private void CometConfigBrowse_Click(object sender, EventArgs e)
{
var fileLoc = new OpenFileDialog
{
InitialDirectory = OutputDirectoryBox.Text,
RestoreDirectory = true,
Filter = "Config Files|*.params|All files|*.*",
CheckFileExists = true,
CheckPathExists = true,
Multiselect = false,
Title = "Comet config file location"
};
if (fileLoc.ShowDialog() == DialogResult.OK)
{
var newConfig = new ConfigFile
{
Name = Path.GetFileName(fileLoc.FileName),
FilePath = fileLoc.FileName,
DestinationProgram = "Comet"
};
CometConfigBox.Tag = newConfig;
CometConfigBox.Text = newConfig.Name;
}
}
public static ConfigFile PepXMLToCustomConfig(string file, string destinationProgram)
{
var newConfig = new ConfigFile
{
DestinationProgram = destinationProgram,
Name = Path.GetFileName(file),
PropertyList = new List<ConfigProperty>()
};
var parameterTypes = Util.parameterTypes;
var cutFile = string.Empty;
var fileStream = new StreamReader(file);
while (!fileStream.EndOfStream)
{
var tempString = fileStream.ReadLine() ?? string.Empty;
if (tempString.Contains("<parameter name=\"Config:"))
cutFile += tempString + System.Environment.NewLine;
else if (cutFile.Length > 0)
break;
}
fileStream.Close();
var entireLine = cutFile.Split(Environment.NewLine.ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
string[] propertySplit;
for (int x = 0; x < entireLine.Length; x++)
{
//get the two meaningful values
entireLine[x] = entireLine[x].Replace("<parameter name=\"Config:", " ");
entireLine[x] = entireLine[x].Replace("\" value=", " ");
entireLine[x] = entireLine[x].Replace("/>", " ");
propertySplit = entireLine[x].Split(" ".ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
propertySplit[0] = propertySplit[0].Trim();
propertySplit[1] = propertySplit[1].Trim();
//check if value is actually meaningful to the editor
if (parameterTypes.ContainsKey(propertySplit[0]))
{
if (parameterTypes[propertySplit[0]] == "bool")
{
propertySplit[1] = propertySplit[1].Trim('\"');
propertySplit[1] = Convert.ToBoolean(int.Parse(propertySplit[1])).ToString().ToLower();
newConfig.PropertyList.Add(new ConfigProperty
{
Name = propertySplit[0],
Value = propertySplit[1],
Type = parameterTypes[propertySplit[0]]
});
}
else if (parameterTypes[propertySplit[0]] == "int"
|| parameterTypes[propertySplit[0]] == "double")
{
propertySplit[1] = propertySplit[1].Trim('\"');
newConfig.PropertyList.Add(new ConfigProperty
{
Name = propertySplit[0],
Value = propertySplit[1],
Type = parameterTypes[propertySplit[0]]
});
}
else if (parameterTypes[propertySplit[0]] == "string")
{
if (propertySplit.Length > 2)
{
for (int i = 2; i < propertySplit.Length; i++)
propertySplit[1] += " " + propertySplit[i];
}
newConfig.PropertyList.Add(new ConfigProperty
{
Name = propertySplit[0],
Value = propertySplit[1],
Type = parameterTypes[propertySplit[0]]
});
}
}
}
return newConfig;
}
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 static ConfigFile TagsFileToEntireFileString(string file)
{
var newConfig = new ConfigFile
{
DestinationProgram = "DirecTag",
Name = Path.GetFileName(file),
PropertyList = new List<ConfigProperty>()
};
var parameterTypes = Util.parameterTypes;
var cutFile = string.Empty;
var fileStream = new StreamReader(file);
while (!fileStream.EndOfStream)
{
var tempString = fileStream.ReadLine() ?? string.Empty;
if (tempString.Contains("TagsParameters"))
{
tempString = fileStream.ReadLine();
while (!string.IsNullOrEmpty(tempString))
{
tempString = tempString.Remove(0, 2);
cutFile += tempString + ",";
tempString = fileStream.ReadLine();
}
cutFile = cutFile.Trim();
break;
}
}
fileStream.Close();
var entireLine = cutFile.Split(",".ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
string[] propertySplit;
foreach (var parameter in entireLine)
{
//get the two meaningful values
propertySplit = parameter.Split(":".ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
propertySplit[0] = propertySplit[0].Trim();
propertySplit[1] = propertySplit[1].Trim();
