private IsotopicAtom AddHevayAtom(string name, string monoAtomName, int isotopicIndex, Dictionary <string, IsotopicAtom> dic)
{
var result = new IsotopicAtom()
{
Name = name
};
result.Isotopics.Add(new Peak(dic[monoAtomName].Isotopics[isotopicIndex].Mz, 1.0));
return(result);
}
public override IEnumerable <string> Process(string fileName)
{
System.Net.WebClient aWebClient = new System.Net.WebClient();
aWebClient.Encoding = System.Text.Encoding.Default;
string html = aWebClient.DownloadString(this.url);
//string html = File.ReadAllText(fileName);
Lexer lexer = new Lexer(html);
Winista.Text.HtmlParser.Parser parser = new Winista.Text.HtmlParser.Parser(lexer);
NodeList htmlNodes = parser.Parse(null);
List <IsotopicAtom> atoms = new List <IsotopicAtom>();
var node = FindFirstNode(htmlNodes, "tbody");
INode nextNode;
IsotopicAtom atom = null;
while ((nextNode = FindFirstNode(node, "tr")) != null)
{
if (nextNode.Children != null)
{
var tds = nextNode.Children.ExtractAllNodesThatMatch(new NameFilter("td"));
if (tds.Count == 1)
{
atom = null;
}
if (tds.Count >= 3 && tds[0].FirstChild != null)
{
var t1 = tds[0].FirstChild.GetText().Trim();
var t2 = tds[1].FirstChild.GetText().Trim();
if (Char.IsDigit(t1[0]) && Char.IsLetter(t2[0]))
{
atom = new IsotopicAtom();
atoms.Add(atom);
atom.Name = tds[1].FirstChild.GetText().Trim();
Peak p = new Peak();
p.Mz = GetDouble(tds[3]);
p.Intensity = GetDouble(tds[4]);
atom.Isotopics.Add(p);
}
else if (atom != null)
{
var txt = tds[0].FirstChild.GetText().Trim();
if (txt.Length > 0 && Char.IsLetter(txt[0]))
{
tds.Remove(0);
}
Peak p = new Peak();
p.Mz = GetDouble(tds[1]);
p.Intensity = GetDouble(tds[2]);
atom.Isotopics.Add(p);
}
}
}
node = nextNode.NextSibling;
if (node == null)
{
break;
}
}
atoms.ForEach(m => m.Isotopics.RemoveAll(n => n.Intensity == 0.0));
atoms.RemoveAll(m => m.Isotopics.Count == 0);
var dic = atoms.ToDictionary(m => m.Name);
var x = new IsotopicAtom();
x.Name = "X";
x.Isotopics.Add(new Peak(1, 0.9));
x.Isotopics.Add(new Peak(2, 0.1));
atoms.Insert(0, x);
atoms.Add(AddHevayAtom("(H2)", "H", 1, dic));
atoms.Add(AddHevayAtom("(C13)", "C", 1, dic));
atoms.Add(AddHevayAtom("(N15)", "N", 1, dic));
atoms.Add(AddHevayAtom("(O18)", "O", 2, dic));
using (StreamWriter sw = new StreamWriter(fileName))
{
atoms.ForEach(m =>
{
sw.WriteLine("{0}\t{1}", m.Name, m.Isotopics.Count);
m.Isotopics.ForEach(n => sw.WriteLine("{0:0.000000}\t{1:0.000000}", n.Mz, n.Intensity));
sw.WriteLine();
});
}
return(new string[] { fileName });
}
