update mzLib, other small changes

smith-chem-wisc · Oct 2, 2020 · e4dbb10 · e4dbb10
1 parent 41b502f
commit e4dbb10
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Showing 7 changed files with 25 additions and 18 deletions.
diff --git a/CMD/CMD.csproj b/CMD/CMD.csproj
@@ -16,7 +16,7 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.7.82" />
     <PackageReference Include="MathNet.Numerics" Version="4.9.0" />
-    <PackageReference Include="mzLib" Version="1.0.472" />
+    <PackageReference Include="mzLib" Version="1.0.476" />
     <PackageReference Include="NetSerializer" Version="4.1.1" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SharpLearning.Common.Interfaces" Version="0.28.0" />

diff --git a/CMD/FlashLFQExecutable.cs b/CMD/FlashLFQExecutable.cs
@@ -1,6 +1,7 @@
 using CommandLine;
 using CommandLine.Text;
 using FlashLFQ;
+using IO.ThermoRawFileReader;
 using System;
 using System.Collections.Generic;
 using System.Diagnostics;
@@ -85,7 +86,7 @@ private static void Run(FlashLfqSettings settings)
 
             if (settings.PrintThermoLicenceViaCommandLine)
             {
-                Console.WriteLine(ThermoRawFileReader.ThermoRawFileReaderLicence.ThermoLicenceText);
+                Console.WriteLine(ThermoRawFileReaderLicence.ThermoLicenceText);
                 return;
             }
 
@@ -106,7 +107,7 @@ private static void Run(FlashLfqSettings settings)
                     else
                     {
                         // decided to write this even if it's on silent mode...
-                        Console.WriteLine(ThermoRawFileReader.ThermoRawFileReaderLicence.ThermoLicenceText);
+                        Console.WriteLine(ThermoRawFileReaderLicence.ThermoLicenceText);
                         Console.WriteLine("\nIn order to search Thermo .raw files, you must agree to the above terms. Do you agree to the above terms? y/n\n");
 
                         string res = Console.ReadLine();

diff --git a/Dockerfile b/Dockerfile
@@ -1,7 +1,7 @@
 ## Base image is the Alpine Linux distro with .NET Core runtime
 FROM mcr.microsoft.com/dotnet/core/runtime:3.1-alpine AS build
 
-## Copies FlashLFQ_CommandLine.zip from the current directory into the Docker image
+## Copies contents of the "publish" folder into the Docker image
 ADD CMD/bin/Release/netcoreapp3.1/publish/ /flashlfq/
 
 ## Set the entrypoint of the Docker image to CMD.dll

diff --git a/GUI/GUI.csproj b/GUI/GUI.csproj
@@ -16,7 +16,7 @@
 
   <ItemGroup>
     <PackageReference Include="MathNet.Numerics" Version="4.9.0" />
-    <PackageReference Include="mzLib" Version="1.0.472" />
+    <PackageReference Include="mzLib" Version="1.0.476" />
     <PackageReference Include="NetSerializer" Version="4.1.1" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SharpLearning.Common.Interfaces" Version="0.28.0" />

diff --git a/GUI/MainWindow.xaml.cs b/GUI/MainWindow.xaml.cs
@@ -1,5 +1,6 @@
 using FlashLFQ;
 using GUI.DataGridObjects;
+using IO.ThermoRawFileReader;
 using System;
 using System.Collections.Generic;
 using System.Collections.ObjectModel;
@@ -57,7 +58,6 @@ public MainWindow()
             idFiles = new ObservableCollection<IdentificationFileForDataGrid>();
             worker = new BackgroundWorker();
             worker.DoWork += new DoWorkEventHandler(RunProgram);
-            worker.RunWorkerCompleted += Worker_RunWorkerCompleted;
 
             flashLfqEngine = new FlashLfqEngine(new List<Identification>());
 
@@ -71,14 +71,6 @@ public MainWindow()
             Console.SetOut(_writer);
         }
 
-        private void Worker_RunWorkerCompleted(object sender, RunWorkerCompletedEventArgs e)
-        {
-            if (e.Error == null)
-            {
-                MessageBox.Show("Run complete");
-            }
-        }
-
         private void PopulateSettings()
         {
             settings = new FlashLfqSettings();
@@ -122,7 +114,7 @@ private void ParseSettings()
             }
 
             settings.ProteinQuantFoldChangeCutoff = double.Parse(FoldChangeCutoffManualTextBox.Text, CultureInfo.InvariantCulture);
-            
+
             // ppm tolerance
             if (double.TryParse(ppmToleranceTextBox.Text, NumberStyles.Number, CultureInfo.InvariantCulture, out double ppmTolerance))
             {
@@ -304,7 +296,7 @@ private void AddAFile(string filePath)
                 if (!licenceAgreement.HasAcceptedThermoLicence)
                 {
                     var thermoLicenceWindow = new ThermoLicenceAgreementWindow();
-                    thermoLicenceWindow.LicenceText.AppendText(ThermoRawFileReader.ThermoRawFileReaderLicence.ThermoLicenceText);
+                    thermoLicenceWindow.LicenceText.AppendText(ThermoRawFileReaderLicence.ThermoLicenceText);
                     var dialogResult = thermoLicenceWindow.ShowDialog();
 
                     if (dialogResult.HasValue && dialogResult.Value == true)
@@ -550,6 +542,18 @@ private void RunFlashLfq()
                 return;
             }
 
+            if (ids.Any(p => p.Ms2RetentionTimeInMinutes > 500))
+            {
+                var res = MessageBox.Show("It seems that some of the retention times in the PSM file(s) are in seconds and not minutes; FlashLFQ requires the RT to be in minutes. " +
+                    "Continue with the FlashLFQ run? (only click yes if the RTs are actually in minutes)",
+                    "Error", MessageBoxButton.YesNo, MessageBoxImage.Hand);
+
+                if (res == MessageBoxResult.No)
+                {
+                    return;
+                }
+            }
+
             // run FlashLFQ engine
             try
             {
@@ -592,6 +596,8 @@ private void RunFlashLfq()
                 {
                     OutputWriter.WriteOutput(Directory.GetParent(spectraFiles.First().FilePath).FullName, results, flashLfqEngine.Silent,
                         outputFolderPath);
+
+                    MessageBox.Show("Run complete");
                 }
                 catch (Exception ex)
                 {

diff --git a/Test/Test.csproj b/Test/Test.csproj
@@ -14,7 +14,7 @@
 
   <ItemGroup>
     <PackageReference Include="MathNet.Numerics" Version="4.9.0" />
-    <PackageReference Include="mzLib" Version="1.0.472" />
+    <PackageReference Include="mzLib" Version="1.0.476" />
     <PackageReference Include="NetSerializer" Version="4.1.1" />
     <PackageReference Include="nunit" Version="3.12.0" />
     <PackageReference Include="NUnit3TestAdapter" Version="3.13.0" />

diff --git a/Util/Util.csproj b/Util/Util.csproj
@@ -14,7 +14,7 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.7.82" />
     <PackageReference Include="MathNet.Numerics" Version="4.9.0" />
-    <PackageReference Include="mzLib" Version="1.0.472" />
+    <PackageReference Include="mzLib" Version="1.0.476" />
     <PackageReference Include="NetSerializer" Version="4.1.1" />
     <PackageReference Include="Nett" Version="0.15.0" />
   </ItemGroup>