//check if value is actually meaningful to the editor
if (parameterTypes.ContainsKey(propertySplit[0]))
{
if (parameterTypes[propertySplit[0]] == "bool")
{
propertySplit[1] = propertySplit[1].Trim('\"');
propertySplit[1] = Convert.ToBoolean(int.Parse(propertySplit[1])).ToString().ToLower();
newConfig.PropertyList.Add(new ConfigProperty
{
Name = propertySplit[0],
Value = propertySplit[1],
Type = parameterTypes[propertySplit[0]]
});
}
else if (parameterTypes[propertySplit[0]] == "int"
|| parameterTypes[propertySplit[0]] == "double")
{
propertySplit[1] = propertySplit[1].Trim('\"');
newConfig.PropertyList.Add(new ConfigProperty
{
Name = propertySplit[0],
Value = propertySplit[1],
Type = parameterTypes[propertySplit[0]]
});
}
else if (parameterTypes[propertySplit[0]] == "string")
{
if (propertySplit.Length > 2)
{
for (int foo = 2; foo < propertySplit.Length; foo++)
propertySplit[1] += " " + propertySplit[foo];
}
newConfig.PropertyList.Add(new ConfigProperty
{
Name = propertySplit[0],
Value = propertySplit[1],
Type = parameterTypes[propertySplit[0]]
});
}
}
}
return newConfig;
}
/// <summary>
/// Sets values of items to values in config
/// </summary>
/// <param name="baseConfig"></param>
private void LoadConfig(ConfigFile baseConfig)
{
var configValues = baseConfig.PropertyList
.ToDictionary(property => property.Name,
property => property.Value.Trim('"'));
foreach (var kvp in _defaults)
{
var root = RootName(kvp.Key.Name);
var value = configValues.ContainsKey(root)
? configValues[root]
: kvp.Value;
if (root == "MaxMissedCleavages" && decimal.Parse(value) > 90000)
value = "-1";
if (root == "TicCutoffPercentage" || root == "LibTicCutoffPercentage")
value = Math.Round(decimal.Parse(value), 2).ToString();
if (root == "PrecursorAdjustmentStep")
value = Math.Round(decimal.Parse(value), 6).ToString();
var isDual = GetDualDependenceValue(kvp.Key);
if (isDual != null)
SetDualDependenceValue(kvp.Key, value);
else if (root == "AppliedMod")
{
var modString = string.Empty;
if (configValues.ContainsKey("StaticMods"))
{
modString += "StaticMods = \"" + configValues["StaticMods"] + "\"" + Environment.NewLine;
}
if (configValues.ContainsKey("DynamicMods"))
{
modString += "DynamicMods = \"" + configValues["DynamicMods"] + "\"" + Environment.NewLine;
}
if (configValues.ContainsKey("PreferredDeltaMasses"))
{
modString += "PreferredDeltaMasses = \"" + configValues["PreferredDeltaMasses"] + "\"";
}
if (!string.IsNullOrEmpty(modString))
{
SetModString(modString.Trim());
}
}
else if (root == "UseAvgMassOfSequences")
((ComboBox)kvp.Key).SelectedIndex = (value == "true") ? 1 : 0;
else if (root == "MinTerminiCleavages" || root == "DeisotopingMode")
((ComboBox)kvp.Key).SelectedIndex = int.Parse(value);
else if (kvp.Key is ComboBox || kvp.Key is TextBox)
kvp.Key.Text = value;
else if (kvp.Key is NumericUpDown)
((NumericUpDown)kvp.Key).Value = decimal.Parse(value);
else if (kvp.Key is CheckBox)
((CheckBox)kvp.Key).Checked = bool.Parse(value);
}
}
public static ISessionFactory CreateSessionFactory()
{
var currentGuiVersion = Assembly.GetExecutingAssembly().GetName().Version.ToString(3);
var newdatabase = false;
var root = Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.ApplicationData), "Bumberdash");
if (!Directory.Exists(root))
{
Directory.CreateDirectory(root);
}
var dataFile = Path.Combine(root, "Bumbershoot " + currentGuiVersion + ".db");
var newfactory = CreateSessionFactory(dataFile, true);
var session = newfactory.OpenSession();
//check that all preloaded templates are present
if (session.QueryOver <ConfigFile>().List().Count < 16)
{
//check for presence of completely empty database
if (session.QueryOver <HistoryItem>().List().Count == 0 &&
session.QueryOver <ConfigFile>().List().Count == 0)
{
newdatabase = true;
}
//load base database
var baseRoot = Path.GetDirectoryName(Process.GetCurrentProcess().MainModule.FileName);
if (baseRoot == null)
{
throw new Exception("Cannot find base database file");
}
