From 1a28c1a9a8bba57152761755b45367f8ca9937d5 Mon Sep 17 00:00:00 2001
From: trishorts <mshort@chem.wisc.edu>
Date: Wed, 13 Sep 2023 11:38:43 -0500
Subject: [PATCH 1/2] Ms2scan with specific mass eliminate unused code (#2303)

* reverted filtering method for psms passed to FlashLFQ

* two unused methods gone

* eliminate space

---------

Co-authored-by: Alex <AlexSolivais@gmail.com>
Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
Co-authored-by: Nic Bollis <nbollis@comcast.net>
---
 .../EngineLayer/Ms2ScanWithSpecificMass.cs    | 41 -------------------
 MetaMorpheus/Test/GPTMDengineTest.cs          |  1 -
 2 files changed, 42 deletions(-)

diff --git a/MetaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs b/MetaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs
index 4e0d8f4c4..394118a1e 100644
--- a/MetaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs
+++ b/MetaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs
@@ -152,46 +152,5 @@ public IsotopicEnvelope[] GetClosestExperimentalIsotopicEnvelopeList(double mini
             IsotopicEnvelope[] isotopicEnvelopes = ExperimentalFragments.Skip(startIndex).Take(length).ToArray();
             return isotopicEnvelopes;
         }
-
-        public double? GetClosestExperimentalFragmentMz(double theoreticalMz, out double? intensity)
-        {
-            if (TheScan.MassSpectrum.XArray.Length == 0)
-            {
-                intensity = null;
-                return null;
-            }
-            intensity = TheScan.MassSpectrum.YArray[GetClosestFragmentMzIndex(theoreticalMz).Value];
-            return TheScan.MassSpectrum.XArray[GetClosestFragmentMzIndex(theoreticalMz).Value];
-        }
-
-        private int? GetClosestFragmentMzIndex(double mz)
-        {
-            if (TheScan.MassSpectrum.XArray.Length == 0)
-            {
-                return null;
-            }
-            int index = Array.BinarySearch(TheScan.MassSpectrum.XArray, mz);
-            if (index >= 0)
-            {
-                return index;
-            }
-            index = ~index;
-
-            if (index >= TheScan.MassSpectrum.XArray.Length)
-            {
-                return index - 1;
-            }
-            if (index == 0)
-            {
-                return index;
-            }
-
-            if (mz - TheScan.MassSpectrum.XArray[index - 1] > TheScan.MassSpectrum.XArray[index] - mz)
-            {
-                return index;
-            }
-            return index - 1;
-
-        }
     }
 }
\ No newline at end of file
diff --git a/MetaMorpheus/Test/GPTMDengineTest.cs b/MetaMorpheus/Test/GPTMDengineTest.cs
index d637e0614..b89790e8e 100644
--- a/MetaMorpheus/Test/GPTMDengineTest.cs
+++ b/MetaMorpheus/Test/GPTMDengineTest.cs
@@ -228,7 +228,6 @@ public static void TestUniProtGptmdConflict()
         {
             // this unit test checks to make sure GPTMD does not annotate mods at residues on 
             // proteins where the equivalent uniprot mod already exists
-
             Modification uniProtPhospho = GlobalVariables.AllModsKnown.First(p => p.ModificationType == "UniProt" && p.IdWithMotif.Contains("Phosphoserine"));
             Modification mmPhospho = GlobalVariables.AllModsKnown.First(p => p.ModificationType == "Common Biological" && p.IdWithMotif.Contains("Phosphorylation on S"));
 

From d9ee5654b63841d23a1c6cfcc4510c800b7d6e3d Mon Sep 17 00:00:00 2001
From: Nic Bollis <nbollis@comcast.net>
Date: Mon, 18 Sep 2023 15:08:53 -0500
Subject: [PATCH 2/2] Added SpectralAveraging.dll to project.wxs (#2310)

* Added averaging dll to project.wxs

* Unhid Button

---------

Co-authored-by: Alexander-Sol <41119316+Alexander-Sol@users.noreply.github.com>
---
 MetaMorpheus/GUI/MainWindow.xaml           | 2 +-
 MetaMorpheus/MetaMorpheusSetup/Product.wxs | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/MetaMorpheus/GUI/MainWindow.xaml b/MetaMorpheus/GUI/MainWindow.xaml
index 1a68e3e86..398e3f961 100644
--- a/MetaMorpheus/GUI/MainWindow.xaml
+++ b/MetaMorpheus/GUI/MainWindow.xaml
@@ -524,7 +524,7 @@
                         <Button Name="AddCalibTaskButton" Grid.Column="0" Content="+ADD CALIBRATION" HorizontalAlignment="Right" Click="AddCalibrateTaskButton_Click" 
                             Style="{StaticResource ImportantButtonStyle}" Margin="0,0,1,0" Width="140"/>
                         <Button Name="AddAveragingTaskButton" Grid.Column="1" Content="+AVERAGE SPECTRA" HorizontalAlignment="Right" Click="AddAveragingTaskButton_OnClick" 
-                                Style="{StaticResource ImportantButtonStyle}" Margin="0, 0, 1, 0" Width="140" FontSize="11" Visibility="Collapsed"/>
+                                Style="{StaticResource ImportantButtonStyle}" Margin="0, 0, 1, 0" Width="140" FontSize="11" Visibility="Visible"/>
                         <Button Name="AddGptmdTaskButton" Grid.Column="2" Content="+ADD PTM DISCOVERY" HorizontalAlignment="Right" Click="AddGPTMDTaskButton_Click" 
                             Style="{StaticResource ImportantButtonStyle}" Margin="0,0,1,0" Width="140"/>
                         <Button Name="AddSearchTaskButton" Grid.Column="3" Content="+ADD SEARCH" HorizontalAlignment="Right" Click="AddSearchTaskButton_Click" 
diff --git a/MetaMorpheus/MetaMorpheusSetup/Product.wxs b/MetaMorpheus/MetaMorpheusSetup/Product.wxs
index 29c84e94c..5d9ec87f8 100644
--- a/MetaMorpheus/MetaMorpheusSetup/Product.wxs
+++ b/MetaMorpheus/MetaMorpheusSetup/Product.wxs
@@ -181,6 +181,9 @@
       <Component Id="src_MassSpectrometry.dll" Guid="d6241678-3d48-4c7a-becf-9c1160fbe06b">
         <File Id="src_MassSpectrometry.dll" Name="MassSpectrometry.dll" Source="$(var.GUI_TargetDir)MassSpectrometry.dll" />
       </Component>
+      <Component Id="src_SpectralAveraging.dll" Guid="{1B9EB148-6FC3-4DA1-82D0-935EDE76E8D7}">
+        <File Id="src_SpectralAveraging.dll" Name="SpectralAveraging.dll" Source="$(var.GUI_TargetDir)SpectralAveraging.dll" />
+      </Component>
       <Component Id="src_MathNet.Numerics.dll" Guid="dea92905-719e-48e1-8a64-e845dca06dac">
         <File Id="src_MathNet.Numerics.dll" Name="MathNet.Numerics.dll" Source="$(var.GUI_TargetDir)MathNet.Numerics.dll" />
       </Component>