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[WIP] Tims tof #2462

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[WIP] Tims tof #2462

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0ebbd89
timsTof search is working?
Alexander-Sol Sep 15, 2024
8b0d539
idk
Alexander-Sol Sep 23, 2024
6d2f1e4
IDK
Alexander-Sol Dec 9, 2024
e74356d
Merge branch 'master' into timsTOF
Alexander-Sol Dec 9, 2024
f63180e
updated mzLib to local version
Alexander-Sol Dec 10, 2024
1ee4858
Updated nuget
Alexander-Sol Jan 30, 2025
9aee1b6
Merge branch 'master' into timsTof
Alexander-Sol Jan 30, 2025
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3 changes: 3 additions & 0 deletions MetaMorpheus/CMD/CMD.csproj
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Expand Up @@ -26,6 +26,9 @@
<PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
<PackageReference Include="mzLib" Version="1.0.558" />
<PackageReference Include="Nett" Version="0.15.0" />
<PackageReference Include="SQLite.Interop.dll" Version="1.0.103" />
<PackageReference Include="System.Data.SQLite" Version="1.0.118" />
<PackageReference Include="System.Data.SQLite.Core" Version="1.0.118" />
</ItemGroup>

<ItemGroup>
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3 changes: 3 additions & 0 deletions MetaMorpheus/EngineLayer/EngineLayer.csproj
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Expand Up @@ -25,6 +25,9 @@
<PackageReference Include="NETStandard.Library" Version="2.0.3" />
<PackageReference Include="Nett" Version="0.15.0" />
<PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
<PackageReference Include="SQLite.Interop.dll" Version="1.0.103" />
<PackageReference Include="System.Data.SQLite" Version="1.0.118" />
<PackageReference Include="System.Data.SQLite.Core" Version="1.0.118" />
<PackageReference Include="TopDownProteomics" Version="0.0.297" />
</ItemGroup>

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10 changes: 10 additions & 0 deletions MetaMorpheus/GUI/GUI.csproj
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Expand Up @@ -19,6 +19,13 @@
<EnableWindowsTargeting>true</EnableWindowsTargeting>
</PropertyGroup>

<PropertyGroup>
<ContentSQLiteInteropFiles>true</ContentSQLiteInteropFiles>
<CopySQLiteInteropFiles>false</CopySQLiteInteropFiles>
<CleanSQLiteInteropFiles>false</CleanSQLiteInteropFiles>
<CollectSQLiteInteropFiles>false</CollectSQLiteInteropFiles>
</PropertyGroup>

<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|AnyCPU'">
<PlatformTarget>x64</PlatformTarget>
</PropertyGroup>
Expand Down Expand Up @@ -63,9 +70,12 @@
<PackageReference Include="SharpLearning.CrossValidation" Version="0.31.8" />
<PackageReference Include="SharpLearning.GradientBoost" Version="0.31.8" />
<PackageReference Include="SharpLearning.Metrics" Version="0.31.8" />
<PackageReference Include="SQLite.Interop.dll" Version="1.0.103" />
<PackageReference Include="System.Buffers" Version="4.5.1" />
<PackageReference Include="System.CodeDom" Version="8.0.0" />
<PackageReference Include="System.Collections.Immutable" Version="8.0.0" />
<PackageReference Include="System.Data.SQLite" Version="1.0.118" />
<PackageReference Include="System.Data.SQLite.Core" Version="1.0.118" />
<PackageReference Include="System.Drawing.Common" Version="8.0.7" />
<PackageReference Include="System.Memory" Version="4.5.5" />
<PackageReference Include="System.Numerics.Vectors" Version="4.5.0" />
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2 changes: 1 addition & 1 deletion MetaMorpheus/GUI/MainWindow.xaml
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Expand Up @@ -458,7 +458,7 @@

<!--Detail text-->
<TextBlock Grid.Row="1" Style="{StaticResource TextBlockStyle}">
Add spectra file(s) in .mzML, .mgf, or Thermo .raw format.
Add spectra file(s) in .mzML, .mgf, Thermo .raw, or Bruker .d formats. Bruker files can only be added by dragging and dropping into the window.
</TextBlock>

<!--Button to add spectra files-->
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24 changes: 17 additions & 7 deletions MetaMorpheus/GUI/MainWindow.xaml.cs
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Expand Up @@ -19,6 +19,7 @@
using System.Windows.Navigation;
using Omics.Modifications;
using TaskLayer;
using System.Text.RegularExpressions;

namespace MetaMorpheusGUI
{
Expand Down Expand Up @@ -516,7 +517,7 @@ private void Window_Drop(object sender, DragEventArgs e)
/// </summary>
private void AddSpectraFile_Click(object sender, RoutedEventArgs e)
{
var openPicker = StartOpenFileDialog("Spectra Files(*.raw;*.mzML;*.mgf)|*.raw;*.mzML;*.mgf");
var openPicker = StartOpenFileDialog("Spectra Files(*.raw;*.mzML;*.mgf;*.d)|*.raw;*.mzML;*.mgf;*.d");

