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stefanks
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Merge pull request #220 from smith-chem-wisc/StefanBranch
Stefan branch
2 parents 7c779aa + e005334 commit bc326f2

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5 files changed

+101
-100
lines changed

5 files changed

+101
-100
lines changed

‎EngineLayer/Analysis/AnalysisResults.cs

+4-4
Original file line numberDiff line numberDiff line change
@@ -24,13 +24,13 @@ public AnalysisResults(AnalysisEngine s, List<NewPsmWithFdr>[] allResultingIdent
2424

2525
#endregion Public Properties
2626

27-
#region Protected Properties
27+
#region Public Methods
2828

2929
public override string ToString()
3030
{
3131
var sb = new StringBuilder();
3232
sb.AppendLine(base.ToString());
33-
sb.Append("\t\tAll PSMS within 1% FDR: " + string.Join(", ", AllResultingIdentifications.Select(b => b.Count(c => c.qValue <= 0.01))));
33+
sb.AppendLine("All PSMS within 1% FDR: " + string.Join(", ", AllResultingIdentifications.Select(b => b.Count(c => c.qValue <= 0.01))));
3434

3535
var check = ProteinGroups.Where(s => s != null);
3636
if (check.Any())
@@ -44,13 +44,13 @@ public override string ToString()
4444
numProteinsList.Add(ProteinGroups[i].Count(c => c.QValue <= 0.01));
4545
}
4646

47-
sb.Append("\n\t\tAll proteins within 1% FDR: " + string.Join(", ", numProteinsList));
47+
sb.Append("All proteins within 1% FDR: " + string.Join(", ", numProteinsList));
4848
}
4949

5050
return sb.ToString();
5151
}
5252

53-
#endregion Protected Properties
53+
#endregion Public Methods
5454

5555
}
5656
}

‎EngineLayer/ClassicSearch/ClassicSearchResults.cs

+3-3
Original file line numberDiff line numberDiff line change
@@ -19,16 +19,16 @@ internal ClassicSearchResults(ClassicSearchEngine searchParams) : base(searchPar
1919

2020
#endregion Public Properties
2121

22-
#region Protected Properties
22+
#region Public Methods
2323

2424
public override string ToString()
2525
{
2626
var sb = new StringBuilder();
27-
sb.AppendLine(base.ToString());
27+
sb.Append(base.ToString());
2828
return sb.ToString();
2929
}
3030

31-
#endregion Protected Properties
31+
#endregion Public Methods
3232

3333
}
3434
}

‎GUI/GPTMDTaskWindow.xaml.cs

+2-1
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,7 @@
33
using System;
44
using System.Collections.ObjectModel;
55
using System.Globalization;
6+
using System.IO;
67
using System.Linq;
78
using System.Windows;
89
using System.Windows.Controls;
@@ -62,7 +63,7 @@ private void Row_DoubleClick(object sender, MouseButtonEventArgs e)
6263
var hm = ye.Content as TextBlock;
6364
if (hm != null && !string.IsNullOrEmpty(hm.Text))
6465
{
65-
System.Diagnostics.Process.Start(hm.Text);
66+
System.Diagnostics.Process.Start(Path.Combine(@"Mods", hm.Text));
6667
}
6768
}
6869

