//Undoes value(sets to null)
private void Unset(object sender, RoutedEventArgs e)
{
int index = ParameterGrid.SelectedIndex;
Parameter a = ParameterGrid.Items[index] as Parameter;
a.Value = null;
if (TempSettings != null)
{
for (int i = 0; i < TempSettings.Length; i++)
{
FileSpecificSettings b = TempSettings.GetValue(i) as FileSpecificSettings;
switch (index)
{
case 0:
b.Protease = null;
break;
case 1:
b.ConserveMemory = null;
break;
case 2:
b.Max_mods_for_peptide = null;
break;
case 3:
b.DeconvolutionIntensityRatio = null;
break;
case 4:
b.DoPrecursorDeconvolution = null;
break;
case 5:
b.UseProvidedPrecursorInfo = null;
break;
case 6:
b.ScoreCutoff = null;
break;
case 7:
b.ProductMassTolerance = null;
break;
case 8:
b.DeconvolutionMaxAssumedChargeState = null;
break;
case 9:
b.TotalPartitions = null;
break;
case 10:
b.MaxModificationIsoforms = null;
break;
case 11:
b.MaxPeptideLength = null;
break;
case 12:
b.MinPeptideLength = null;
break;
case 13:
b.MaxMissedCleavages = null;
break;
case 14:
b.InitiatorMethionineBehavior = 0;
break;
case 15:
b.DeconvolutionMassTolerance = null;
break;
case 16:
b.TrimMsMsPeaks = null;
break;
case 17:
b.TrimMs1Peaks = null;
break;
case 18:
b.MinRatio = null;
break;
case 19:
b.TopNpeaks = null;
break;
case 20:
b.ToleranceType = null;
break;
}
}
}
ParameterGrid.Items.Refresh();
}
//Window that is opened if user wishes to change file specific settings (TOML) for
//individual or multiple spectra files. Creates a toml file where settings can be
//viewed, loaded, and changed from it.
public ChangeParametersWindow(ObservableCollection <RawDataForDataGrid> selectedRaw)
{
SelectedRaw = selectedRaw;
FileSpecificSettingsList = new FileSpecificSettings[selectedRaw.Count];
InitializeComponent();
tempParamList = InitializeParameterList();
paramList = InitializeParameterList();
ParameterGrid.Items.RemoveAt(0);
for (int i = 0; i < paramList.Count(); i++)
{
ParameterGrid.Items.Add(paramList[i]);
}
ParameterGrid.Items.Refresh();
FileSpecificSettingsList = new FileSpecificSettings[selectedRaw.Count];
//If changing settins of single file
if (selectedRaw.Count == 1)
{
string tomlFileName = System.IO.Path.ChangeExtension(SelectedRaw[0].FilePath, ".toml");
Dictionary <string, KeyValuePair <string, Nett.TomlObject> > tomlSettingsList;
if (File.Exists(tomlFileName))
{
var paramFile = Toml.ReadFile(tomlFileName, MetaMorpheusTask.tomlConfig);
tomlSettingsList = paramFile.ToDictionary(p => p.Key);
FileSpecificSettings settings = new FileSpecificSettings(tomlSettingsList);
Array.Copy(paramList, tempParamList, paramList.Length);
UpdateAndPopulateFields(settings);
}
else
{
tomlSettingsList = new Dictionary <string, KeyValuePair <string, TomlObject> >();
FileSpecificSettings settings = new FileSpecificSettings(tomlSettingsList);
settings.ConserveMemory = null;
settings.DoPrecursorDeconvolution = null;
settings.UseProvidedPrecursorInfo = null;
Array.Copy(paramList, tempParamList, paramList.Length);
UpdateAndPopulateFields(settings);
}
}
//if more than one file selected have to do processing to check equality.