if (!File.Exists(Path.Combine(baseRoot, "lib\\Bumbershoot.db")))
{
throw new Exception("Looking for \"" + Path.Combine(baseRoot, "lib\\Bumbershoot.db") + "\", however I cant find it");
}
var baseFactory = CreateSessionFactory(Path.Combine(baseRoot, "lib\\Bumbershoot.db"), false);
var baseSession = baseFactory.OpenSession();
//load base templates
var connectedBaseConfigs = baseSession.QueryOver <ConfigFile>().List();
var baseConfigs = new List <ConfigFile>();
foreach (var config in connectedBaseConfigs)
{
var newInstrument = new ConfigFile
{
Name = config.Name,
DestinationProgram = config.DestinationProgram,
FilePath = config.FilePath,
PropertyList = new List <ConfigProperty>()
};
foreach (var property in config.PropertyList)
{
var newProperty = new ConfigProperty
{
ConfigAssociation = newInstrument,
Name = property.Name,
Type = property.Type,
Value = property.Value
};
newInstrument.PropertyList.Add(newProperty);
}
baseConfigs.Add(newInstrument);
}
//delete old templates (if any remain) and load base template
foreach (var config in baseConfigs)
{
ConfigFile config1 = config;
var deleteList = session.QueryOver <ConfigFile>()
.Where(x => x.Name == config1.Name &&
x.DestinationProgram == config1.DestinationProgram)
.List();
foreach (var item in deleteList)
{
session.Delete(item);
}
session.Flush();
var newInstrument = new ConfigFile()
{
Name = config.Name,
DestinationProgram = config.DestinationProgram,
FilePath = config.FilePath
};
session.SaveOrUpdate(newInstrument);
session.Flush();
foreach (var property in config.PropertyList)
{
var newProperty = new ConfigProperty()
{
ConfigAssociation = newInstrument,
Name = property.Name,
Type = property.Type,
Value = property.Value
};
session.SaveOrUpdate(newProperty);
}
session.Flush();
}
//automatically try to recover old history items if database is flagged as new
if (newdatabase)
{
//if database structure is ever changed this will need to be updated to include conversion (probably in the form of basic sqlite queries)
var directoryInfo = new DirectoryInfo(root);
var bdFiles = directoryInfo.GetFiles("Bumbershoot*.db").Select(file => file.Name).ToList();
bdFiles.Sort();
if (bdFiles.Count > 1)
{
//reorder to proper location
if (bdFiles[bdFiles.Count - 1] == "Bumbershoot.db")
{
bdFiles.RemoveAt(bdFiles.Count - 1);
bdFiles.Insert(0, "Bumbershoot.db");
}
var restorePath = Path.Combine(root, bdFiles[bdFiles.Count - 2]);
var restoreFactory = CreateSessionFactory(restorePath, true);
var restoreSession = restoreFactory.OpenSession();
var restoreJobs = restoreSession.QueryOver <HistoryItem>().List <HistoryItem>();
var restoredConfigs = new Dictionary <int, ConfigFile>();
//start restoring jobs
foreach (var job in restoreJobs)
{
var newjob = new HistoryItem
{
Cpus = job.Cpus, CurrentStatus = job.CurrentStatus,
EndTime = job.EndTime, JobName = job.JobName,
JobType = job.JobType, OutputDirectory = job.OutputDirectory,
ProteinDatabase = job.ProteinDatabase, RowNumber = job.RowNumber,
SpectralLibrary = job.SpectralLibrary, StartTime = job.StartTime
};
if (!restoredConfigs.ContainsKey(job.InitialConfigFile.ConfigId))
{
var newConfig = new ConfigFile
{
DestinationProgram = job.InitialConfigFile.DestinationProgram,
FilePath = job.InitialConfigFile.FilePath,
FirstUsedDate = job.InitialConfigFile.FirstUsedDate,
Name = job.InitialConfigFile.Name
};
session.SaveOrUpdate(newConfig);
session.Flush();
foreach (var property in job.InitialConfigFile.PropertyList)
{
var newProperty = new ConfigProperty
{
Name = property.Name,
ConfigAssociation = newConfig,
Type = property.Type,
Value = property.Value
};
session.SaveOrUpdate(newProperty);
}
session.Flush();
newjob.InitialConfigFile = newConfig;
restoredConfigs.Add(job.InitialConfigFile.ConfigId, newConfig);
}
else
{
newjob.InitialConfigFile = restoredConfigs[job.InitialConfigFile.ConfigId];
}
if (job.TagConfigFile != null)
{
if (!restoredConfigs.ContainsKey(job.TagConfigFile.ConfigId))
{
var newConfig = new ConfigFile
{
