[WIP] Enable saving of multiple settings for tasks

MetaMorpheus.sln

@@ -0,0 +1,134 @@
+
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio Version 17
+VisualStudioVersion = 17.1.32228.430
+MinimumVisualStudioVersion = 10.0.40219.1
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "CMD", "CMD\CMD.csproj", "{FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "GUI", "GUI\GUI.csproj", "{C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "EngineLayer", "EngineLayer\EngineLayer.csproj", "{FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "TaskLayer", "TaskLayer\TaskLayer.csproj", "{9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}"
+EndProject
+Project("{930C7802-8A8C-48F9-8165-68863BCCD9DD}") = "MetaMorpheusSetup", "MetaMorpheusSetup\MetaMorpheusSetup.wixproj", "{BE72541A-66A4-4958-9D19-56ACC7D3876B}"
+ ProjectSection(ProjectDependencies) = postProject
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD} = {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}
+ EndProjectSection
+EndProject
+Project("{930C7802-8A8C-48F9-8165-68863BCCD9DD}") = "Bootstrapper1", "Bootstrapper1\Bootstrapper1.wixproj", "{FBA0315B-076D-4470-AFB0-64C8AB4A65A9}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "GuiFunctions", "GuiFunctions\GuiFunctions.csproj", "{653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Test", "Test\Test.csproj", "{7EE028A9-75A2-450F-A9A7-76559ED15419}"
+EndProject
+Global
+ GlobalSection(SolutionConfigurationPlatforms) = preSolution
+ Debug|Any CPU = Debug|Any CPU
+ Debug|x64 = Debug|x64
+ Debug|x86 = Debug|x86
+ Release|Any CPU = Release|Any CPU
+ Release|x64 = Release|x64
+ Release|x86 = Release|x86
+ EndGlobalSection
+ GlobalSection(ProjectConfigurationPlatforms) = postSolution
+ {FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+ {FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Debug|Any CPU.Build.0 = Debug|Any CPU
+ {FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Debug|x64.ActiveCfg = Debug|Any CPU
+ {FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Debug|x64.Build.0 = Debug|Any CPU
+ {FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Debug|x86.ActiveCfg = Debug|Any CPU
+ {FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Debug|x86.Build.0 = Debug|Any CPU
+ {FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|Any CPU.ActiveCfg = Release|Any CPU
+ {FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|Any CPU.Build.0 = Release|Any CPU
+ {FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|x64.ActiveCfg = Release|Any CPU
+ {FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|x64.Build.0 = Release|Any CPU
+ {FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|x86.ActiveCfg = Release|Any CPU
+ {FD20EBBA-F4C5-40D6-AD61-48A7EB255DAE}.Release|x86.Build.0 = Release|Any CPU
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|Any CPU.Build.0 = Debug|Any CPU
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|x64.ActiveCfg = Debug|Any CPU
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|x64.Build.0 = Debug|Any CPU
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|x86.ActiveCfg = Debug|Any CPU
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Debug|x86.Build.0 = Debug|Any CPU
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|Any CPU.ActiveCfg = Release|Any CPU
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|Any CPU.Build.0 = Release|Any CPU
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|x64.ActiveCfg = Release|Any CPU
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|x64.Build.0 = Release|Any CPU
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|x86.ActiveCfg = Release|Any CPU
+ {C654FC97-FBD1-43D7-9F61-35FDD1A4E0AD}.Release|x86.Build.0 = Release|Any CPU
+ {FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+ {FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Debug|Any CPU.Build.0 = Debug|Any CPU
+ {FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Debug|x64.ActiveCfg = Debug|Any CPU
+ {FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Debug|x64.Build.0 = Debug|Any CPU
+ {FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Debug|x86.ActiveCfg = Debug|Any CPU
+ {FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Debug|x86.Build.0 = Debug|Any CPU
+ {FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Release|Any CPU.ActiveCfg = Release|Any CPU
+ {FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Release|Any CPU.Build.0 = Release|Any CPU
+ {FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Release|x64.ActiveCfg = Release|Any CPU
+ {FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Release|x64.Build.0 = Release|Any CPU
+ {FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Release|x86.ActiveCfg = Release|Any CPU
+ {FFAE3A5E-B5AE-4CD0-ABF9-703C91F1C7D6}.Release|x86.Build.0 = Release|Any CPU
