private ConfigFile GetConfigFile(string destinationProgram)
{
if (destinationProgram == "MyriMatch" ||
destinationProgram == "DirecTag" ||
destinationProgram == "TagRecon" ||
destinationProgram == "Pepitome")
{
var config = new ConfigFile()
{
DestinationProgram = destinationProgram,
PropertyList = new List<ConfigProperty>(),
FilePath = "--Custom--"
};
var tolerance = double.Parse(PrecursorToleranceBox.Text);
if (destinationProgram == "DirecTag")
{
if (PrecursorToleranceUnitsBox.Text == "ppm")
tolerance /= 1000;
config.PropertyList.Add(new ConfigProperty
{
Name = "PrecursorMzTolerance",
Value = tolerance.ToString(CultureInfo.InvariantCulture),
Type = "string",
ConfigAssociation = config
});
}
else if (destinationProgram == "TagRecon")
config.PropertyList.Add(new ConfigProperty
{
Name = "PrecursorMzTolerance",
Value = "\"" + tolerance.ToString(CultureInfo.InvariantCulture) + PrecursorToleranceUnitsBox.Text + "\"",
Type = "string",
ConfigAssociation = config
});
else
config.PropertyList.Add(new ConfigProperty
{
Name = "MonoPrecursorMzTolerance",
Value = "\"" + tolerance.ToString(CultureInfo.InvariantCulture) + PrecursorToleranceUnitsBox.Text + "\"",
Type = "string",
ConfigAssociation = config
});
if (!destinationProgram.Contains("Tag") && PrecursorToleranceUnitsBox.Text == "mz" && double.Parse(PrecursorToleranceBox.Text) > 0.2)
config.PropertyList.Add(new ConfigProperty
{
Name = "MonoisotopeAdjustmentSet",
Value = "\"0\"",
Type = "string",
ConfigAssociation = config
});
tolerance = double.Parse(FragmentToleranceBox.Text);
if (destinationProgram == "DirecTag")
{
if (FragmentToleranceUnitsBox.Text == "ppm")
tolerance /= 1000;
config.PropertyList.Add(new ConfigProperty
{
Name = "FragmentMzTolerance",
Value = tolerance.ToString(CultureInfo.InvariantCulture),
Type = "string",
ConfigAssociation = config
});
config.PropertyList.Add(new ConfigProperty
{
Name = "ComplementMzTolerance",
Value = tolerance.ToString(CultureInfo.InvariantCulture),
Type = "string",
ConfigAssociation = config
});
config.PropertyList.Add(new ConfigProperty
{
Name = "IsotopeMzTolerance",
Value = tolerance.ToString(CultureInfo.InvariantCulture),
Type = "string",
ConfigAssociation = config
});
}
else
config.PropertyList.Add(new ConfigProperty
{
Name = "FragmentMzTolerance",
Value = "\"" + tolerance.ToString(CultureInfo.InvariantCulture) + FragmentToleranceUnitsBox.Text + "\"",
Type = "string",
ConfigAssociation = config
});
if (destinationProgram != "DirecTag")
{
if (SuffixBox.Checked)
config.PropertyList.Add(new ConfigProperty
{
Name = "OutputSuffix",
Value = "\"" + PrimarySuffixBox.Text + "\"",
Type = "string",
ConfigAssociation = config
});
config.PropertyList.Add(new ConfigProperty
{
Name = "CleavageRules",
Value = "\"" + CleavageAgentBox.Text + "\"",
Type = "string",
ConfigAssociation = config
});
config.PropertyList.Add(new ConfigProperty
{
Name = "MinTerminiCleavages",
Value = SpecificityBox.SelectedIndex.ToString(CultureInfo.InvariantCulture),
Type = "int",
ConfigAssociation = config
});
config.PropertyList.Add(new ConfigProperty
{
Name = "DecoyPrefix",
Value = "XXX_",
Type = "string",
ConfigAssociation = config
});
}
if (destinationProgram == "TagRecon" && BlindModBox.Checked)
config.PropertyList.Add(new ConfigProperty
{
Name = "ExplainUnknownMassShiftsAs",
Value = "\"blindptms\"",
Type = "string",
ConfigAssociation = config
});
var staticMods = new List<string>();
var dynamicMods = new List<string>();
for (var x = 0; x < ModBox.Rows.Count; x++)
{
var residue = ModBox.Rows[x].Cells[0].Value.ToString();
var massString = ModBox.Rows[x].Cells[1].Value.ToString();
