static void Main(string[] args)
{
if(args.Length > 0)
{
Arguments arguments = new Arguments(args);
List<string> data = new List<string>(arguments["d"].Split(','));
int min_assumed_precursor_charge_state = 2;
if(arguments["minprecz"] != null)
{
min_assumed_precursor_charge_state = int.Parse(arguments["minprecz"]);
}
int max_assumed_precursor_charge_state = 4;
if(arguments["maxprecz"] != null)
{
max_assumed_precursor_charge_state = int.Parse(arguments["maxprecz"]);
}
double abs_threshold = -1.0;
if(arguments["at"] != null)
{
abs_threshold = double.Parse(arguments["at"], CultureInfo.InvariantCulture);
}
double rel_threshold_percent = -1.0;
if(arguments["rt"] != null)
{
rel_threshold_percent = double.Parse(arguments["rt"], CultureInfo.InvariantCulture);
}
int max_peaks = 400;
if(arguments["mp"] != null)
{
max_peaks = int.Parse(arguments["mp"]);
}
bool assign_charge_states = true;
if(arguments["acs"] != null)
{
assign_charge_states = bool.Parse(arguments["acs"]);
}
bool deisotope = true;
if(arguments["di"] != null)
{
deisotope = bool.Parse(arguments["di"]);
}
string database = arguments["db"];
bool append_decoys;
if(arguments["ad"] != null)
{
append_decoys = bool.Parse(arguments["ad"]);
}
else
{
append_decoys = !ProteinFastaReader.HasDecoyProteins(database);
}
ProteaseDictionary proteases = ProteaseDictionary.Instance;
Protease protease = proteases["trypsin (no proline rule)"];
if(arguments["p"] != null)
{
protease = proteases[arguments["p"]];
}
int max_missed_cleavages = 2;
if(arguments["mmc"] != null)
{
max_missed_cleavages = int.Parse(arguments["mmc"]);
}
InitiatorMethionineBehavior initiator_methionine_behavior = InitiatorMethionineBehavior.Variable;
if(arguments["imb"] != null)
{
initiator_methionine_behavior = (InitiatorMethionineBehavior)Enum.Parse(typeof(InitiatorMethionineBehavior), arguments["imb"], true);
}
ModificationDictionary mods = ModificationDictionary.Instance;
List<Modification> fixed_mods = new List<Modification>();
if(arguments["fm"] != null)
{
foreach(string fixed_mod in arguments["fm"].Split(','))
{
fixed_mods.Add(mods[fixed_mod]);
}
}
List<Modification> variable_mods = new List<Modification>();
if(arguments["vm"] != null)
{
foreach(string variable_mod in arguments["vm"].Split(','))
{
variable_mods.Add(mods[variable_mod]);
}
}
int max_variable_mod_isoforms_per_peptide = 1024;
if(arguments["mvmi"] != null)
{
max_variable_mod_isoforms_per_peptide = int.Parse(arguments["mvmi"]);
}
double precursor_mass_tolerance_value = 2.1;
if(arguments["precmtv"] != null)
{
precursor_mass_tolerance_value = double.Parse(arguments["precmtv"], CultureInfo.InvariantCulture);
}
MassToleranceUnits precursor_mass_tolerance_units = MassToleranceUnits.Da;
if(arguments["precmtu"] != null)
{
precursor_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["precmtu"], true);
}
MassTolerance precursor_mass_tolerance = new MassTolerance(precursor_mass_tolerance_value, precursor_mass_tolerance_units);
MassType precursor_mass_type = MassType.Monoisotopic;
if(arguments["precmt"] != null)
{
precursor_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["precmt"], true);
}
bool prec_mono_correction = false;
if(arguments["pmc"] != null)
{
prec_mono_correction = bool.Parse(arguments["pmc"]);
}
int min_prec_mono_offset = -3;
if(arguments["minpmo"] != null)
{
min_prec_mono_offset = int.Parse(arguments["minpmo"]);
}
int max_prec_mono_offset = 1;
if(arguments["maxpmo"] != null)
{
max_prec_mono_offset = int.Parse(arguments["maxpmo"]);
}
double product_mass_tolerance_value = 0.025;
if(arguments["prodmtv"] != null)
{
product_mass_tolerance_value = double.Parse(arguments["prodmtv"], CultureInfo.InvariantCulture);
