/**
* Add a SmallMolecule record.
*
* @param lineNumber SHOULD be positive integer
* @param smallMolecule SHOULD NOT set null.
*
* @throws ArgumentException if there exists SmallMolecule object for assigned lineNumber
*/
public void addSmallMolecule(int lineNumber, SmallMolecule smallMolecule)
{
if (smallMolecule == null){
throw new NullReferenceException("Small Molecule record is null!");
}
if (lineNumber <= 0){
throw new ArgumentException("Line number should be positive integer");
}
if (smallMolecules.ContainsKey(lineNumber)){
throw new ArgumentException("There already exist small molecule record in line number " +
lineNumber);
}
smallMolecules.Add(lineNumber, smallMolecule);
}
/**
* 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 Small Molecule record.
*
* @param smallMolecule SHOULD NOT set null.
*/
public void addSmallMolecule(SmallMolecule smallMolecule)
{
if (smallMolecule == null){
throw new NullReferenceException("Small Molecule record is null!");
}
int position = smallMolecules.Count == 0 ? 1 : smallMolecules.Last().Key + 1;
smallMolecules.Add(position, smallMolecule);
}