DestinationProgram = job.TagConfigFile.DestinationProgram,
FilePath = job.TagConfigFile.FilePath,
FirstUsedDate = job.TagConfigFile.FirstUsedDate,
Name = job.TagConfigFile.Name
};
session.SaveOrUpdate(newConfig);
session.Flush();
foreach (var property in job.TagConfigFile.PropertyList)
{
var newProperty = new ConfigProperty
{
Name = property.Name,
ConfigAssociation = newConfig,
Type = property.Type,
Value = property.Value
};
session.SaveOrUpdate(newProperty);
}
session.Flush();
newjob.TagConfigFile = newConfig;
restoredConfigs.Add(job.TagConfigFile.ConfigId, newConfig);
}
else
{
newjob.TagConfigFile = restoredConfigs[job.TagConfigFile.ConfigId];
}
}
session.SaveOrUpdate(newjob);
session.Flush();
foreach (var file in job.FileList)
{
var newFile = new InputFile {
FilePath = file.FilePath, HistoryItem = newjob
};
session.SaveOrUpdate(newFile);
session.Flush();
}
}
}
}
}
session.Close();
return(newfactory);
}
private List<ConfigProperty> GetProperties(List<Control> items, ConfigFile newConfig)
{
var propertyList = new List<ConfigProperty>();
foreach (var item in items)
{
var root = RootName(item.Name);
var isDual = GetDualDependenceValue(item);
if (isDual != null)
propertyList.Add(new ConfigProperty
{
Name = root,
Type = "string",
ConfigAssociation = newConfig,
Value = isDual
});
else if (root == "AppliedMod")
{
var modProperties = GetModProperties((DataGridView)item);
foreach (var property in modProperties)
property.ConfigAssociation = newConfig;
propertyList.AddRange(modProperties);
}
else if (root == "UseAvgMassOfSequences")
propertyList.Add(new ConfigProperty
{
Name = root,
Type = "string",
ConfigAssociation = newConfig,
Value = (((ComboBox)item).SelectedIndex == 1).ToString().ToLower()
});
else if (root == "MinTerminiCleavages" || root == "DeisotopingMode")
propertyList.Add(new ConfigProperty
{
Name = root,
Type = "string",
ConfigAssociation = newConfig,
Value = ((ComboBox)item).SelectedIndex.ToString()
});
else if (root == "UnimodXML" && TRUnimodXMLBox.Text == "Default")
propertyList.Add(new ConfigProperty
{
Name = root,
Type = "string",
ConfigAssociation = newConfig,
Value = Path.Combine(Application.StartupPath, @"lib\Bumbershoot\TagRecon\unimod.xml")
});
else if (root == "Blosum" && TRBlosumBox.Text == "Default")
propertyList.Add(new ConfigProperty
{
Name = root,
Type = "string",
ConfigAssociation = newConfig,
Value = Path.Combine(Application.StartupPath, @"lib\Bumbershoot\TagRecon\blosum62.fas")
});
else if (root == "DeisotopingMode")
propertyList.Add(new ConfigProperty
{
Name = root,
Type = "string",
ConfigAssociation = newConfig,
Value = ((ComboBox)item).SelectedIndex.ToString()
});
else if (item is ComboBox || item is TextBox)
{
double x;
propertyList.Add(new ConfigProperty
{
Name = root,
Type = "string",
ConfigAssociation = newConfig,
Value = double.TryParse(item.Text, out x)
? item.Text
: string.Format("\"{0}\"", item.Text)
});
}
if (item is NumericUpDown)
propertyList.Add(new ConfigProperty
{
Name = root,
Type = "string",
ConfigAssociation = newConfig,
Value = ((NumericUpDown) item).Value.ToString()
});
if (item is CheckBox)
propertyList.Add(new ConfigProperty
{
Name = root,
Type = "string",
ConfigAssociation = newConfig,
Value = ((CheckBox) item).Checked.ToString().ToLower()
});
}
return propertyList;
}
/// <summary>
/// Returns properties from the given config file (newline seperated, in format "Property = Value")
/// </summary>
/// <param name="config"></param>
/// <returns></returns>
private static string CreatePropertyStringFromConfig(ConfigFile config)
{
var tempString = new StringBuilder();
foreach (var param in config.PropertyList)
tempString.AppendLine(string.Format("{0} = {1}", param.Name, param.Value));
return tempString.ToString().Trim();
}
public ConfigFile GetCometConfig()
{
if (!ProgramSelectComet.Checked)
return null;
var newConfig = new ConfigFile
{
DestinationProgram = "Comet",
Name = "--Custom--",
FilePath = "--Custom--",
PropertyList = new List<ConfigProperty>()