var type = ModBox.Rows[x].Cells[2].Value.ToString();
double mass;
if (string.IsNullOrEmpty(residue) || string.IsNullOrEmpty(massString) ||
!double.TryParse(massString, out mass) || string.IsNullOrEmpty(type))
continue;
if (type == "Static")
{
staticMods.Add(residue);
staticMods.Add(mass.ToString(CultureInfo.InvariantCulture));
}
else
{
dynamicMods.Add(residue);
dynamicMods.Add("*");
dynamicMods.Add(mass.ToString(CultureInfo.InvariantCulture));
}
}
if (staticMods.Count > 0)
config.PropertyList.Add(new ConfigProperty
{
Name = "StaticMods",
Value = "\"" + string.Join(" ", staticMods) + "\"",
Type = "string",
ConfigAssociation = config
});
if (dynamicMods.Count > 0)
config.PropertyList.Add(new ConfigProperty
{
Name = "DynamicMods",
Value = "\"" + string.Join(" ", dynamicMods) + "\"",
Type = "string",
ConfigAssociation = config
});
return config;
}
if (destinationProgram == "Comet")
{
CometParams cometParams;
if (FragmentLowRadio.Checked)
cometParams = CometParams.GetIonTrapParams();
else if (FragmentMidRadio.Checked)
cometParams = CometParams.GetTofParams();
else
cometParams = CometParams.GetHighResParams();
cometParams.PrecursorTolerance = double.Parse(PrecursorToleranceBox.Text);
cometParams.PrecursorUnit = PrecursorToleranceUnitsBox.Text == "mz"
? CometParams.PrecursorUnitOptions.Daltons
: CometParams.PrecursorUnitOptions.PPM;
cometParams.OutputSuffix = CometSuffixBox.Text;
if (CometParams.CleavageAgentOptions.ContainsKey(CleavageAgentBox.Text))
cometParams.CleavageAgent = CometParams.CleavageAgentOptions[CleavageAgentBox.Text];
else
MessageBox.Show("[Comet] Cannot use " + CleavageAgentBox.Text +
" as a digestive enzyme for comet searches. Results may be unpredictable.");
cometParams.Specificity = SpecificityBox.Text == "Fully-Specific"
? CometParams.SpecificityOptions.Tryptic
: CometParams.SpecificityOptions.SemiTryptic;
for (var x = 0; x < ModBox.Rows.Count; x++)
{
var residue = ModBox.Rows[x].Cells[0].Value.ToString();
var massString = ModBox.Rows[x].Cells[1].Value.ToString();
var type = ModBox.Rows[x].Cells[2].Value.ToString();
double mass;
if (string.IsNullOrEmpty(residue) || string.IsNullOrEmpty(massString) ||
!double.TryParse(massString, out mass) || string.IsNullOrEmpty(type))
continue;
if (type == "Static" && residue == "C")
{
cometParams.StaticCysteineMod = mass;
continue;
}
//for now can only do static on cystine
if (type == "Static")
MessageBox.Show("[Comet] Warning, BumberDash can only apply static modifications "+
"to cystine at this time. Applying \'" +residue + ";" + mass + "\' as dynamic");
cometParams.DynamicModifications.Add(new CometParams.Modification(residue, mass));
}
var config = new ConfigFile
{
DestinationProgram = "Comet",
FilePath = "--Custom--"
};
config.PropertyList = new List<ConfigProperty>
{
new ConfigProperty
{
Name = "config",
Value = CometHandler.CometParamsToFileContents(cometParams),
Type = "string",
ConfigAssociation = config
}
};
return config;
}
if (destinationProgram == "MSGF")
{
var msgfParams = new MSGFParams();
msgfParams.PrecursorTolerance = double.Parse(PrecursorToleranceBox.Text);
msgfParams.PrecursorToleranceUnits = PrecursorToleranceUnitsBox.Text == "mz"
? MSGFParams.PrecursorToleranceUnitOptions.Daltons
: MSGFParams.PrecursorToleranceUnitOptions.PPM;
//msgfParams.FragmentationMethod = FragmentLowRadio.Checked
// ? MSGFParams.FragmentationMethodOptions.CID
// : MSGFParams.FragmentationMethodOptions.HCD;
if (PrecursorLowRadio.Checked || FragmentLowRadio.Checked)
msgfParams.Instrument = MSGFParams.InstrumentOptions.LowResLTQ;
else if (PrecursorMidRadio.Checked || FragmentMidRadio.Checked)