}
MassToleranceUnits product_mass_tolerance_units = MassToleranceUnits.Da;
if(arguments["prodmtu"] != null)
{
product_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["prodmtu"], true);
}
MassTolerance product_mass_tolerance = new MassTolerance(product_mass_tolerance_value, product_mass_tolerance_units);
MassType product_mass_type = MassType.Monoisotopic;
if(arguments["prodmt"] != null)
{
product_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["prodmt"], true);
}
double max_fdr = 0.01;
if(arguments["fdr"] != null)
{
max_fdr = double.Parse(arguments["fdr"], CultureInfo.InvariantCulture) / 100.0;
}
bool consider_mods_unique = false;
if(arguments["cmu"] != null)
{
consider_mods_unique = bool.Parse(arguments["cmu"]);
}
int max_threads = Environment.ProcessorCount;
if(arguments["mt"] != null)
{
max_threads = int.Parse(arguments["mt"]);
}
bool minimize_memory_usage = false;
if(arguments["mmu"] != null)
{
minimize_memory_usage = bool.Parse(arguments["mmu"]);
}
string output_folder = Environment.CurrentDirectory;
if(arguments["o"] != null)
{
output_folder = arguments["o"];
}
DatabaseSearcher database_searcher = new DatabaseSearcher(data,
min_assumed_precursor_charge_state, max_assumed_precursor_charge_state,
abs_threshold, rel_threshold_percent, max_peaks,
assign_charge_states, deisotope,
database, append_decoys,
protease, max_missed_cleavages, initiator_methionine_behavior,
fixed_mods, variable_mods, max_variable_mod_isoforms_per_peptide,
precursor_mass_tolerance, precursor_mass_type,
prec_mono_correction, min_prec_mono_offset, max_prec_mono_offset,
product_mass_tolerance, product_mass_type,
max_fdr, consider_mods_unique,
max_threads, minimize_memory_usage,
output_folder);
database_searcher.Starting += HandleStarting;
database_searcher.StartingFile += HandleStartingFile;
database_searcher.UpdateStatus += HandleUpdateStatus;
database_searcher.UpdateProgress += HandleUpdateProgress;
database_searcher.ThrowException += HandleThrowException;
database_searcher.FinishedFile += HandleFinishedFile;
database_searcher.Finished += HandleFinished;
database_searcher.Search();
}
else
{
Console.WriteLine("USAGE");
}
}
private void btnSearch_Click(object sender, EventArgs e)
{
if(lstData.Items.Count == 0)
{
MessageBox.Show("No data files selected");
btnAdd.Focus();
return;
}
List<string> data_filepaths = new List<string>(lstData.Items.Count);
foreach(string data_filepath in lstData.Items)
{
data_filepaths.Add(data_filepath);
}
bool assign_charge_states = chkAssignChargeStates.Checked;
bool deisotope = chkDeisotope.Checked;
string fasta_filepath = txtFastaFile.Text;
if(!File.Exists(fasta_filepath))
{
if(fasta_filepath.Length > 0)
{
MessageBox.Show("Invalid protein database file: " + fasta_filepath);
}
else
{
MessageBox.Show("Invalid protein database file");
}
txtFastaFile.Focus();
return;
}
bool on_the_fly_decoys = chkOnTheFlyDecoys.Checked;
Protease protease = (Protease)cboProtease.SelectedItem;
int max_missed_cleavages = (int)numMaxMissedCleavages.Value;
InitiatorMethionineBehavior initiator_methionine_behavior = (InitiatorMethionineBehavior)Enum.Parse(typeof(InitiatorMethionineBehavior), cboInitiatorMethionineBehavior.Text, true);
List<Modification> fixed_modifications = new List<Modification>(clbFixedModifications.CheckedItems.Count);
foreach(object fixed_modification in clbFixedModifications.CheckedItems)
{
fixed_modifications.Add((Modification)fixed_modification);
}
List<Modification> variable_modifications = new List<Modification>(clbVariableModifications.CheckedItems.Count);