+ {9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+ {9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}.Debug|Any CPU.Build.0 = Debug|Any CPU
+ {9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}.Debug|x64.ActiveCfg = Debug|Any CPU
+ {9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}.Debug|x64.Build.0 = Debug|Any CPU
+ {9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}.Debug|x86.ActiveCfg = Debug|Any CPU
+ {9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}.Debug|x86.Build.0 = Debug|Any CPU
+ {9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}.Release|Any CPU.ActiveCfg = Release|Any CPU
+ {9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}.Release|Any CPU.Build.0 = Release|Any CPU
+ {9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}.Release|x64.ActiveCfg = Release|Any CPU
+ {9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}.Release|x64.Build.0 = Release|Any CPU
+ {9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}.Release|x86.ActiveCfg = Release|Any CPU
+ {9CD3D75C-4E3C-40AC-A3D8-C32DD528DB7F}.Release|x86.Build.0 = Release|Any CPU
+ {BE72541A-66A4-4958-9D19-56ACC7D3876B}.Debug|Any CPU.ActiveCfg = Debug|x64
+ {BE72541A-66A4-4958-9D19-56ACC7D3876B}.Debug|Any CPU.Build.0 = Debug|x64
+ {BE72541A-66A4-4958-9D19-56ACC7D3876B}.Debug|x64.ActiveCfg = Debug|x64
+ {BE72541A-66A4-4958-9D19-56ACC7D3876B}.Debug|x64.Build.0 = Debug|x64
+ {BE72541A-66A4-4958-9D19-56ACC7D3876B}.Debug|x86.ActiveCfg = Debug|x64
+ {BE72541A-66A4-4958-9D19-56ACC7D3876B}.Release|Any CPU.ActiveCfg = Release|x64
+ {BE72541A-66A4-4958-9D19-56ACC7D3876B}.Release|Any CPU.Build.0 = Release|x64
+ {BE72541A-66A4-4958-9D19-56ACC7D3876B}.Release|x64.ActiveCfg = Release|x64
+ {BE72541A-66A4-4958-9D19-56ACC7D3876B}.Release|x64.Build.0 = Release|x64
+ {BE72541A-66A4-4958-9D19-56ACC7D3876B}.Release|x86.ActiveCfg = Release|x64
+ {FBA0315B-076D-4470-AFB0-64C8AB4A65A9}.Debug|Any CPU.ActiveCfg = Debug|x86
+ {FBA0315B-076D-4470-AFB0-64C8AB4A65A9}.Debug|x64.ActiveCfg = Debug|x86
+ {FBA0315B-076D-4470-AFB0-64C8AB4A65A9}.Debug|x86.ActiveCfg = Debug|x86
+ {FBA0315B-076D-4470-AFB0-64C8AB4A65A9}.Debug|x86.Build.0 = Debug|x86
+ {FBA0315B-076D-4470-AFB0-64C8AB4A65A9}.Release|Any CPU.ActiveCfg = Release|x86
+ {FBA0315B-076D-4470-AFB0-64C8AB4A65A9}.Release|Any CPU.Build.0 = Release|x86
+ {FBA0315B-076D-4470-AFB0-64C8AB4A65A9}.Release|x64.ActiveCfg = Release|x86
+ {FBA0315B-076D-4470-AFB0-64C8AB4A65A9}.Release|x64.Build.0 = Release|x86
+ {FBA0315B-076D-4470-AFB0-64C8AB4A65A9}.Release|x86.ActiveCfg = Release|x86
+ {FBA0315B-076D-4470-AFB0-64C8AB4A65A9}.Release|x86.Build.0 = Release|x86
+ {653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+ {653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}.Debug|Any CPU.Build.0 = Debug|Any CPU
+ {653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}.Debug|x64.ActiveCfg = Debug|Any CPU
+ {653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}.Debug|x64.Build.0 = Debug|Any CPU
+ {653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}.Debug|x86.ActiveCfg = Debug|Any CPU
+ {653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}.Debug|x86.Build.0 = Debug|Any CPU
+ {653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}.Release|Any CPU.ActiveCfg = Release|Any CPU
+ {653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}.Release|Any CPU.Build.0 = Release|Any CPU
+ {653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}.Release|x64.ActiveCfg = Release|Any CPU
+ {653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}.Release|x64.Build.0 = Release|Any CPU
+ {653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}.Release|x86.ActiveCfg = Release|Any CPU
+ {653015B3-CC5A-4D1C-AAD3-1CE2A0C4D197}.Release|x86.Build.0 = Release|Any CPU
+ {7EE028A9-75A2-450F-A9A7-76559ED15419}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+ {7EE028A9-75A2-450F-A9A7-76559ED15419}.Debug|Any CPU.Build.0 = Debug|Any CPU
+ {7EE028A9-75A2-450F-A9A7-76559ED15419}.Debug|x64.ActiveCfg = Debug|Any CPU
+ {7EE028A9-75A2-450F-A9A7-76559ED15419}.Debug|x64.Build.0 = Debug|Any CPU
+ {7EE028A9-75A2-450F-A9A7-76559ED15419}.Debug|x86.ActiveCfg = Debug|Any CPU
+ {7EE028A9-75A2-450F-A9A7-76559ED15419}.Debug|x86.Build.0 = Debug|Any CPU
+ {7EE028A9-75A2-450F-A9A7-76559ED15419}.Release|Any CPU.ActiveCfg = Release|Any CPU
+ {7EE028A9-75A2-450F-A9A7-76559ED15419}.Release|Any CPU.Build.0 = Release|Any CPU
+ {7EE028A9-75A2-450F-A9A7-76559ED15419}.Release|x64.ActiveCfg = Release|Any CPU
+ {7EE028A9-75A2-450F-A9A7-76559ED15419}.Release|x64.Build.0 = Release|Any CPU
+ {7EE028A9-75A2-450F-A9A7-76559ED15419}.Release|x86.ActiveCfg = Release|Any CPU
+ {7EE028A9-75A2-450F-A9A7-76559ED15419}.Release|x86.Build.0 = Release|Any CPU
+ EndGlobalSection
+ GlobalSection(SolutionProperties) = preSolution
+ HideSolutionNode = FALSE
+ EndGlobalSection
+ GlobalSection(ExtensibilityGlobals) = postSolution
+ SolutionGuid = {4735EA49-310B-4478-BF26-64F03519DB48}
+ EndGlobalSection
+EndGlobal