‎GUI/MainWindow.xaml

+86-71
Original file line numberDiff line numberDiff line change
@@ -5,9 +5,9 @@
55
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
66
xmlns:local="clr-namespace:MetaMorpheusGUI"
77
mc:Ignorable="d"
8-
Title="MetaMorpheus Not a release" Drop="Window_Drop" AllowDrop="true" WindowStartupLocation="CenterScreen">
9-
<StackPanel Margin="5">
10-
<Menu x:Name="menu">
8+
Title="MetaMorpheus Not a release" Drop="Window_Drop" AllowDrop="true" WindowStartupLocation="CenterScreen" MinHeight="400" MinWidth="650" Height="500" Width="700">
9+
<DockPanel>
10+
<Menu x:Name="menu" DockPanel.Dock="Top">
1111
<MenuItem Header="Databases">
1212
<MenuItem Header="External Databases" />
1313
<MenuItem Header="Custom Modification Databases" />
@@ -22,31 +22,38 @@
2222
<ColumnDefinition Width="1*" />
2323
<ColumnDefinition Width="1*" />
2424
</Grid.ColumnDefinitions>
25-
<Grid.RowDefinitions>
26-
<RowDefinition Height="1*" />
27-
<RowDefinition Height="1*" />
28-
</Grid.RowDefinitions>
29-
<StackPanel>
30-
<Border BorderBrush="Black" BorderThickness="2" Margin="5">
31-
<StackPanel Margin="5" x:Name="XMLdbPanel">
32-
<Label x:Name="xmlLabel" Content="Protein Databases" HorizontalAlignment="Center" />
33-
<DataGrid x:Name="dataGridXMLs" ItemsSource="{Binding}" CanUserSortColumns="False" CanUserResizeColumns="False" CanUserReorderColumns="False" Height="100">
25+
<Grid>
26+
<Grid.RowDefinitions>
27+
<RowDefinition Height="1*" />
28+
<RowDefinition Height="1*" />
29+
<RowDefinition Height="1*" />
30+
</Grid.RowDefinitions>
31+
<GroupBox Header="Protein Databases" Name="proteinDatabasesGroupBox">
32+
<Grid>
33+
<Grid.RowDefinitions>
34+
<RowDefinition Height="*" />
35+
<RowDefinition Height="20" />
36+
</Grid.RowDefinitions>
37+
<DataGrid x:Name="dataGridXMLs" ItemsSource="{Binding}" CanUserSortColumns="False" CanUserResizeColumns="False" CanUserReorderColumns="False">
3438
<DataGrid.Resources>
3539
<Style TargetType="DataGridCell">
3640
<EventSetter Event="MouseDoubleClick" Handler="Row_DoubleClick" />
3741
</Style>
3842
</DataGrid.Resources>
3943
</DataGrid>
40-
<StackPanel Orientation="Horizontal" HorizontalAlignment="Center">
44+
<StackPanel Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="1">
4145
<Button x:Name="AddXML" Content="Add" Click="AddXML_Click" />
4246
<Button x:Name="ClearXML" Content="Clear" Click="ClearXML_Click" />
4347
</StackPanel>
44-
</StackPanel>
45-
</Border>
46-
<Border BorderBrush="Black" BorderThickness="2" Margin="5">
47-
<StackPanel x:Name="DatafilesStackPanel" Margin="5">
48-
<Label x:Name="DatafilesLabel" Content="Datafiles" HorizontalAlignment="Center" />
49-
<DataGrid x:Name="dataGridDatafiles" ItemsSource="{Binding}" CanUserSortColumns="False" CanUserResizeColumns="False" CanUserReorderColumns="False" Height="150">
48+
</Grid>
49+
</GroupBox>
50+
<GroupBox Header="Datafiles" Grid.Row="1" Name="datafilesGroupBox">
51+
<Grid>
52+
<Grid.RowDefinitions>
53+
<RowDefinition Height="*" />
54+
<RowDefinition Height="20" />
55+
</Grid.RowDefinitions>
56+
<DataGrid x:Name="dataGridDatafiles" ItemsSource="{Binding}" CanUserSortColumns="False" CanUserResizeColumns="False" CanUserReorderColumns="False" DockPanel.Dock="Top">
5057
<DataGrid.Resources>
5158
<ResourceDictionary>
5259
<Style x:Key="{x:Type DataGridCell}" TargetType="{x:Type DataGridCell}">
@@ -85,40 +92,50 @@
8592
</ResourceDictionary>
8693
</DataGrid.Resources>
8794
</DataGrid>
88-
<StackPanel Orientation="Horizontal" HorizontalAlignment="Center">
95+
<StackPanel Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="1">
8996
<Button x:Name="AddRaw" Content="Add" Click="AddRaw_Click" />
9097
<Button x:Name="ClearRaw" Content="Clear" Click="ClearRaw_Click" />
9198
</StackPanel>
92-
</StackPanel>
93-
</Border>
94-
</StackPanel>
95-
<Border BorderBrush="Black" BorderThickness="2" Grid.Row="1" Margin="5">
96-
<StackPanel x:Name="OutputFilesStackPanel" Margin="5">
97-
<Label x:Name="outputFilesLabel" Content="Output Files" HorizontalAlignment="Center" />
98-
<DataGrid x:Name="outputFilesDataGrid" ItemsSource="{Binding}" CanUserSortColumns="False" CanUserResizeColumns="False" CanUserReorderColumns="False">
99-
<DataGrid.Resources>
100-
<Style TargetType="DataGridCell">
101-
<EventSetter Event="MouseDoubleClick" Handler="Row_DoubleClick" />
102-
</Style>
103-
</DataGrid.Resources>
104-
</DataGrid>
105-
<StackPanel Orientation="Horizontal" HorizontalAlignment="Center">
106-
<Button x:Name="ClearOutput" Content="Clear" Click="ClearOutput_Click" />
107-
</StackPanel>
108-
</StackPanel>
109-
</Border>
110-
<StackPanel x:Name="RightPanel" Grid.Column="1">
111-
<StackPanel Orientation="Horizontal" HorizontalAlignment="Center">
112-
<Button x:Name="addSearchTaskButton" Content="Add Search Task" Click="addSearchTaskButton_Click" />
113-
<Button x:Name="addCalibrateTaskButton" Content="Add Calibrate Task" Click="addCalibrateTaskButton_Click" />