};
var cometConfig = CometInstrumentBox.SelectedIndex == 0
? CometParams.GetIonTrapParams()
: CometInstrumentBox.SelectedIndex == 0
? CometParams.GetTofParams()
: CometParams.GetHighResParams();
if (CometParams.CleavageAgentOptions.ContainsKey(MyriCleavageRulesBox.Text))
cometConfig.CleavageAgent = CometParams.CleavageAgentOptions[MyriCleavageRulesBox.Text];
foreach (DataGridViewRow row in MyriAppliedModBox.Rows)
{
if (row.Cells[MyriTypeColumn.Index].Value.ToString() == "Dynamic")
cometConfig.DynamicModifications.Add(
new CometParams.Modification(row.Cells[MyriMotifColumn.Index].Value.ToString(),
double.Parse(row.Cells[MyriMassColumn.Index].Value.ToString())));
else if (row.Cells[MyriMotifColumn.Index].Value.ToString() == "C")
cometConfig.StaticCysteineMod = double.Parse(row.Cells[MyriMassColumn.Index].Value.ToString());
}
cometConfig.MaxMissedCleavages = (int)MyriMaxMissedCleavagesBox.Value;
cometConfig.MaxMods = (int)MyriMaxDynamicModsBox.Value;
cometConfig.OutputSuffix = CometOutputSuffixBox.Text;
cometConfig.PrecursorTolerance = Double.Parse(MyriMonoPrecursorMzToleranceBox.Text);
cometConfig.PrecursorUnit = MyriMonoPrecursorMzToleranceUnitsList.SelectedIndex == 0
? CometParams.PrecursorUnitOptions.Daltons
: CometParams.PrecursorUnitOptions.PPM;
cometConfig.Specificity = MyriMinTerminiCleavagesBox.SelectedIndex;
newConfig.PropertyList.Add(new ConfigProperty
{
Name = "config",
Type = "string",
ConfigAssociation = newConfig,
Value = CometHandler.CometParamsToFileContents(cometConfig)
});
return newConfig;
}
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;
}
private void SaveTemplateButton_Click(object sender, EventArgs e)
{
var parameterType = Util.parameterTypes;
string prefix;
var newTemplate = false;
try
{
ConfigFile currentConfig;
if (ProgramModeBox.Text == "MyriMatch")
{
if (MyriInstrumentList.SelectedIndex > 0)
currentConfig = _myriTemplateList[MyriInstrumentList.SelectedIndex - 1];
else
{
currentConfig = new ConfigFile
{
DestinationProgram = "MyriMatch",
FilePath = "Template",
PropertyList = new List<ConfigProperty>()
};
newTemplate = true;
}
prefix = "Myri";
}
else if (ProgramModeBox.Text == "DirecTag")
{
if (DTInstrumentList.SelectedIndex > 0)
currentConfig = _DTTemplateList[DTInstrumentList.SelectedIndex-1];
else
{
currentConfig = new ConfigFile
{
DestinationProgram = "DirecTag",
FilePath = "Template",
PropertyList = new List<ConfigProperty>()
};
newTemplate = true;
}
prefix = "DT";
}
else if (ProgramModeBox.Text == "TagRecon")
{
if (TRInstrumentList.SelectedIndex > 0)
currentConfig = _TRTemplateList[TRInstrumentList.SelectedIndex-1];
else
{
currentConfig = new ConfigFile
{
DestinationProgram = "TagRecon",
FilePath = "Template",
PropertyList = new List<ConfigProperty>()
};
newTemplate = true;
}
prefix = "TR";
}
else
{
if (PepInstrumentList.SelectedIndex > 0)
currentConfig = _pepTemplateList[PepInstrumentList.SelectedIndex - 1];
else
{
currentConfig = new ConfigFile
{
DestinationProgram = "Pepitome",
FilePath = "Template",
PropertyList = new List<ConfigProperty>()
};
newTemplate = true;
}
prefix = "Pep";
}
if (newTemplate)
{
var namebox = new TextPromptBox("Instrument Name", string.Empty);
if (namebox.ShowDialog() == DialogResult.OK)
currentConfig.Name = namebox.GetText();
else
return;
}
currentConfig.PropertyList.Clear();
foreach (var kvp in _labelAssociation
.Where(kvp => kvp.Key.Name.StartsWith(prefix))
.Where(kvp => kvp.Value.ForeColor != DefaultForeColor
&& kvp.Value.ForeColor != Color.Blue))
{
currentConfig.PropertyList.Add(new ConfigProperty
{
Name = RootName(kvp.Key.Name),
Value = GetControlValueString(kvp.Key),
Type = parameterType.ContainsKey(RootName(kvp.Key.Name))
? parameterType[RootName(kvp.Key.Name)]
: "unknown",
ConfigAssociation = currentConfig
});
}
_session.SaveOrUpdate(currentConfig);
_session.Flush();
ResetTemplateLists();
MessageBox.Show("Save successful");
}
catch
{
MessageBox.Show("Unable to save");
}
}
/// <summary>
