protected override IProcessor GetProcessor()
{
string dbFile;
if (fastaFile.Exists)
{
dbFile = fastaFile.FullName;
}
else
{
dbFile = databaseFile.FullName;
}
var options = new PNovoSAPValidatorOptions()
{
PnovoFiles = pNovoFiles.SelectedFileNames,
DatabaseFastaFile = dbFile,
TitleParser = titleParsers.SelectedItem,
AccessNumberParser = acParsers.SelectedItem,
Enzyme = ProteaseManager.GetProteaseByName(proteases.SelectedItem),
MinScore = minScore.Value,
ThreadCount = threadCount.Value,
IgnoreNtermMutation = ignoreNTerm.Checked,
IgnoreDeamidatedMutation = ignoreDeamidatedMutation.Checked,
IgnoreMultipleNucleotideMutation = ignoreMultipleNucleotideMutation.Checked,
MinLength = minLength.Value,
TargetDirectory = targetDirectory.FullName,
TargetFastaFile = databaseFile.FullName
};
return(new PNovoSAPValidator(options));
}
public PNovoSAPValidator(PNovoSAPValidatorOptions options)
{
this.options = options;
if (this.options.ThreadCount < 1)
{
this.options.ThreadCount = 1;
}
}