114-
<Button x:Name="addGPTMDTaskButton" Content="Add GPTMD Task" Click="addGPTMDTaskButton_Click" />
115-
</StackPanel>
116-
<Border BorderBrush="Black" BorderThickness="2" Margin="5">
117-
<StackPanel x:Name="tasksPanel" Margin="5">
99+
</Grid>
100+
</GroupBox>
101+
<GroupBox Header="Output Files" Grid.Row="2">
102+
<Grid>
103+
<Grid.RowDefinitions>
104+
<RowDefinition Height="*" />
105+
<RowDefinition Height="20" />
106+
</Grid.RowDefinitions>
107+
<DataGrid x:Name="outputFilesDataGrid" ItemsSource="{Binding}" CanUserSortColumns="False" CanUserResizeColumns="False" CanUserReorderColumns="False">
108+
<DataGrid.Resources>
109+
<Style TargetType="DataGridCell">
110+
<EventSetter Event="MouseDoubleClick" Handler="Row_DoubleClick" />
111+
</Style>
112+
</DataGrid.Resources>
113+
</DataGrid>
114+
<StackPanel Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="1">
115+
<Button x:Name="ClearOutput" Content="Clear" Click="ClearOutput_Click" />
116+
</StackPanel>
117+
</Grid>
118+
</GroupBox>
119+
</Grid>
120+
<Grid Grid.Column="1">
121+
<Grid.RowDefinitions>
122+
<RowDefinition Height="1*" />
123+
<RowDefinition Height="1*" />
124+
</Grid.RowDefinitions>
125+
<GroupBox Header="Tasks" Name="tasksGroupBox">
126+
<Grid>
127+
<Grid.RowDefinitions>
128+
<RowDefinition Height="20" />
129+
<RowDefinition Height="*" />
130+
<RowDefinition Height="20" />
131+
<RowDefinition Height="40" />
132+
</Grid.RowDefinitions>
118133
<StackPanel Orientation="Horizontal" HorizontalAlignment="Center">
119-
<Label x:Name="labelTasks" Content="Tasks" HorizontalAlignment="Center" />
134+
<Button x:Name="addSearchTaskButton" Content="Add Search Task" Click="addSearchTaskButton_Click" />
135+
<Button x:Name="addCalibrateTaskButton" Content="Add Calibrate Task" Click="addCalibrateTaskButton_Click" />
136+
<Button x:Name="addGPTMDTaskButton" Content="Add GPTMD Task" Click="addGPTMDTaskButton_Click" />
120137
</StackPanel>
121-
<DataGrid x:Name="tasksDataGrid" ItemsSource="{Binding}" CanUserSortColumns="False" CanUserResizeColumns="False" CanUserResizeRows="False" CanUserReorderColumns="False" SelectionMode="Single" MouseDoubleClick="tasksDataGrid_MouseDoubleClick" IsReadOnly="True">
138+
<DataGrid x:Name="tasksDataGrid" ItemsSource="{Binding}" CanUserSortColumns="False" CanUserResizeColumns="False" CanUserResizeRows="False" CanUserReorderColumns="False" SelectionMode="Single" MouseDoubleClick="tasksDataGrid_MouseDoubleClick" IsReadOnly="True" Grid.Row="1">
122139
<DataGrid.Resources>
123140
<ResourceDictionary>
124141
<Style x:Key="{x:Type DataGridCell}" TargetType="{x:Type DataGridCell}">
@@ -156,31 +173,29 @@
156173
</ResourceDictionary>
157174
</DataGrid.Resources>
158175
</DataGrid>
159-
<StackPanel Orientation="Horizontal" HorizontalAlignment="Center">
176+
<StackPanel Orientation="Horizontal" HorizontalAlignment="Center" Grid.Row="2">
160177
<Button x:Name="ClearTasksButton" Content="Clear" Click="ClearTasks_Click" />
161178
<Button x:Name="RemoveLastTaskButton" Content="Remove Last Task" Click="RemoveLastTask_Click" />
162179
</StackPanel>
163-
<Button x:Name="RunTasksButton" Content="Run all tasks!" Click="RunAllTasks_Click" Margin="10" FontSize="24" />
164-
</StackPanel>
165-
</Border>
166-
</StackPanel>
167-
168-
<Border BorderBrush="Black" BorderThickness="2" Margin="5" Grid.Column="1" Grid.Row="1">
169-
<StackPanel Margin="5">
170-
<StackPanel Orientation="Horizontal" HorizontalAlignment="Center">
171-
<Label x:Name="labelStatus" Content="Status:" HorizontalAlignment="Center" />
172-
<Label x:Name="statusLabel" Content="Ready" HorizontalAlignment="Center" />
173-
</StackPanel>
174-
<ProgressBar x:Name="outProgressBar" Height="15" />
175-
<RichTextBox x:Name="outRichTextBox" Height="200" VerticalScrollBarVisibility="Visible" IsReadOnly="True">
176-
<RichTextBox.Resources>
177-
<Style TargetType="{x:Type Paragraph}">
178-
<Setter Property="Margin" Value="0" />
179-
</Style>
180-
</RichTextBox.Resources>
181-
</RichTextBox>
182-
</StackPanel>
183-
</Border>
180+
<Button x:Name="RunTasksButton" Content="Run all tasks!" Click="RunAllTasks_Click" FontSize="24" Grid.Row="3"/>
181+
</Grid>
182+
</GroupBox>
183+
<GroupBox Header="Status" Grid.Row="1">
184+
<DockPanel>
185+
<StackPanel Orientation="Horizontal" HorizontalAlignment="Center" DockPanel.Dock="Top">
186+
<Label x:Name="statusLabel" Content="Ready" HorizontalAlignment="Center" />
187+
</StackPanel>
188+
<ProgressBar x:Name="outProgressBar" DockPanel.Dock="Top" Height="20"/>
189+
<RichTextBox x:Name="outRichTextBox" VerticalScrollBarVisibility="Visible" IsReadOnly="True">
190+
<RichTextBox.Resources>
191+
<Style TargetType="{x:Type Paragraph}">
192+
<Setter Property="Margin" Value="0" />
193+
</Style>
194+
</RichTextBox.Resources>
195+
</RichTextBox>
196+
</DockPanel>
197+
</GroupBox>
198+
</Grid>
184199
</Grid>
185-
</StackPanel>
200+
</DockPanel>
186201
</Window>