/// Create ConfigForm in edit/clone mode
/// </summary>
/// <param name="baseConfig"></param>
/// <param name="baseDirectory"></param>
/// <param name="defaultName"></param>
/// <param name="templates"></param>
public ConfigForm(ConfigFile baseConfig, string baseDirectory, string defaultName, IEnumerable<ConfigFile> templates)
{
InitializeComponent();
ProgramModeBox.Text = baseConfig.DestinationProgram;
_defaults = new Dictionary<Control, string>();
_templateDefaults = new Dictionary<Control, string>(); //starts as blank for comparison purposes
_labelAssociation = new Dictionary<Control, Control>();
_itemList = new Dictionary<string, List<Control>>
{
{baseConfig.DestinationProgram, new List<Control>()}
};
_filePath = baseConfig.FilePath;
_baseDirectory = baseDirectory;
_defaultName = defaultName;
if (!File.Exists(_filePath))
SaveOverOldButton.Visible = false;
_nonTemplate = new HashSet<Control>();
_changedItems = new HashSet<Control>();
SetInitialValues();
switch (baseConfig.DestinationProgram)
{
case "MyriMatch":
this.Text = "MyriMatch Configuration Editor";
_myriTemplateList = templates.Where(x => x.DestinationProgram == "MyriMatch").ToList();
InitializePane(MyriGenPanel);
InitializePane(MyriAdvPanel);
MyriInstrumentList.Items.Add("New");
foreach (var item in _myriTemplateList)
MyriInstrumentList.Items.Add(item.Name);
MyriInstrumentList.Text = "New";
break;
case "DirecTag":
this.Text = "DirecTag Configuration Editor";
_DTTemplateList = templates.Where(x => x.DestinationProgram == "DirecTag").ToList();
InitializePane(DTGenPanel);
InitializePane(DTAdvPanel);
DTInstrumentList.Items.Add("New");
foreach (var item in _DTTemplateList)
DTInstrumentList.Items.Add(item.Name);
DTInstrumentList.Text = "New";
break;
case "TagRecon":
this.Text = "TagRecon Configuration Editor";
_TRTemplateList = templates.Where(x => x.DestinationProgram == "TagRecon").ToList();
InitializePane(TRGenPanel);
InitializePane(TRAdvPanel);
TRInstrumentList.Items.Add("New");
foreach (var item in _TRTemplateList)
TRInstrumentList.Items.Add(item.Name);
TRInstrumentList.Text = "New";
break;
case "Pepitome":
this.Text = "Pepitome Configuration Editor";
_pepTemplateList = templates.Where(x => x.DestinationProgram == "Pepitome").ToList();
InitializePane(PepGenPanel);
InitializePane(PepAdvPanel);
PepInstrumentList.Items.Add("New");
foreach (var item in _pepTemplateList)
PepInstrumentList.Items.Add(item.Name);
PepInstrumentList.Text = "New";
break;
}
mainTabControl.TabPages.Remove(AdvTab);
LoadConfig(baseConfig);
}
internal ConfigFile GetMainConfigFile()
{
if (ProgramModeBox.Text == "MyriMatch" && !ProgramSelectMyri.Checked)
return null;
var changed = new List<Control>();
if (_isCustom)
foreach (var item in _itemList[ProgramModeBox.Text])
{
var value = GetControlValueString(item);
var compareValue = value.Trim('"');
var root = RootName(item.Name);
var isModBox = root == "AppliedMod";
if (isModBox && compareValue.Length > 0)
compareValue += "\"";
if (compareValue != _defaults[item] || (isModBox && !ModStringsEqual(compareValue, _defaults[item])))
changed.Add(item);
}
var newConfig = new ConfigFile();
newConfig.DestinationProgram = ProgramModeBox.Text;
newConfig.Name = "--Custom--";
newConfig.PropertyList = _isCustom ? GetProperties(changed, newConfig) : null;
newConfig.FilePath = _isCustom ? "--Custom--" : _filePath;
return newConfig;
}
public static ISessionFactory CreateSessionFactory()
{
var currentGuiVersion = Assembly.GetExecutingAssembly().GetName().Version.ToString(3);
var newdatabase = false;
var root = Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.ApplicationData),"Bumberdash");
if (!Directory.Exists(root))
Directory.CreateDirectory(root);
var dataFile = Path.Combine(root, "Bumbershoot " + currentGuiVersion + ".db");
var newfactory = CreateSessionFactory(dataFile, true);
var session = newfactory.OpenSession();
//check that all preloaded templates are present
if (session.QueryOver<ConfigFile>().List().Count<16)
{