foreach(object variable_modification in clbVariableModifications.CheckedItems)
{
variable_modifications.Add((Modification)variable_modification);
}
int max_variable_mod_isoforms = (int)numMaxVariableModIsoforms.Value;
int min_assumed_precursor_charge_state = (int)numMinimumAssumedPrecursorChargeState.Value;
int max_assumed_precursor_charge_state = (int)numMaximumAssumedPrecursorChargeState.Value;
double absolute_threshold = -1.0;
if(chkAbsoluteThreshold.Checked)
{
if(!double.TryParse(txtAbsoluteThreshold.Text, NumberStyles.Float | NumberStyles.AllowThousands, CultureInfo.InvariantCulture, out absolute_threshold))
{
MessageBox.Show("Cannot parse absolute MS/MS peak threshold: " + txtAbsoluteThreshold.Text);
txtAbsoluteThreshold.Focus();
return;
}
}
double relative_threshold_percent = -1.0;
if(chkRelativeThreshold.Checked)
{
if(!double.TryParse(txtRelativeThresholdPercent.Text, NumberStyles.Float | NumberStyles.AllowThousands, CultureInfo.InvariantCulture, out relative_threshold_percent))
{
MessageBox.Show("Cannot parse relative MS/MS peak threshold: " + txtRelativeThresholdPercent.Text);
txtRelativeThresholdPercent.Focus();
return;
}
}
int max_peaks = -1;
if(chkMaxNumPeaks.Checked)
{
max_peaks = (int)numMaxPeaks.Value;
}
MassTolerance precursor_mass_tolerance = new MassTolerance((double)numPrecursorMassTolerance.Value, (MassToleranceUnits)cboPrecursorMassToleranceUnits.SelectedIndex);
MassType precursor_mass_type = (MassType)cboPrecursorMassType.SelectedIndex;
List<double> accepted_precursor_mass_errors = new List<double>();
if(txtAcceptedPrecursorMassErrors.Text.Length > 0)
{
foreach(string accepted_precursor_mass_error_text in txtAcceptedPrecursorMassErrors.Text.Split(';'))
{
double accepted_precursor_mass_error;
if(!double.TryParse(accepted_precursor_mass_error_text, NumberStyles.Float | NumberStyles.AllowThousands, CultureInfo.InvariantCulture, out accepted_precursor_mass_error))
{
MessageBox.Show("Cannot parse accepted precursor mass errors: " + txtRelativeThresholdPercent.Text);
txtAcceptedPrecursorMassErrors.Focus();
return;
}
accepted_precursor_mass_errors.Add(accepted_precursor_mass_error);
}
}
else
{
accepted_precursor_mass_errors.Add(0.0);
}
MassTolerance product_mass_tolerance = new MassTolerance((double)numProductMassTolerance.Value, (MassToleranceUnits)cboProductMassToleranceUnits.SelectedIndex);
MassType product_mass_type = (MassType)cboProductMassType.SelectedIndex;
double max_false_discovery_rate = (double)numMaximumFalseDiscoveryRatePercent.Value / 100.0;
bool consider_modified_unique = chkConsiderModifiedUnique.Checked;
int max_threads = (int)numMaxThreads.Value;
bool minimize_memory_usage = chkMinimizeMemoryUsage.Checked;
string output_folder = txtOutputFolder.Text;
if(!Directory.Exists(output_folder))
{
try
{
Directory.CreateDirectory(output_folder);
}
catch
{
if(output_folder.Length > 0)
{
MessageBox.Show("Invalid output folder: " + output_folder);
}
else
{
MessageBox.Show("Invalid output folder");
}
txtOutputFolder.Focus();
return;
}
}
DatabaseSearcher database_searcher = new DatabaseSearcher(data_filepaths,
min_assumed_precursor_charge_state, max_assumed_precursor_charge_state,
absolute_threshold, relative_threshold_percent, max_peaks,
assign_charge_states, deisotope,
fasta_filepath, on_the_fly_decoys,
protease, max_missed_cleavages, initiator_methionine_behavior,
fixed_modifications, variable_modifications, max_variable_mod_isoforms,
precursor_mass_tolerance, precursor_mass_type,
accepted_precursor_mass_errors,
product_mass_tolerance, product_mass_type,
max_false_discovery_rate, consider_modified_unique,
max_threads, minimize_memory_usage,
output_folder);
