private void Read(string filePath)
{
var ratioProbDictionary = _ratioTargetProbDictionary;
var isotopeIntensityCorrTargetProbDictionary = new Dictionary <GroupParameter, Dictionary <int, Dictionary <int, double> > >();
var isotopeIntensityCorrDecoyProbDictionary = new Dictionary <GroupParameter, Dictionary <int, Dictionary <int, double> > >();
var isotopeIntensityCorrProbDictionary = isotopeIntensityCorrTargetProbDictionary;
var noIonTargetProbDictionary = new Dictionary <GroupParameter, double>();
var noIonDecoyProbDictionary = new Dictionary <GroupParameter, double>();
var noIonProbDictionary = noIonTargetProbDictionary;
var stremaReader = new StreamReader(filePath);
string s;
var mode = -1;
GroupParameter groupParameter = null;
List <int> ionTypeIndices = null;
while ((s = stremaReader.ReadLine()) != null)
{
if (s.StartsWith("###DECOY"))
{
ratioProbDictionary = _ratioDecoyProbDictionary;
isotopeIntensityCorrProbDictionary = isotopeIntensityCorrDecoyProbDictionary;
noIonProbDictionary = noIonDecoyProbDictionary;
continue;
}
if (s.StartsWith("##IONTYPES"))
{
mode = 1;
continue;
}
if (s.StartsWith("##ISOTOPE"))
{
mode = 2;
continue;
}
if (s.StartsWith("##RATIO"))
{
mode = 3;
continue;
}
if (s.StartsWith("##NOION"))
{
mode = 4;
continue;
}
var token = s.Split('\t');
if (s.StartsWith("#G"))
{
groupParameter = GroupParameter.Parse(token[1]);
continue;
}
if (s.StartsWith("#I"))
{
if (mode == 1)
{
var ionType = IonType.Parse(token[1]);
if (groupParameter == null || ionType == null)
{
continue;
}
if (!_ionTypeDictionary.ContainsKey(groupParameter))
{
_ionTypeDictionary[groupParameter] = new List <IonType>();
}
_ionTypeDictionary[groupParameter].Add(ionType);
}
else
{
ionTypeIndices = new List <int>();
for (var i = 1; i < token.Length; i++)
{
ionTypeIndices.Add(int.Parse(token[i]));
}
}
continue;
}
if (!s.StartsWith("#") && token.Length > 0)
{
if (mode == 2)
{
if (groupParameter == null || ionTypeIndices == null || ionTypeIndices.Count == 0)
{
continue;
}
if (!isotopeIntensityCorrProbDictionary.ContainsKey(groupParameter))
{
isotopeIntensityCorrProbDictionary[groupParameter] = new Dictionary <int, Dictionary <int, double> >();
}
var si = isotopeIntensityCorrProbDictionary[groupParameter];
if (!si.ContainsKey(ionTypeIndices[0]))
{
si[ionTypeIndices[0]] = new Dictionary <int, double>();
}
var ssi = si[ionTypeIndices[0]];
foreach (var scoreStr in token)
{
var st = scoreStr.Split(',');
if (st.Length == 2)
{
ssi[int.Parse(st[0])] = double.Parse(st[1]);
}
}
}
else if (mode == 3)
{
if (groupParameter == null || ionTypeIndices == null || ionTypeIndices.Count < 2)
{
continue;
}
if (!ratioProbDictionary.ContainsKey(groupParameter))
{
ratioProbDictionary[groupParameter] = new Dictionary <Tuple <int, int>, Dictionary <int, double> >();
}
var sr = ratioProbDictionary[groupParameter];
var key = new Tuple <int, int>(ionTypeIndices[0], ionTypeIndices[1]);
if (!sr.ContainsKey(key))
{
sr[key] = new Dictionary <int, double>();
}
var ssr = sr[key];
foreach (var scoreStr in token)
{
var st = scoreStr.Split(',');
if (st.Length == 2)
{
ssr[int.Parse(st[0])] = double.Parse(st[1]);
}
}
}
else if (mode == 4)
{
if (groupParameter == null)
{
continue;
}
noIonProbDictionary[groupParameter] = double.Parse(s);
}
}
}
foreach (var k in noIonTargetProbDictionary.Keys)
{
_noIonScore[k] = GetLogLRScore(noIonTargetProbDictionary[k], noIonDecoyProbDictionary[k]);
}
GetScoreDictionariesFromProbDictionaries();
}