‎GUI/MainWindow.xaml.cs

+6-21
Original file line numberDiff line numberDiff line change
@@ -41,13 +41,6 @@ public MainWindow()
4141
tasksDataGrid.DataContext = taskEngineObservableCollection;
4242
outputFilesDataGrid.DataContext = finishedFileObservableCollection;
4343

44-
//proteinDbObservableCollection.Add(new XMLdb(@"C:\Users\stepa\Data\CalibrationPaperData\OrigData\uniprot-mouse-reviewed-1-23-2017.xml"));
45-
//proteinDbObservableCollection.Add(new XMLdb(@"C:\Users\stepa\Data\CalibrationPaperData\OrigData\uniprot-human-reviewed-1-23-2017.xml"));
46-
47-
//rawDataObservableCollection.Add(new RawData(@"C:\Users\stepa\Downloads\small.pwiz.1.1.mzML"));
48-
49-
//rawDataObservableCollection.Add(new RawData(@"C:\Users\stepa\Data\CalibrationPaperData\OrigData\Mouse\2017-01-30-19-07-49\Task1Calibrate\04-30-13_CAST_Frac5_4uL-Calibrated.mzML"));
50-
5144
EverythingRunnerEngine.newDbsHandler += AddNewDB;
5245
EverythingRunnerEngine.newSpectrasHandler += AddNewSpectra;
5346

@@ -408,13 +401,9 @@ private void NewSuccessfullyStartingAllTasks(object sender, EventArgs e)
408401
}
409402
else
410403
{
411-
//TODO: Check those
412-
XMLdbPanel.IsEnabled = false;
413-
DatafilesStackPanel.IsEnabled = false;
414-
addSearchTaskButton.IsEnabled = false;
415-
addCalibrateTaskButton.IsEnabled = false;
416-
addGPTMDTaskButton.IsEnabled = false;
417-
tasksPanel.IsEnabled = false;
404+
proteinDatabasesGroupBox.IsEnabled = false;
405+
datafilesGroupBox.IsEnabled = false;
406+
tasksGroupBox.IsEnabled = false;
418407

419408
statusLabel.Content = "Starting all tasks...";
420409
outProgressBar.IsIndeterminate = true;
@@ -431,13 +420,9 @@ private void NewSuccessfullyFinishedAllTasks(object sender, EventArgs e)
431420
}
432421
else
433422
{
434-
//TODO: Check those
435-
XMLdbPanel.IsEnabled = true;
436-
DatafilesStackPanel.IsEnabled = true;
437-
addSearchTaskButton.IsEnabled = true;
438-
addCalibrateTaskButton.IsEnabled = true;
439-
addGPTMDTaskButton.IsEnabled = true;
440-
tasksPanel.IsEnabled = true;
423+
proteinDatabasesGroupBox.IsEnabled = true;
424+
datafilesGroupBox.IsEnabled = true;
425+
tasksGroupBox.IsEnabled = true;
441426

442427
statusLabel.Content = "Finished all tasks!";
443428
outProgressBar.IsIndeterminate = false;

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