//check for presence of completely empty database
if (session.QueryOver<HistoryItem>().List().Count == 0 &&
session.QueryOver<ConfigFile>().List().Count == 0)
newdatabase = true;
//load base database
var baseRoot = Path.GetDirectoryName(Process.GetCurrentProcess().MainModule.FileName);
if (baseRoot == null)
throw new Exception("Cannot find base database file");
if (!File.Exists(Path.Combine(baseRoot, "lib\\Bumbershoot.db")))
throw new Exception("Looking for \"" + Path.Combine(baseRoot, "lib\\Bumbershoot.db") + "\", however I cant find it");
var baseFactory = CreateSessionFactory(Path.Combine(baseRoot, "lib\\Bumbershoot.db"), false);
var baseSession = baseFactory.OpenSession();
//load base templates
var connectedBaseConfigs = baseSession.QueryOver<ConfigFile>().List();
var baseConfigs = new List<ConfigFile>();
foreach (var config in connectedBaseConfigs)
{
var newInstrument = new ConfigFile
{
Name = config.Name,
DestinationProgram = config.DestinationProgram,
FilePath = config.FilePath,
PropertyList = new List<ConfigProperty>()
};
foreach (var property in config.PropertyList)
{
var newProperty = new ConfigProperty
{
ConfigAssociation = newInstrument,
Name = property.Name,
Type = property.Type,
Value = property.Value
};
newInstrument.PropertyList.Add(newProperty);
}
baseConfigs.Add(newInstrument);
}
//delete old templates (if any remain) and load base template
foreach (var config in baseConfigs)
{
ConfigFile config1 = config;
var deleteList = session.QueryOver<ConfigFile>()
.Where(x => x.Name == config1.Name &&
x.DestinationProgram == config1.DestinationProgram)
.List();
foreach (var item in deleteList)
session.Delete(item);
session.Flush();
var newInstrument = new ConfigFile()
{
Name = config.Name,
DestinationProgram = config.DestinationProgram,
FilePath = config.FilePath
};
session.SaveOrUpdate(newInstrument);
session.Flush();
foreach (var property in config.PropertyList)
{
var newProperty = new ConfigProperty()
{
ConfigAssociation = newInstrument,
Name = property.Name,
Type = property.Type,
Value = property.Value
};
session.SaveOrUpdate(newProperty);
}
session.Flush();
}
//automatically try to recover old history items if database is flagged as new
if (newdatabase)
{
//if database structure is ever changed this will need to be updated to include conversion (probably in the form of basic sqlite queries)
var directoryInfo = new DirectoryInfo(root);
var bdFiles = directoryInfo.GetFiles("Bumbershoot*.db").Select(file => file.Name).ToList();
bdFiles.Sort();
if (bdFiles.Count > 1)
{
//reorder to proper location
if (bdFiles[bdFiles.Count - 1] == "Bumbershoot.db")
{
bdFiles.RemoveAt(bdFiles.Count - 1);
bdFiles.Insert(0, "Bumbershoot.db");
}
var restorePath = Path.Combine(root, bdFiles[bdFiles.Count - 2]);
var restoreFactory = CreateSessionFactory(restorePath, true);
var restoreSession = restoreFactory.OpenSession();
var restoreJobs = restoreSession.QueryOver<HistoryItem>().List<HistoryItem>();
var restoredConfigs = new Dictionary<int,ConfigFile>();
//start restoring jobs
foreach (var job in restoreJobs)
{
var newjob = new HistoryItem
{
Cpus = job.Cpus, CurrentStatus = job.CurrentStatus,
EndTime = job.EndTime, JobName = job.JobName,
JobType = job.JobType, OutputDirectory = job.OutputDirectory,
ProteinDatabase = job.ProteinDatabase, RowNumber = job.RowNumber,
SpectralLibrary = job.SpectralLibrary, StartTime = job.StartTime
};
if (!restoredConfigs.ContainsKey(job.InitialConfigFile.ConfigId))
{
var newConfig = new ConfigFile
{
DestinationProgram = job.InitialConfigFile.DestinationProgram,
FilePath = job.InitialConfigFile.FilePath,
FirstUsedDate = job.InitialConfigFile.FirstUsedDate,
Name = job.InitialConfigFile.Name
};
session.SaveOrUpdate(newConfig);
session.Flush();
foreach (var property in job.InitialConfigFile.PropertyList)
{
var newProperty = new ConfigProperty
{
Name = property.Name,
ConfigAssociation = newConfig,
Type = property.Type,
Value = property.Value
};
session.SaveOrUpdate(newProperty);
}