else
{
string[] tomlFileNames = new string[SelectedRaw.Count];
List <string> nonEqualValueNames = new List <string>();
List <Dictionary <string, KeyValuePair <string, Nett.TomlObject> > > tomlSettingsListList = new List <Dictionary <string, KeyValuePair <string, Nett.TomlObject> > >();
//Set tomlSettingListList (list of tomlSettings)
for (int i = 0; i < selectedRaw.Count; i++)
{
tomlFileNames[i] = System.IO.Path.ChangeExtension(SelectedRaw[i].FilePath, ".toml");
if (File.Exists(tomlFileNames[i]))
{
var paramFile = Toml.ReadFile(tomlFileNames[i], MetaMorpheusTask.tomlConfig);
tomlSettingsListList.Add(paramFile.ToDictionary(p => p.Key));
}
else
{
tomlSettingsListList.Add(new Dictionary <string, KeyValuePair <string, TomlObject> >());
}
}
//check every value against every other value; if same, then add to list to set 'different in multiple files' later in Parameter Object
for (int i = 0; i < tomlSettingsListList.Count; i++)
{
for (int j = 0; j < tomlSettingsListList.Count; j++)
{
foreach (var key in tomlSettingsListList[j].Keys)
{
if (tomlSettingsListList[i].ContainsKey(key))
{
if (tomlSettingsListList[j].ContainsKey(tomlSettingsListList[i][key].Key))
{
//Need to convert first letter to uppercase to match Type
string h = tomlSettingsListList[j][key].Value.ReadableTypeName;
//convert string to appropritate format
if (!string.IsNullOrEmpty(h))
{
h = h.First().ToString().ToUpper() + h.Substring(1);
}
if (h == "Int")
{
h = "Int32";
}
if (h == "Bool")
{
h = "Boolean";
}
if (h == "Float")
{
h = "Single";
}
Type typeAsString = Type.GetType("System." + h);
var a = tomlSettingsListList[j][key].Value.Get(typeAsString);
var b = tomlSettingsListList[i][key].Value.Get(typeAsString);
if (!a.Equals(b))
{
nonEqualValueNames.Add(tomlSettingsListList[j][key].Key);
}
}
}
//add different checked if null and others are not
else
{
nonEqualValueNames.Add(key);
}
}
}
}
//now set settings so that it reflects if values are different
FileSpecificSettings settings = new FileSpecificSettings(tomlSettingsListList[0]);
foreach (string key in nonEqualValueNames)
{
if (key == "Protease")
{
paramList[0].Different = true;
}
if (key == "ConserveMemory")
{
paramList[1].Different = true;
}
if (key == "Max_mods_for_peptide")
{
paramList[2].Different = true;
}
if (key == "DeconvolutionIntensityRatio")
{
paramList[3].Different = true;
}
if (key == "DoPrecursorDeconvolution")
{
paramList[4].Different = true;
}
if (key == "UseProvidedPrecursorInfo")
{
paramList[5].Different = true;
}
if (key == "ScoreCutoff")
{
paramList[6].Different = true;
}
if (key == "ProductMassTolerance")
{
paramList[7].Different = true;
}
if (key == "DeconvolutionMaxAssumedChargeState")
{
paramList[8].Different = true;
}
if (key == "TotalPartitions")
{
paramList[9].Different = true;
}
if (key == "MaxModificationIsoforms")
{
paramList[10].Different = true;
}
if (key == "MaxPeptideLength")
{
paramList[11].Different = true;
}
if (key == "MinPeptideLength")
{
paramList[12].Different = true;
}
if (key == "MaxMissedCleavages")
{
paramList[13].Different = true;
}
if (key == "InitiatorMethionineBehavior")
{
paramList[14].Different = true;
}
if (key == "DeconvolutionMassTolerance")
{
paramList[15].Different = true;
}
if (key == "TrimMsMsPeaks")
{
paramList[16].Different = true;
}
if (key == "TrimMs1Peaks")
{
paramList[17].Different = true;
}
if (key == "MinRatio")
{
paramList[18].Different = true;
}
if (key == "TopNpeaks")
{
paramList[19].Different = true;