database_searcher.Starting += HandleStarting;
database_searcher.StartingFile += HandleStartingFile;
database_searcher.UpdateStatus += HandleUpdateStatus;
database_searcher.ReportTaskWithoutProgress += HandleReportTaskWithoutProgress;
database_searcher.ReportTaskWithProgress += HandleReportTaskWithProgress;
database_searcher.UpdateProgress += HandleUpdateProgress;
database_searcher.ThrowException += HandleThrowException;
database_searcher.FinishedFile += HandleFinishedFile;
database_searcher.Finished += HandleFinished;
lstData.SelectedItem = null;
tspbProgress.Value = tspbProgress.Minimum;
Thread thread = new Thread(new ThreadStart(database_searcher.Search));
thread.IsBackground = true;
thread.Start();
}
static void Main(string[] args)
{
if(args.Length > 0)
{
Arguments arguments = new Arguments(args);
List<string> data = new List<string>(arguments["d"].Split(','));
int min_assumed_precursor_charge_state = 2;
if(arguments["minprecz"] != null)
{
min_assumed_precursor_charge_state = int.Parse(arguments["minprecz"]);
}
int max_assumed_precursor_charge_state = 4;
if(arguments["maxprecz"] != null)
{
max_assumed_precursor_charge_state = int.Parse(arguments["maxprecz"]);
}
double abs_threshold = -1.0;
if(arguments["at"] != null)
{
abs_threshold = double.Parse(arguments["at"], CultureInfo.InvariantCulture);
}
double rel_threshold_percent = -1.0;
if(arguments["rt"] != null)
{
rel_threshold_percent = double.Parse(arguments["rt"], CultureInfo.InvariantCulture);
}
int max_peaks = 400;
if(arguments["mp"] != null)
{
max_peaks = int.Parse(arguments["mp"]);
}
bool assign_charge_states = true;
if(arguments["acs"] != null)
{
assign_charge_states = bool.Parse(arguments["acs"]);
}
bool deisotope = true;
if(arguments["di"] != null)
{
deisotope = bool.Parse(arguments["di"]);
}
string database = arguments["db"];
Dictionary<string, Modification> known_variable_modifications = null;
HashSet<Modification> variable_mods = new HashSet<Modification>();
if(Path.GetExtension(database).Equals(".xml", StringComparison.InvariantCultureIgnoreCase))
{
bool no_uniprot_mods = false;
if(arguments["noup"] != null)
{
no_uniprot_mods = bool.Parse(arguments["noup"]);
}
if (!no_uniprot_mods)
{
known_variable_modifications = ProteomeDatabaseReader.ReadUniProtXmlModifications(database);
variable_mods.UnionWith(known_variable_modifications.Values);
}
}
bool append_decoys = false;
if(arguments["ad"] != null)
{
append_decoys = bool.Parse(arguments["ad"]);
}
else
{
append_decoys = Path.GetExtension(database).Equals(".xml", StringComparison.InvariantCultureIgnoreCase) || !ProteomeDatabaseReader.HasDecoyProteins(database);
}
ProteaseDictionary proteases = ProteaseDictionary.Instance;
Protease protease = proteases["trypsin (no proline rule)"];
if(arguments["p"] != null)
{
protease = proteases[arguments["p"]];
}
int max_missed_cleavages = 2;
if(arguments["mmc"] != null)
{
max_missed_cleavages = int.Parse(arguments["mmc"]);
}
InitiatorMethionineBehavior initiator_methionine_behavior = InitiatorMethionineBehavior.Variable;
if(arguments["imb"] != null)
{
initiator_methionine_behavior = (InitiatorMethionineBehavior)Enum.Parse(typeof(InitiatorMethionineBehavior), arguments["imb"], true);
}
ModificationDictionary mods = ModificationDictionary.Instance;
List<Modification> fixed_mods = new List<Modification>();
if(arguments["fm"] != null)
{
foreach(string fixed_mod in arguments["fm"].Split(';'))
{
fixed_mods.Add(mods[fixed_mod]);
}
}
if(arguments["vm"] != null)
{
foreach(string variable_mod in arguments["vm"].Split(';'))
{
Modification mod;
if(!mods.TryGetValue(variable_mod, out mod))
{
