm = new PSM(factory, metadata);
psm.Sequence = Sequence;
psm.PSM_ID = PSM_ID;
psm.Accession = Accession;
psm.Unique = Unique;
psm.Database = Database;
psm.DatabaseVersion = DatabaseVersion;
psm.SearchEngine = SearchEngine;
psm.SearchEngineScore = SearchEngineScore;
psm.Reliability = Reliability;
psm.Modifications = Modifications;
psm.RetentionTime = RetentionTime;
psm.Charge = Charge;
psm.ExpMassToCharge = ExpMassToCharge;
psm.CalcMassToCharge = CalcMassToCharge;
psm.URI = URI;
psm.SpectraRef = SpectraRef;
psm.Post = Post;
psm.Pre = Pre;
psm.Start = Start;
psm.End = End;
return psm;
}
/**
* Add a PSM record.
*
* @param psm SHOULD NOT set null.
*/
public void addPSM(PSM psm)
{
if (psm == null){
throw new NullReferenceException("PSM record is null!");
}
int position = psms.Count == 0 ? 1 : psms.Last().Key + 1;
psms.Add(position, psm);
}
/**
* Add a PSM record.
*
* @param lineNumber SHOULD be positive integer
* @param psm SHOULD NOT set null.
*
* @throws ArgumentException if there exists PSM object for assigned lineNumber
*/
public void addPSM(int lineNumber, PSM psm)
{
if (psm == null){
throw new NullReferenceException("PSM record is null!");
}
if (lineNumber <= 0){
throw new ArgumentException("Line number should be positive integer");
}
if (psms.ContainsKey(lineNumber)){
throw new ArgumentException("There already exist PSM record in line number " + lineNumber);
}
psms.Add(lineNumber, psm);
}
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);
}