}
if (key == "ToleranceType")
{
paramList[20].Different = true;
}
}
TempSettings = new FileSpecificSettings[selectedRaw.Count];
Array.Copy(paramList, tempParamList, paramList.Length);
for (int i = 0; i < tomlSettingsListList.Count(); i++)
{
TempSettings[i] = new FileSpecificSettings(tomlSettingsListList[i]);
}
UpdateAndPopulateFields(settings);
}
}
//upon clicking save button, settings are saved to memory in FileSettingsList in order to be
//written to a toml file later
private void Save_Click(object sender, RoutedEventArgs e)
{
ParameterGrid.Items.Refresh();
Array.Copy(tempParamList, paramList, paramList.Length);
for (int file = 0; file < FileSpecificSettingsList.Count(); file++)
{
FileSpecificSettingsList[file] = new FileSpecificSettings();
int?index = paramList[0].Value as int?;
int?index2 = paramList[20].Value as int?;
//Cases for each Parameter:
//1. If one file with Changed value: write value to File settings
//2. If one file with unchanged Value: Do nothing; will be null
//3. If multiple files editing the same setting: write same setting to each file
/* 4. If multiple files with different values for an attribute that is unchanged, then get each paramter setting
* from Temporary Settings. If this parameter is changed, then it will be the same so going to temp settings
* is Not necesarry
*/
//Tolerance Type
if (index2.HasValue && index2 >= 0)
{
FileSpecificSettingsList[file].ToleranceType = paramList[20].ProductMassToleranceList[index2.Value];
}
else if ((index2 == -1 || !index2.HasValue) && (paramList[7].Value != null || paramList[15].Value != null))
{
MessageBox.Show("Please Select a Tolerance Type", "Confirmation", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].ToleranceType != null && FileSpecificSettingsList[file].ToleranceType == null)
{
FileSpecificSettingsList[file].ToleranceType = TempSettings[file].ToleranceType;
}
//Protease
if (index.HasValue && index >= 0 && paramList[0].HasChanged)
{
FileSpecificSettingsList[file].Protease = paramList[0].ProtList[index.Value];
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].Protease != null && FileSpecificSettingsList[file].Protease == null)
{
FileSpecificSettingsList[file].Protease = TempSettings[file].Protease;
}
//Conserve Memory
if (paramList[1].Value != null)
{
FileSpecificSettingsList[file].ConserveMemory = paramList[1].Value as bool?;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].ConserveMemory != null && FileSpecificSettingsList[file].ConserveMemory == null)
{
FileSpecificSettingsList[file].ConserveMemory = TempSettings[file].ConserveMemory;
}
//Max Mods for Peptide
if (paramList[2].Value != null)
{
int.TryParse(paramList[2].Value.ToString(), out var a);
FileSpecificSettingsList[file].Max_mods_for_peptide = a;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].Max_mods_for_peptide != null && FileSpecificSettingsList[file].Max_mods_for_peptide == null)
{
FileSpecificSettingsList[file].Max_mods_for_peptide = TempSettings[file].Max_mods_for_peptide;
}
//Deconvolution Intensity Ratio
if (paramList[3].Value != null)
{
int.TryParse(paramList[3].Value.ToString(), out var a);
FileSpecificSettingsList[file].DeconvolutionIntensityRatio = a;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].DeconvolutionIntensityRatio != null && FileSpecificSettingsList[file].DeconvolutionIntensityRatio == null)
{
FileSpecificSettingsList[file].DeconvolutionIntensityRatio = TempSettings[file].DeconvolutionIntensityRatio;
