public DeconToolsFilterLoader(string filterTableTextFile)
{
if (!File.Exists(filterTableTextFile))
{
Logger.Log("File not found error. DeconTools filter settings could not be loaded.");
throw new FileNotFoundException("File not found error. DeconTools filter settings could not be loaded.");
}
using (var sr = new StreamReader(filterTableTextFile))
{
sr.ReadLine(); //headerline
while (sr.Peek() != -1)
{
var line = sr.ReadLine();
if (line == null)
{
continue;
}
var parsedLine = line.Split('\t');
if (parsedLine.Length != 6)
{
Logger.Log("Error loading DeconTools filter settings file.");
throw new ArgumentException("Error loading DeconTools filter settings file.");
}
var zMin = Convert.ToInt32(parsedLine[0]);
var zMax = Convert.ToInt32(parsedLine[1]);
var abundanceMin = Convert.ToInt32(parsedLine[2]);
var abundanceMax = Convert.ToInt32(parsedLine[3]);
var iscoreCutoff = Convert.ToDouble(parsedLine[4]);
var fitScoreCutoff = Convert.ToDouble(parsedLine[5]);
var f = new DeconToolsFilter(zMin, zMax, abundanceMin, abundanceMax, fitScoreCutoff, iscoreCutoff);
DeconToolsFilterList.Add(f);
}
}
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="deconToolsFilterFilePath"></param>
public DeconToolsFilterLoader(string deconToolsFilterFilePath)
{
if (!File.Exists(deconToolsFilterFilePath))
{
var errorMessage = "DeconTools filter settings could not be loaded; File not found: " + deconToolsFilterFilePath;
Logger.LogError(errorMessage);
throw new FileNotFoundException(errorMessage);
}
var linesRead = 0;
DeconToolsFilterList.Clear();
using (var reader = new StreamReader(deconToolsFilterFilePath))
{
if (reader.EndOfStream)
{
var errorMessage = "DeconTools filter file is empty: " + deconToolsFilterFilePath;
Logger.LogError(errorMessage);
throw new ArgumentException(errorMessage);
}
// Skip the header line, which should have 6 columns:
// chargeMin chargeMax abundanceMin abundanceMax iscoreCutoff fitScoreCutoff
reader.ReadLine();
linesRead++;
while (!reader.EndOfStream)
{
var dataLine = reader.ReadLine();
linesRead++;
if (string.IsNullOrWhiteSpace(dataLine))
{
continue;
}
var parsedLine = dataLine.Split('\t');
if (parsedLine.Length < 6)
{
var errorMessage = string.Format(
"Error loading DeconTools filter settings file; the file should have six tab-delimited columns, but line {0} has {1} columns",
linesRead, parsedLine.Length);
Logger.LogError(errorMessage);
throw new ArgumentException(errorMessage);
}
try
{
var zMin = Convert.ToInt32(parsedLine[0]);
var zMax = Convert.ToInt32(parsedLine[1]);
var abundanceMin = Convert.ToInt32(parsedLine[2]);
var abundanceMax = Convert.ToInt32(parsedLine[3]);
// Interference score cutoff (0 means no interference; 1 means lots of interference)
var iscoreCutoff = Convert.ToDouble(parsedLine[4]);
// Isotopic fit score cutoff
var fitScoreCutoff = Convert.ToDouble(parsedLine[5]);
var f = new DeconToolsFilter(zMin, zMax, abundanceMin, abundanceMax, fitScoreCutoff, iscoreCutoff);
DeconToolsFilterList.Add(f);
}
catch (Exception ex)
{
var errorMessage = string.Format(
"Error reading data from the DeconTools filter settings file on line {0}, {1}",
linesRead, dataLine);
Logger.LogError(errorMessage, ex);
throw new Exception(errorMessage + ": " + ex.Message);
}
}
}
}