msgfParams.Instrument = MSGFParams.InstrumentOptions.TOF;
else
msgfParams.Instrument = MSGFParams.InstrumentOptions.HighResLTQ;
msgfParams.OutputSuffix = MSGFSuffixBox.Text;
if (MSGFParams.CleavageAgentOptions.ContainsKey(CleavageAgentBox.Text))
msgfParams.CleavageAgent = MSGFParams.CleavageAgentOptions[CleavageAgentBox.Text];
else if (CleavageAgentBox.Text != "Trypsin/P")
MessageBox.Show("[MSGF] Cannot use " + CleavageAgentBox.Text +
" as a digestive enzyme for MS-GF+ searches. Results may be unpredictable.");
msgfParams.Specificity = SpecificityBox.Text == "Fully-Specific"
? MSGFParams.SpecificityOptions.Tryptic
: MSGFParams.SpecificityOptions.SemiTryptic;
var msgfMods = new List<Util.Modification>();
for (var x = 0; x < ModBox.Rows.Count; x++)
{
var residue = ModBox.Rows[x].Cells[0].Value.ToString();
var massString = ModBox.Rows[x].Cells[1].Value.ToString();
var type = ModBox.Rows[x].Cells[2].Value.ToString();
double mass;
if (string.IsNullOrEmpty(residue) || string.IsNullOrEmpty(massString) ||
!double.TryParse(massString, out mass) || string.IsNullOrEmpty(type))
continue;
msgfMods.Add(new Util.Modification {Residue = residue, Mass = mass, Type = type});
}
var config = new ConfigFile
{
DestinationProgram = "MSGF",
FilePath = "--Custom--"
};
config.PropertyList = new List<ConfigProperty>
{
new ConfigProperty
{
Name = "config",
Value = MSGFHandler.MSGFParamsToOverload(msgfParams),
Type = "string",
ConfigAssociation = config
},
new ConfigProperty
{
Name = "mods",
Value = MSGFHandler.ModListToModString(msgfMods, 2),
Type = "string",
ConfigAssociation = config
}
};
return config;
}
throw new Exception("Invalid destination program, can't construct configuration");
}
public ConfigFile GetMSGFConfig()
{
if (!ProgramSelectMSGF.Checked)
return null;
var newConfig = new ConfigFile
{
DestinationProgram = "MSGF",
Name = "--Custom--",
FilePath = "--Custom--",
PropertyList = new List<ConfigProperty>()
};
var msgfConfig = new MSGFParams();
if (MSGFParams.CleavageAgentOptions.ContainsKey(MyriCleavageRulesBox.Text))
msgfConfig.CleavageAgent = MSGFParams.CleavageAgentOptions[MyriCleavageRulesBox.Text];
//msgfConfig.FragmentationMethod = MSGFFragmentMethodBox.SelectedIndex;
msgfConfig.Instrument = MSGFInstrumentBox.SelectedIndex;
msgfConfig.OutputSuffix = MSGFOutputSuffixBox.Text;
msgfConfig.PrecursorTolerance = Double.Parse(MyriMonoPrecursorMzToleranceBox.Text);
msgfConfig.PrecursorToleranceUnits = MyriMonoPrecursorMzToleranceUnitsList.SelectedIndex == 0
? MSGFParams.PrecursorToleranceUnitOptions.Daltons
: MSGFParams.PrecursorToleranceUnitOptions.PPM;
msgfConfig.Protocol = MSGFPhosphoBox.Checked
? MSGFiTRAQBox.Checked
? MSGFParams.ProtocolOptions.iTRAQPhospho
: MSGFParams.ProtocolOptions.Phosphorylation
: MSGFiTRAQBox.Checked
? MSGFParams.ProtocolOptions.iTRAQ
: MSGFParams.ProtocolOptions.NoProtocol;
msgfConfig.Specificity = MyriMinTerminiCleavagesBox.SelectedIndex;
var modList = new List<Util.Modification>();
foreach (DataGridViewRow row in MyriAppliedModBox.Rows)
{
modList.Add(new Util.Modification
{
Mass = double.Parse(row.Cells[MyriMassColumn.Index].Value.ToString()),
Residue = row.Cells[MyriMotifColumn.Index].Value.ToString(),
Type = row.Cells[MyriTypeColumn.Index].Value.ToString()
});
}
newConfig.PropertyList.Add(new ConfigProperty
{
Name = "config",
Type = "string",
ConfigAssociation = newConfig,
Value = MSGFHandler.MSGFParamsToOverload(msgfConfig)
});
newConfig.PropertyList.Add(new ConfigProperty
{
Name = "mods",
Type = "string",
ConfigAssociation = newConfig,
Value = MSGFHandler.ModListToModString(modList, (int) MyriMaxDynamicModsBox.Value)
});
return newConfig;
}