}
//Precursor Deconvolution
if (paramList[4].Value != null)
{
FileSpecificSettingsList[file].DoPrecursorDeconvolution = paramList[4].Value as bool?;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].DoPrecursorDeconvolution != null && FileSpecificSettingsList[file].DoPrecursorDeconvolution == null)
{
FileSpecificSettingsList[file].DoPrecursorDeconvolution = TempSettings[file].DoPrecursorDeconvolution;
}
//Use Provided Precursor Info
if (paramList[5].Value != null)
{
FileSpecificSettingsList[file].UseProvidedPrecursorInfo = paramList[5].Value as bool?;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].UseProvidedPrecursorInfo != null && FileSpecificSettingsList[file].UseProvidedPrecursorInfo == null)
{
FileSpecificSettingsList[file].UseProvidedPrecursorInfo = TempSettings[file].UseProvidedPrecursorInfo;
}
//Score Cutoff
if (paramList[6].Value != null)
{
double.TryParse(paramList[6].Value.ToString(), out var a);
FileSpecificSettingsList[file].ScoreCutoff = a;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].ScoreCutoff != null && FileSpecificSettingsList[file].ScoreCutoff == null)
{
FileSpecificSettingsList[file].ScoreCutoff = TempSettings[file].ScoreCutoff;
}
//Product Mass Tolerance
if (paramList[7].Value != null)
{
FileSpecificSettingsList[file].ProductMassTolerance = Tolerance.ParseToleranceString(paramList[7].Value + " " + FileSpecificSettingsList[file].ToleranceType);
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].ProductMassTolerance != null && FileSpecificSettingsList[file].ProductMassTolerance == null)
{
FileSpecificSettingsList[file].ProductMassTolerance = TempSettings[file].ProductMassTolerance;
}
//Deconvolution Max ASsumed Charge State
if (paramList[8].Value != null)
{
int.TryParse(paramList[8].Value.ToString(), out var a);
FileSpecificSettingsList[file].DeconvolutionMaxAssumedChargeState = a;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].DeconvolutionMaxAssumedChargeState != null && FileSpecificSettingsList[file].DeconvolutionMaxAssumedChargeState == null)
{
FileSpecificSettingsList[file].DeconvolutionMaxAssumedChargeState = TempSettings[file].DeconvolutionMaxAssumedChargeState;
}
//Total Partitions
if (paramList[9].Value != null)
{
int.TryParse(paramList[9].Value.ToString(), out var a);
FileSpecificSettingsList[file].TotalPartitions = a;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].TotalPartitions != null && FileSpecificSettingsList[file].TotalPartitions == null)
{
FileSpecificSettingsList[file].TotalPartitions = TempSettings[file].TotalPartitions;
}
//Max Modification Isoforms
if (paramList[10].Value != null)
{
int.TryParse(paramList[10].Value.ToString(), out var a);
FileSpecificSettingsList[file].MaxModificationIsoforms = a;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].MaxModificationIsoforms != null && FileSpecificSettingsList[file].MaxModificationIsoforms == null)
{
FileSpecificSettingsList[file].MaxModificationIsoforms = TempSettings[file].MaxModificationIsoforms;
}
//Max Pep Length
if (paramList[11].Value != null)
{
int.TryParse(paramList[11].Value.ToString(), out var a);
FileSpecificSettingsList[file].MaxPeptideLength = a;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].MaxPeptideLength != null && FileSpecificSettingsList[file].MaxPeptideLength == null)
{
FileSpecificSettingsList[file].MaxPeptideLength = TempSettings[file].MaxPeptideLength;
}
//Min Pep Length
