/// <summary>
/// Populate a mod brick object with the appropriate date
/// </summary>
/// <param name="title">Unique designation of mod brick, usually a single letter</param>
/// <param name="fullName">full name</param>
/// <param name="monoMass">monoisotopic mass</param>
/// <param name="avgMass">average mass</param>
/// <param name="formula">Chemical formula</param>
public ModBrick(string title, string fullName, double monoMass, double avgMass, ChemFormula formula)
{
_title = title;
_fullName = fullName;
_monoMass = monoMass;
_avgMass = avgMass;
_formula = formula;
}
/// <summary>
/// Populate an AminoAcid object with the appropriate date
/// </summary>
/// <param name="title">Unique designation of Amino Acid, usually a single letter</param>
/// <param name="shortName">3 letter name</param>
/// <param name="fullName">full name</param>
/// <param name="monoMass">monoisotopic mass</param>
/// <param name="avgMass">average mass</param>
/// <param name="formula">Chemical formula</param>
public AminoAcid(string title, string shortName, string fullName, double monoMass, double avgMass, ChemFormula formula)
{
_title = title;
_shortName = shortName;
_fullName = fullName;
_monoMass = monoMass;
_avgMass = avgMass;
_formula = formula;
}
/// <summary>
/// Populate a modification object with the appropriate data
/// </summary>
/// <param name="title">Modification title</param>
/// <param name="fullName">Modification full name</param>
/// <param name="monoMass">Modification monoisotopic mass</param>
/// <param name="avgMass">Modification average mass</param>
/// <param name="comp">Modifcation composition (UNIMOD style)</param>
/// <param name="id">UNIMOD record id for modification</param>
/// <param name="formula">Chemical formula of modification</param>
public Modification(string title, string fullName, double monoMass, double avgMass, string comp, int id, ChemFormula formula)
{
_title = title;
_fullName = fullName;
_monoMass = monoMass;
_avgMass = avgMass;
_composition = comp;
_recordId = id;
_formula = formula;
}
/// <summary>
/// Read the chemical formula of an item from unimod.xml
/// </summary>
/// <param name="reader">XmlReader that is only valid for the scope containing the chemical formula</param>
/// <returns>List containing the chemical formula</returns>
private static ChemFormula ReadFormula(XmlReader reader)
{
var formula = new ChemFormula();
reader.MoveToContent();
while (reader.ReadToFollowing("umod:element"))
{
var symbol = reader.GetAttribute("symbol");
var number = Convert.ToInt32(reader.GetAttribute("number"));
formula.Add(symbol, number);
}
return(formula);
}
/// <summary>
/// Handle a single umod:brick element and child nodes
/// Called by ReadModBricks (xml hierarchy)
/// </summary>
/// <param name="reader">XmlReader that is only valid for the scope of the single umod:brick element</param>
private static void ReadModBrick(XmlReader reader)
{
reader.MoveToContent(); // Move to the "aa" element
string title = reader.GetAttribute("title");
string fullName = reader.GetAttribute("full_name");
double monoMass = Convert.ToDouble(reader.GetAttribute("mono_mass"));
double avgMass = Convert.ToDouble(reader.GetAttribute("avge_mass"));
ChemFormula formula = ReadFormula(reader.ReadSubtree());
var brick = new ModBrick(title, fullName, monoMass, avgMass, formula);
ModBricks.Add(title, brick);
reader.Close();
}
/// <summary>
/// Handle a single umod:aa element and child nodes
/// Called by ReadAminoAcids (xml hierarchy)
/// </summary>
/// <param name="reader">XmlReader that is only valid for the scope of the single umod:aa element</param>
private static void ReadAminoAcid(XmlReader reader)
{
reader.MoveToContent(); // Move to the "aa" element
string title = reader.GetAttribute("title");
string shortName = reader.GetAttribute("three_letter");
string fullName = reader.GetAttribute("full_name");
double monoMass = Convert.ToDouble(reader.GetAttribute("mono_mass"));
double avgMass = Convert.ToDouble(reader.GetAttribute("avge_mass"));
ChemFormula formula = ReadFormula(reader.ReadSubtree());
var amAcid = new AminoAcid(title, shortName, fullName, monoMass, avgMass, formula);
AminoAcids.Add(title, amAcid);
reader.Close();
}
/// <summary>
/// Handle a single umod:mod element and child nodes
/// Called by ReadModifications (xml hierarchy)
/// </summary>
/// <param name="reader">XmlReader that is only valid for the scope of the single umod:mod element</param>
private static void ReadModification(XmlReader reader)
{
reader.MoveToContent();
string title = reader.GetAttribute("title");
string fullName = reader.GetAttribute("full_name");
int recordId = Convert.ToInt32(reader.GetAttribute("record_id"));
reader.ReadToDescendant("umod:delta");
double monoMass = Convert.ToDouble(reader.GetAttribute("mono_mass"));
double avgMass = Convert.ToDouble(reader.GetAttribute("avge_mass"));
string composition = reader.GetAttribute("composition");
ChemFormula formula = ReadFormula(reader.ReadSubtree());
var mod = new Modification(title, fullName, monoMass, avgMass, composition, recordId, formula);
ModList.Add(title, mod);
reader.Close();
}