session.Flush();
newjob.InitialConfigFile = newConfig;
restoredConfigs.Add(job.InitialConfigFile.ConfigId, newConfig);
}
else
newjob.InitialConfigFile = restoredConfigs[job.InitialConfigFile.ConfigId];
if (job.TagConfigFile != null)
{
if (!restoredConfigs.ContainsKey(job.TagConfigFile.ConfigId))
{
var newConfig = new ConfigFile
{
DestinationProgram = job.TagConfigFile.DestinationProgram,
FilePath = job.TagConfigFile.FilePath,
FirstUsedDate = job.TagConfigFile.FirstUsedDate,
Name = job.TagConfigFile.Name
};
session.SaveOrUpdate(newConfig);
session.Flush();
foreach (var property in job.TagConfigFile.PropertyList)
{
var newProperty = new ConfigProperty
{
Name = property.Name,
ConfigAssociation = newConfig,
Type = property.Type,
Value = property.Value
};
session.SaveOrUpdate(newProperty);
}
session.Flush();
newjob.TagConfigFile = newConfig;
restoredConfigs.Add(job.TagConfigFile.ConfigId,newConfig);
}
else
newjob.TagConfigFile = restoredConfigs[job.TagConfigFile.ConfigId];
}
session.SaveOrUpdate(newjob);
session.Flush();
foreach (var file in job.FileList)
{
var newFile = new InputFile {FilePath = file.FilePath, HistoryItem = newjob};
session.SaveOrUpdate(newFile);
session.Flush();
}
}
}
}
}
session.Close();
return newfactory;
}
/// <summary>
/// Takes a template config and populates the template defaults dictionary
/// </summary>
/// <param name="baseConfig"></param>
private void SetTemplateDefaults(ConfigFile baseConfig)
{
_templateDefaults = new Dictionary<Control, string>();
var configValues = new Dictionary<string, string>();
foreach (var item in baseConfig.PropertyList)
if (!configValues.ContainsKey(item.Name))
configValues.Add(item.Name, item.Value.Trim('"'));
if (configValues.ContainsKey("AppliedMod") && configValues["AppliedMod"].Length > 0)
configValues["AppliedMod"] += "\"";
//Set values
foreach (var item in _itemList[ProgramModeBox.Text])
{
var root = RootName(item.Name);
if (configValues.ContainsKey(root))
_templateDefaults.Add(item, configValues[root]);
}
foreach (var item in _itemList[ProgramModeBox.Text])
CheckForChange(item, null);
}
/// <summary>
/// Returns list of output templates
/// </summary>
/// <returns></returns>
internal List<ConfigFile> GetConfigs()
{
var list = from DataGridViewRow row in OutputDGV.Rows
select (ConfigFile) row.Tag;
var newList = new List<ConfigFile>();
foreach (var item in list)
{
var newconfig = new ConfigFile
{
Name = item.Name,
DestinationProgram = item.DestinationProgram,
FilePath = item.FilePath,
PropertyList = new List<ConfigProperty>()
};
foreach (var property in item.PropertyList)
newconfig.PropertyList.Add(new ConfigProperty
{
Name = property.Name,
Type = property.Type,
Value = property.Value,
ConfigAssociation = newconfig
});
newList.Add(newconfig);
}
return newList;
}
/// <summary>
/// Reloads database representation of a valid config file
/// </summary>
/// <param name="config"></param>
private void ReloadConfig(ConfigFile config)
{
if (Path.GetExtension(config.FilePath) == ".cfg")
{
if (File.Exists(config.FilePath))
{
var parameterType = Util.parameterTypes;
var fileIn = new StreamReader(config.FilePath);
var completeFile = fileIn.ReadToEnd();
fileIn.Close();
fileIn.Dispose();
var propertyList = completeFile.Split(Environment.NewLine.ToCharArray(),
StringSplitOptions.RemoveEmptyEntries);
config.PropertyList.Clear();
foreach (var line in propertyList)
{
var breakDown = line.Split("=".ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
config.PropertyList.Add(new ConfigProperty
{
Name = breakDown[0].Trim(),
Value = breakDown[1].Trim(),
Type = parameterType.ContainsKey(breakDown[0].Trim())
? parameterType[breakDown[0].Trim()]
: "unknown",
ConfigAssociation = config
});
}
_session.SaveOrUpdate(config);
_session.Flush();
}
else
{
//Occurs when the file has been deleted, convert to custom config
config.Name = "File missing (" + config.FilePath + ")";
config.FilePath = "--Custom--";
_session.SaveOrUpdate(config);
_session.Flush();
}
}
}