if (paramList[12].Value != null)
{
int.TryParse(paramList[12].Value.ToString(), out var a);
FileSpecificSettingsList[file].MinPeptideLength = a;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].MinPeptideLength != null && FileSpecificSettingsList[file].MinPeptideLength == null)
{
FileSpecificSettingsList[file].MinPeptideLength = TempSettings[file].MinPeptideLength;
}
//Max Missed Cleavages
if (paramList[13].Value != null)
{
int.TryParse(paramList[13].Value.ToString(), out var a);
FileSpecificSettingsList[file].MaxMissedCleavages = a;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].MaxMissedCleavages != null && FileSpecificSettingsList[file].MaxMissedCleavages == null)
{
FileSpecificSettingsList[file].MaxMissedCleavages = TempSettings[file].MaxMissedCleavages;
}
//Init Methonine Behavior
if (paramList[14].Value != null)
{
if (!paramList[14].Value.Equals("Undefined"))
{
FileSpecificSettingsList[file].InitiatorMethionineBehavior = (InitiatorMethionineBehavior)paramList[14].Value;
}
else
{
paramList[14].Value = null;
}
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].InitiatorMethionineBehavior != 0 && FileSpecificSettingsList[file].InitiatorMethionineBehavior == 0)
{
FileSpecificSettingsList[file].InitiatorMethionineBehavior = TempSettings[file].InitiatorMethionineBehavior;
}
//Deconvolution Mass Tolerance
if (paramList[15].Value != null)
{
FileSpecificSettingsList[file].DeconvolutionMassTolerance = Tolerance.ParseToleranceString(paramList[15].Value + " " + FileSpecificSettingsList[file].ToleranceType);
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].DeconvolutionMassTolerance != null && FileSpecificSettingsList[file].DeconvolutionMassTolerance == null)
{
FileSpecificSettingsList[file].DeconvolutionMassTolerance = TempSettings[file].DeconvolutionMassTolerance;
}
//Trim Ms/Ms Peaks
if (paramList[16].Value != null)
{
FileSpecificSettingsList[file].TrimMsMsPeaks = paramList[16].Value as bool?;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].TrimMsMsPeaks != null && FileSpecificSettingsList[file].TrimMsMsPeaks == null)
{
FileSpecificSettingsList[file].TrimMsMsPeaks = TempSettings[file].TrimMsMsPeaks;
}
//TrimMs1Peaks
if (paramList[17].Value != null)
{
FileSpecificSettingsList[file].TrimMs1Peaks = paramList[17].Value as bool?;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].TrimMs1Peaks != null && FileSpecificSettingsList[file].TrimMs1Peaks == null)
{
FileSpecificSettingsList[file].TrimMs1Peaks = TempSettings[file].TrimMs1Peaks;
}
//min Ratio
if (paramList[18].Value != null)
{
int.TryParse(paramList[18].Value.ToString(), out var a);
FileSpecificSettingsList[file].MinRatio = a;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].MinRatio != null && FileSpecificSettingsList[file].MinRatio == null)
{
FileSpecificSettingsList[file].MinRatio = TempSettings[file].MinRatio;
}
//Top N Peaks
if (paramList[19].Value != null)
{
int.TryParse(paramList[19].Value.ToString(), out var a);
FileSpecificSettingsList[file].TopNpeaks = a;
}
else if (FileSpecificSettingsList.Count() > 1 && TempSettings[file].TopNpeaks != null && FileSpecificSettingsList[file].TopNpeaks == null)
{
FileSpecificSettingsList[file].TopNpeaks = TempSettings[file].TopNpeaks;
}
}
DialogResult = true;
}
//Updates fields of display so that it reflects current settings
private void UpdateAndPopulateFields(FileSpecificSettings settings)
{
var a = ParameterGrid.Items.GetItemAt(0) as Parameter;
