protected Dictionary <string, string> ParseSection(StreamReader sr, string sectionName, string lineRegexStr, bool required = true)
{
string line;
SectionClass sc = new SectionClass(sectionName);
while ((line = sr.ReadLine()) != null)
{
if (sc.IsStartLine(line))
{
break;
}
}
if (line == null)
{
if (required)
{
throw new Exception("Cannot find " + sectionName + " information when parsing dat file.");
}
else
{
return(new Dictionary <string, string>());
}
}
Regex lineRegex = null;
if (lineRegexStr != null && lineRegexStr.Length > 0)
{
lineRegex = new Regex(lineRegexStr);
}
var result = new Dictionary <string, string>();
while ((line = sr.ReadLine()) != null)
{
if (IsSectionEnd(line))
{
break;
}
if (line.Trim().Length == 0)
{
continue;
}
if (lineRegex == null || lineRegex.Match(line).Success)
{
Match m = this.keyValueRegex.Match(line);
if (m.Success)
{
result[m.Groups[1].Value] = m.Groups[2].Value.Trim();
}
}
}
return(result);
}
protected Protease ParseEnzyme(StreamReader sr)
{
SectionClass sc = new SectionClass("enzyme");
string line;
//find enzyme section
while ((line = sr.ReadLine()) != null)
{
if (sc.IsStartLine(line))
{
break;
}
}
string name = "";
string cleavage = "";
string uncleavage = "";
bool cterm = false;
bool semiSpecific = false;
while ((line = sr.ReadLine()) != null)
{
if (IsSectionEnd(line))
{
break;
}
if (line.StartsWith("Title"))
{
name = line.Substring(line.IndexOf(':') + 1);
}
else if (line.StartsWith("Cleavage"))
{
cleavage = line.Substring(line.IndexOf(':') + 1);
}
else if (line.StartsWith("Restrict"))
{
uncleavage = line.Substring(line.IndexOf(':') + 1);
}
else if (line.StartsWith("Cterm"))
{
cterm = true;
}
else if (line.StartsWith("SemiSpecific"))
{
semiSpecific = true;
}
}
return(new Protease(name, cterm, cleavage, uncleavage)
{
IsSemiSpecific = semiSpecific
});
}
protected Dictionary <int, MascotQueryItem> ParseQueryItems(StreamReader sr, int queryCount, string prefix = "")
{
string line;
SectionClass sc = new SectionClass(prefix + "summary");
while ((line = sr.ReadLine()) != null)
{
if (sc.IsStartLine(line))
{
break;
}
}
var result = new Dictionary <int, MascotQueryItem>();
while ((line = sr.ReadLine()) != null)
{
if (IsSectionEnd(line))
{
break;
}
if (line.StartsWith("qmass"))
{
Match m = queryIdRegex.Match(line);
var item = new MascotQueryItem();
item.QueryId = Convert.ToInt32(m.Groups[1].Value);
item.ExperimentalMass = MyConvert.ToDouble(m.Groups[2].Value);
line = sr.ReadLine();
Match precursor = this.precursorRegex.Match(line);
if (precursor.Success)
{
item.Observed = MyConvert.ToDouble(precursor.Groups[1].Value);
item.Charge = int.Parse(precursor.Groups[2].Value);
}
else
{
var pmr = this.precursorMrRegex.Match(line);
item.Observed = MyConvert.ToDouble(pmr.Groups[1].Value);
item.Charge = 0;
}
line = sr.ReadLine();
if (line.StartsWith("qintensity"))
{
item.Intensity = MyConvert.ToDouble(GetValue(line));
line = sr.ReadLine();
}
if (line.StartsWith("qmatch"))
{
item.MatchCount = Convert.ToInt32(GetValue(line));
line = sr.ReadLine();
}
if (line.StartsWith("qplughole"))
{
item.HomologyScore = Convert.ToDouble(GetValue(line));
}
result[item.QueryId] = item;
}
}
return(result);
}
public void TestSectionClass()
{
SectionClass sc = new SectionClass("parameters");
Assert.IsTrue(sc.IsStartLine("Content-Type: application/x-Mascot; name=\"parameters\""));
}