MetaMorpheus/GUI/MainWindow.xaml

@@ -450,32 +450,33 @@
  <RowDefinition Height="50"/>
  <RowDefinition Height="50"/>
  <RowDefinition Height="25"/>
- <RowDefinition Height="1*"/>
+ <RowDefinition Height="41*"/>
+ <RowDefinition Height="153*"/>
  </Grid.RowDefinitions>
 
  <!--Header label-->
  <Label Content="Spectra" Grid.Row="0" Style="{StaticResource HeaderLabelStyle}" />
 
  <!--Detail text-->
- <TextBlock Grid.Row="1" Style="{StaticResource TextBlockStyle}">
+ <TextBlock Grid.Row="1" Style="{StaticResource TextBlockStyle}" Margin="15,0,10,0">
  Add spectra file(s) in .mzML, .mgf, or Thermo .raw format.
  </TextBlock>
 
  <!--Button to add spectra files-->
- <Button Name="AddSpectraButton" Grid.Row="2" Content="+ADD SPECTRA" Click="AddSpectraFile_Click" HorizontalAlignment="Right" 
- Style="{StaticResource ImportantButtonStyle}" Margin="0,0,10,0"/>
+ <Button Name="AddSpectraButton" Grid.Row="2" Content="+ADD SPECTRA" Click="AddSpectraFile_Click" HorizontalAlignment="Left" 
+ Style="{StaticResource ImportantButtonStyle}" Margin="634,0,0,0"/>
 
  <Button Name="SetFileSpecificSettingsButton" Grid.Row="2" Content="SET FILE-SPECIFIC SETTINGS" Click="SetFileSpecificParameters_Click" 
- HorizontalAlignment="Right" Style="{StaticResource ImportantButtonStyle}"
- Margin="0,0,211,0"/>
+ HorizontalAlignment="Left" Style="{StaticResource ImportantButtonStyle}"
+ Margin="433,0,0,0"/>
 
  <Button Name="SetExperimentalDesignButton" Grid.Row="2" Content="SET EXPERIMENTAL DESIGN" Click="SetExperimentalDesign_Click" 
- HorizontalAlignment="Right" Style="{StaticResource ImportantButtonStyle}"
- Margin="0,0,412,0"/>
+ HorizontalAlignment="Left" Style="{StaticResource ImportantButtonStyle}"
+ Margin="232,0,0,0"/>
 
  <!--The list of spectra files-->
  <DataGrid Name="dataGridSpectraFiles" ItemsSource="{Binding}" Grid.Row="3" Style="{StaticResource x:DataGridStyle}"
- ColumnHeaderStyle="{StaticResource DataGridColumnHeaderStyle}" PreviewKeyDown="Window_PreviewKeyDown">
+ ColumnHeaderStyle="{StaticResource DataGridColumnHeaderStyle}" PreviewKeyDown="Window_PreviewKeyDown" Margin="10,0,10,10" Grid.RowSpan="2">
  <DataGrid.RowStyle>
  <Style TargetType="{x:Type DataGridRow}" BasedOn="{StaticResource SpectraFileDataGridItemStyle}" />
  </DataGrid.RowStyle>
@@ -493,7 +494,7 @@
  </TabItem>
 
  <!--Workflow tab-->
- <TabItem Name="TasksTab" Header="Tasks" TabIndex="0" Style="{StaticResource TabItemStyle}">
+ <TabItem Name="TasksTab" Header="Tasks" TabIndex="0" Style="{StaticResource TabItemStyle}" Height="35" Margin="0,0,2,0" VerticalAlignment="Bottom">
  <Grid Style="{StaticResource PageGridStyle}">
  <Grid.RowDefinitions>
  <RowDefinition Height="50"/>

MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml

@@ -45,6 +45,13 @@
  </TextBox.Style>
  </TextBox>
  </StackPanel>
+
+ <StackPanel DockPanel.Dock="Top" Margin="10">
+ <!-- save settings -->
+ <local:SaveSettingsControl x:Name="TaskSettingsCtrl" 
+ DataContext="{Binding TaskSettingViewModel}"/>
+ </StackPanel>
+
  <GroupBox Header="Search Parameters" DockPanel.Dock="Top">
  <Expander x:Name="SearchModeExpander">
  <StackPanel>

MetaMorpheus/GUI/TaskWindows/CalibrateTaskWindow.xaml.cs

@@ -28,15 +28,19 @@ public partial class CalibrateTaskWindow : Window
  private readonly ObservableCollection<ModTypeForLoc> LocalizeModTypeForTreeViewObservableCollection = new ObservableCollection<ModTypeForLoc>();
  private bool AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
  private CustomFragmentationWindow CustomFragmentationWindow;
+ private TaskSettingViewModel TaskSettingViewModel;
 
  public CalibrateTaskWindow(CalibrationTask myCalibrateTask)
  {
  InitializeComponent();
+ PopulateChoices();
  TheTask = myCalibrateTask ?? new CalibrationTask();
 
+ var updateFieldsFromNewTaskAction = (MetaMorpheusTask task) => UpdateFieldsFromTask(task as CalibrationTask);
+ TaskSettingViewModel = new(TheTask, updateFieldsFromNewTaskAction, GetTaskFromGui);
+ TaskSettingsCtrl.DataContext = TaskSettingViewModel;
+
  AutomaticallyAskAndOrUpdateParametersBasedOnProtease = false;
- PopulateChoices();
- UpdateFieldsFromTask(TheTask);
  AutomaticallyAskAndOrUpdateParametersBasedOnProtease = true;
 
  if (myCalibrateTask == null)
@@ -187,15 +191,25 @@ private void CancelButton_Click(object sender, RoutedEventArgs e)
  }
 
  private void SaveButton_Click(object sender, RoutedEventArgs e)
+ {
+ CalibrationTask task = GetTaskFromGui();
+ if (task == null)
+ return;
+
+ TheTask = task;
+ DialogResult = true;
+ }
+
+ private CalibrationTask GetTaskFromGui()
  {
  string fieldNotUsed = "1";
 
  if (!GlobalGuiSettings.CheckTaskSettingsValidity(PrecursorMassToleranceTextBox.Text, ProductMassToleranceTextBox.Text, MissedCleavagesTextBox.Text,
  MaxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, MaxThreadsTextBox.Text, MinScoreAllowed.Text,
- fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, null, null, fieldNotUsed, MaxModsPerPeptideTextBox.Text, fieldNotUsed, 
+ fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, fieldNotUsed, null, null, fieldNotUsed, MaxModsPerPeptideTextBox.Text, fieldNotUsed,
  null, null, null))
  {
- return;
+ return null;
  }
 
  Protease protease = (Protease)ProteaseComboBox.SelectedItem;
@@ -226,7 +240,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
 
  if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
  {
- return;
+ return null;
  }
 
  var listOfModsFixed = new List<(string, string)>();
@@ -296,7 +310,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
  }
 
  TheTask.CalibrationParameters.WriteIndexedMzml = writeIndexMzmlCheckbox.IsChecked.Value;
- DialogResult = true;
+ return TheTask;
  }
 
  private void CheckIfNumber(object sender, TextCompositionEventArgs e)
@@ -357,7 +371,7 @@ private void OnClosing(object sender, CancelEventArgs e)
  // remove event handler from timer
  // keeping it will trigger an exception because the closed window stops existing
 
- CustomFragmentationWindow.Close();
+ CustomFragmentationWindow?.Close();
  }
 
  private void SaveAsDefault_Click(object sender, RoutedEventArgs e)

MetaMorpheus/GUI/TaskWindows/GPTMDTaskWindow.xaml

@@ -45,6 +45,14 @@
  </TextBox.Style>
  </TextBox>
  </StackPanel>
+
+ <StackPanel DockPanel.Dock="Top" Margin="10">
+
+ <!-- save settings -->
+ <local:SaveSettingsControl x:Name="TaskSettingsCtrl" 
+ DataContext="{Binding TaskSettingViewModel}"/>
+ </StackPanel>
+
  <GroupBox Header="File Loading Parameters" DockPanel.Dock="Top">
  <Expander x:Name="FileLoadExpander" >
  <StackPanel>