int?index = paramList[0].ProtList.IndexOf(settings.Protease);
if (index.HasValue)
{
a.Value = index;
}
if (paramList[0].Different)
{
a.Value = null;
}
var b = ParameterGrid.Items.GetItemAt(1) as Parameter;
b.Value = settings.ConserveMemory;
if (paramList[1].Different)
{
b.Value = null;
}
var c = ParameterGrid.Items.GetItemAt(2) as Parameter;
c.Value = settings.Max_mods_for_peptide;
if (paramList[2].Different)
{
c.Value = null;
}
var d = ParameterGrid.Items.GetItemAt(3) as Parameter;
d.Value = settings.DeconvolutionIntensityRatio;
paramList[3].Value = d.Value;
if (paramList[3].Different)
{
d.Value = null;
}
var e = ParameterGrid.Items.GetItemAt(4) as Parameter;
e.Value = settings.DoPrecursorDeconvolution;
if (paramList[4].Different)
{
e.Value = null;
}
var f = ParameterGrid.Items.GetItemAt(5) as Parameter;
f.Value = settings.UseProvidedPrecursorInfo;
if (paramList[5].Different)
{
f.Value = null;
}
var g = ParameterGrid.Items.GetItemAt(6) as Parameter;
g.Value = settings.ScoreCutoff;
if (paramList[6].Different)
{
g.Value = null;
}
var h = ParameterGrid.Items.GetItemAt(7) as Parameter;
if (settings.ProductMassTolerance != null)
{
h.Value = settings.ProductMassTolerance.Value;
}
if (paramList[7].Different)
{
h.Value = null;
}
var i = ParameterGrid.Items.GetItemAt(8) as Parameter;
i.Value = settings.DeconvolutionMaxAssumedChargeState;
if (paramList[8].Different)
{
i.Value = null;
}
var j = ParameterGrid.Items.GetItemAt(9) as Parameter;
j.Value = settings.TotalPartitions;
if (paramList[9].Different)
{
j.Value = null;
}
var k = ParameterGrid.Items.GetItemAt(10) as Parameter;
k.Value = settings.MaxModificationIsoforms;
if (paramList[10].Different)
{
k.Value = null;
}
var l = ParameterGrid.Items.GetItemAt(11) as Parameter;
l.Value = settings.MaxPeptideLength;
if (paramList[11].Different)
{
l.Value = null;
}
var m = ParameterGrid.Items.GetItemAt(12) as Parameter;
m.Value = settings.MinPeptideLength;
if (paramList[12].Different)
{
m.Value = null;
}
var n = ParameterGrid.Items.GetItemAt(13) as Parameter;
n.Value = settings.MaxMissedCleavages;
if (paramList[13].Different)
{
n.Value = null;
}
int?index2 = paramList[0].InitList.IndexOf(settings.InitiatorMethionineBehavior.ToString());
var o = ParameterGrid.Items.GetItemAt(14) as Parameter;
if (index2.HasValue && index2.Value != 0)
{
o.Value = index2;
}
else
{
o.Value = null;
}
if (paramList[14].Different)
{
o.Value = null;
}
var p = ParameterGrid.Items.GetItemAt(15) as Parameter;
if (settings.DeconvolutionMassTolerance != null)
{
p.Value = settings.DeconvolutionMassTolerance.Value;
}
if (paramList[15].Different)
{
p.Value = null;
}
var q = ParameterGrid.Items.GetItemAt(16) as Parameter;
q.Value = settings.TrimMsMsPeaks;
if (paramList[16].Different)
{
q.Value = null;
}
var r = ParameterGrid.Items.GetItemAt(17) as Parameter;
r.Value = settings.TrimMs1Peaks;
if (paramList[17].Different)
{
r.Value = null;
}
var s = ParameterGrid.Items.GetItemAt(18) as Parameter;
s.Value = settings.MinRatio;
if (paramList[18].Different)
{
s.Value = null;
}
var t = ParameterGrid.Items.GetItemAt(19) as Parameter;
t.Value = settings.TopNpeaks;
if (paramList[19].Different)
{
t.Value = null;
}
//tolerance type
int?index3 = paramList[20].ProductMassToleranceList.IndexOf(settings.ToleranceType);
var w = ParameterGrid.Items.GetItemAt(20) as Parameter;
if (index.HasValue)
{
w.Value = index3;
}
if (paramList[20].Different)
{
w.Value = null;
}
ParameterGrid.Items.Refresh();
}