if (openPicker.ShowDialog() == true)
{
Expand Down Expand Up @@ -1513,14 +1514,14 @@ private void AddPreRunFiles(IEnumerable<string> paths)
{
foreach (string path in paths.OrderBy(p => Path.GetFileName(p)))
{
if (Directory.Exists(path))
if (Directory.Exists(path) & !Regex.IsMatch(path, @".d$")) // don't add directories that end in ".d" (bruker data files)
{
foreach (string file in Directory.EnumerateFiles(path, "*.*", SearchOption.AllDirectories))
{
AddPreRunFile(file);
}
}
else if (File.Exists(path))
else if (File.Exists(path) || Regex.IsMatch(path, @".d$"))
{
AddPreRunFile(path);
}
Expand Down Expand Up @@ -1571,13 +1572,13 @@ private void AddPreRunFile(string filePath)
return;
}
}

goto case ".mzml";

case ".mgf":
NotificationHandler(null, new StringEventArgs(".mgf files lack MS1 spectra, which are needed for quantification and searching for coisolated peptides. All other features of MetaMorpheus will function.", null));
goto case ".mzml";

case ".d": // Bruker data files are directories that contain .d files
NotificationHandler(null, new StringEventArgs("Quantification and calibration are not currently supported for Bruker data files. All other features of MetaMorpheus will function.", null));
goto case ".mzml";
case ".mzml":
if (compressed) // not implemented yet
{
Expand All @@ -1592,7 +1593,6 @@ private void AddPreRunFile(string filePath)
UpdateFileSpecificParamsDisplay(Path.ChangeExtension(filePath, ".toml"));
UpdateOutputFolderTextbox();
break;

case ".xml":
case ".fasta":
case ".fa":
Expand Down Expand Up @@ -1700,6 +1700,16 @@ private OpenFileDialog StartOpenFileDialog(string filter)
return openFileDialog;
}

private OpenFolderDialog StartOpenFolderDialog(string filter)
{
OpenFolderDialog openFileDialog = new OpenFolderDialog
{
Multiselect = true
};

return openFileDialog;
}

private void OpenNewTaskWindow(MyTask taskType)
{
Window dialog = null;
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3 changes: 3 additions & 0 deletions MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj
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Expand Up @@ -53,6 +53,9 @@
</ProjectReference>
</ItemGroup>
<ItemGroup>
<PackageReference Include="SQLite.Interop.dll" Version="1.0.103" />
<PackageReference Include="System.Data.SQLite" Version="1.0.118" />
<PackageReference Include="System.Data.SQLite.Core" Version="1.0.118" />
<PackageReference Include="WixToolset.Util.wixext" Version="5.0.1" />
<PackageReference Include="WixToolset.UI.wixext" Version="5.0.1" />
</ItemGroup>
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13 changes: 13 additions & 0 deletions MetaMorpheus/MetaMorpheusSetup/Product.wxs
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Expand Up @@ -285,6 +285,19 @@
<Component Id="src_ThermoFisher.CommonCore.RawFileReader.dll" Guid="F5EDAA70-06CD-49E7-932F-016C679B07C7">
<File Id="src_ThermoFisher.CommonCore.RawFileReader.dll" Name="ThermoFisher.CommonCore.RawFileReader.dll" Source="$(var.GUI_TargetDir)ThermoFisher.CommonCore.RawFileReader.dll" />
</Component>

<Component Id="src_System.Data.SQLite.dll" Guid="b447a0f4-4f79-45aa-a225-069c27912fe3">
<File Id="src_System.Data.SQLite.dll" Name="System.Data.SQLite.dll" Source="$(var.GUI_TargetDir)System.Data.SQLite.dll" />
</Component>
<Component Id="src_System.Data.SQLite.EF6.dll" Guid="287eac83-051e-491f-8f75-f28cb742c35c">
<File Id="src_System.Data.SQLite.EF6.dll" Name="System.Data.SQLite.EF6.dll" Source="$(var.GUI_TargetDir)System.Data.SQLite.EF6.dll" />
</Component>

<Component Id="src_timsdata.dll" Guid="c40543fb-86cc-4fcc-a4f8-d7c536cab5ec">
<File Id="src_timsdata.dll" Name="timsdata.dll" Source="$(var.GUI_TargetDir)timsdata.dll" />
</Component>


<Component Id="src_BayesianEstimation.dll" Guid="100F4A2E-F4FE-4D25-8C5F-66A7092A2622">
<File Id="src_BayesianEstimation.dll" Name="BayesianEstimation.dll" Source="$(var.GUI_TargetDir)BayesianEstimation.dll" />
</Component>
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3 changes: 3 additions & 0 deletions MetaMorpheus/TaskLayer/TaskLayer.csproj
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,9 @@
<PackageReference Include="mzLib" Version="1.0.558" />
<PackageReference Include="NetSerializer" Version="4.1.2" />
<PackageReference Include="Nett" Version="0.15.0" />
<PackageReference Include="SQLite.Interop.dll" Version="1.0.103" />
<PackageReference Include="System.Data.SQLite" Version="1.0.118" />
<PackageReference Include="System.Data.SQLite.Core" Version="1.0.118" />
</ItemGroup>

<ItemGroup>
Expand Down