known_variable_modifications.TryGetValue(variable_mod, out mod);
}
variable_mods.Add(mod);
}
}
int max_variable_mod_isoforms_per_peptide = 1024;
if(arguments["mvmi"] != null)
{
max_variable_mod_isoforms_per_peptide = int.Parse(arguments["mvmi"]);
}
double precursor_mass_tolerance_value = 2.1;
if(arguments["precmtv"] != null)
{
precursor_mass_tolerance_value = double.Parse(arguments["precmtv"], CultureInfo.InvariantCulture);
}
MassToleranceUnits precursor_mass_tolerance_units = MassToleranceUnits.Da;
if(arguments["precmtu"] != null)
{
precursor_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["precmtu"], true);
}
MassTolerance precursor_mass_tolerance = new MassTolerance(precursor_mass_tolerance_value, precursor_mass_tolerance_units);
MassType precursor_mass_type = MassType.Monoisotopic;
if(arguments["precmt"] != null)
{
precursor_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["precmt"], true);
}
List<double> accepted_precursor_mass_errors = new List<double>();
if(arguments["apme"] != null && arguments["apme"].Length > 0)
{
foreach(string accepted_precursor_mass_error in arguments["apme"].Split(';'))
{
accepted_precursor_mass_errors.Add(double.Parse(accepted_precursor_mass_error, CultureInfo.InvariantCulture));
}
}
else
{
accepted_precursor_mass_errors.Add(0.0);
}
double product_mass_tolerance_value = 0.015;
if(arguments["prodmtv"] != null)
{
product_mass_tolerance_value = double.Parse(arguments["prodmtv"], CultureInfo.InvariantCulture);
}
MassToleranceUnits product_mass_tolerance_units = MassToleranceUnits.Da;
if(arguments["prodmtu"] != null)
{
product_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["prodmtu"], true);
}
MassTolerance product_mass_tolerance = new MassTolerance(product_mass_tolerance_value, product_mass_tolerance_units);
MassType product_mass_type = MassType.Monoisotopic;
if(arguments["prodmt"] != null)
{
product_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["prodmt"], true);
}
double max_fdr = 0.01;
if(arguments["fdr"] != null)
{
max_fdr = double.Parse(arguments["fdr"], CultureInfo.InvariantCulture) / 100.0;
}
bool consider_mods_unique = false;
if(arguments["cmu"] != null)
{
consider_mods_unique = bool.Parse(arguments["cmu"]);
}
int max_threads = Environment.ProcessorCount;
if(arguments["mt"] != null)
{
max_threads = int.Parse(arguments["mt"]);
}
bool minimize_memory_usage = false;
if(arguments["mmu"] != null)
{
minimize_memory_usage = bool.Parse(arguments["mmu"]);
}
string output_folder = Environment.CurrentDirectory;
if(arguments["o"] != null)
{
output_folder = arguments["o"];
}
DatabaseSearcher database_searcher = new DatabaseSearcher(data,
min_assumed_precursor_charge_state, max_assumed_precursor_charge_state,
abs_threshold, rel_threshold_percent, max_peaks,
assign_charge_states, deisotope,
database, append_decoys,
protease, max_missed_cleavages, initiator_methionine_behavior,
fixed_mods, variable_mods, max_variable_mod_isoforms_per_peptide,
precursor_mass_tolerance, precursor_mass_type,
accepted_precursor_mass_errors,
product_mass_tolerance, product_mass_type,
max_fdr, consider_mods_unique,
max_threads, minimize_memory_usage,
output_folder);
database_searcher.Starting += HandleStarting;
database_searcher.StartingFile += HandleStartingFile;
database_searcher.UpdateStatus += HandleUpdateStatus;
database_searcher.UpdateProgress += HandleUpdateProgress;
database_searcher.ThrowException += HandleThrowException;
database_searcher.FinishedFile += HandleFinishedFile;
database_searcher.Finished += HandleFinished;
database_searcher.Search();
}
else
{
Console.WriteLine(Program.GetProductNameAndVersion() + " USAGE");
}
}
