public MSAmandaSearchWrapper()
{
Settings = new MSAmandaSettings();
helper = new MSHelper();
helper.InitLogWriter(_baseDir.DirPath);
helper.SearchProgressChanged += Helper_SearchProgressChanged;
var folderForMappings = Path.Combine(_baseDir.DirPath, AmandaMap);
// creates dir if not existing
Directory.CreateDirectory(folderForMappings);
mzID = new OutputMzid(folderForMappings);
AvailableSettings = new SettingsFile(helper, Settings, mzID);
AvailableSettings.AllEnzymes = new List <MSAmandaEnzyme>();
AvailableSettings.AllModifications = new List <Modification>();
using (var d = new CurrentDirectorySetter(Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location)))
{
if (!AvailableSettings.ParseEnzymeFile(ENZYME_FILENAME, "", AvailableSettings.AllEnzymes))
{
throw new Exception(string.Format(Resources.DdaSearch_MSAmandaSearchWrapper_enzymes_file__0__not_found, ENZYME_FILENAME));
}
if (!AvailableSettings.ParseUnimodFile(UNIMOD_FILENAME, AvailableSettings.AllModifications))
{
throw new Exception(string.Format(Resources.DdaSearch_MSAmandaSearchWrapper_unimod_file__0__not_found, UNIMOD_FILENAME));
}
if (!AvailableSettings.ParseOboFiles())
{
throw new Exception(Resources.DdaSearch_MSAmandaSearchWrapper_Obo_files_not_found);
}
if (!AvailableSettings.ReadInstrumentsFile(INSTRUMENTS_FILENAME))
{
throw new Exception(string.Format(Resources.DdaSearch_MSAmandaSearchWrapper_Instruments_file_not_found, INSTRUMENTS_FILENAME));
}
}
AdditionalSettings = new Dictionary <string, Setting>
{
{ MAX_LOADED_PROTEINS_AT_ONCE, new Setting(MAX_LOADED_PROTEINS_AT_ONCE, 100000, 10, int.MaxValue) },
{ MAX_LOADED_SPECTRA_AT_ONCE, new Setting(MAX_LOADED_SPECTRA_AT_ONCE, 10000, 100, int.MaxValue) }
};
CurrentFile = 0;
}