<commit_before><?xml version="1.0" encoding="UTF-8"?>
<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi">

  <!--Shorthand way of getting the install directory-->
  <?define GUI_TargetDir=$(var.GUI.TargetDir)?>

  <!--Product compiles into an msi file. Only one can be present.-->
  <!--Version needs to be replaced automatically-->
  <Product Id="*" Name="MetaMorpheus" Language="1033" Version="!(bind.FileVersion.MetaMorpheusGUI.exe)" Manufacturer="Smith Group" UpgradeCode="438ad6ff-f027-423a-ab0b-c73384c0e2e5">

    <!--Properties about the package to be placed in the Summary Information Stream.-->
    <!--These are visible from COM through the IStream interface, and these properties can be seen on the package in Explorer.-->
    <Package Id="*" InstallerVersion="500" Compressed="yes" InstallScope="perMachine" Platform="x64"/>
    <MajorUpgrade AllowSameVersionUpgrades="yes" Schedule="afterInstallValidate" DowngradeErrorMessage="A newer version of MetaMorpheus is already installed."/>

    <Condition Message="This application is only supported on Windows 7 or higher.">
      <![CDATA[Installed OR (VersionNT >= 601)]]>
    </Condition>

    <Condition Message="This application requires 64-bit windows">
      <![CDATA[Installed OR VersionNT64]]>
    </Condition>

    <MediaTemplate EmbedCab="yes"/>



    <!--A feature for the Feature table. Features are the smallest installable unit.-->
    <Feature Id="ProductFeature" Level="1">

      <!-- ComponentGroupRef creates a reference to a ComponentGroup in another Fragment-->
      <ComponentGroupRef Id="ExecutablesAndLibrariesComponentGroup" />
      <!--ComponentRef creates a reference to a Component element in another Fragment-->
      <ComponentRef Id="MetaMorpheusProgramMenuFolderComponent"/>
      <!--App Data Section-->

      <ComponentGroupRef Id="Appsrc_Mods_files"/>
      <ComponentGroupRef Id="Appsrc_Data_files"/>
      <ComponentGroupRef Id="Appsrc_NeoData_files" />
      <ComponentGroupRef Id="Appsrc_NeoTomlFiles_files" />
      <ComponentRef Id="RemoveNeo"/>
      <ComponentRef Id="MetaAppsettings.toml"/>
      <ComponentRef Id="MetaAppGUIsettings.toml"/>
      <ComponentRef Id="RemoveApp"/>
      <ComponentRef Id="DesktopShortcut"/>
    </Feature>

    <Directory Id="TARGETDIR" Name="SourceDir">
      <!--Desktop Shortcut Installation-->
      <Directory Id="DesktopFolder" Name="Desktop">
        <Component Id="DesktopShortcut" Guid="ef1fd292-b162-4990-80cb-cd2a0c839d4b">
          <Condition>INSTALLDESKTOPSHORTCUT</Condition>
          <RegistryKey Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Action="createAndRemoveOnUninstall">
            <RegistryValue Name="MetaMorpheusDeskTop" Value="1" Type="integer" KeyPath="yes"/>
          </RegistryKey>
          <Shortcut Id="AppDeskTopSC" Name="MetaMorpheus" Description="Shortcut to App" Target="[#MetaMorpheusGUI.exe]" WorkingDirectory="MetaMorpheusInstallFolder" />
        </Component>
      </Directory>

      <Directory Id="ProgramFiles64Folder">
        <Directory Id="MetaMorpheusInstallFolder" Name="MetaMorpheus">
          <Directory Id="DataFolder" Name="Data" />
          <Directory Id="ModsFolder" Name="Mods" />
          <Directory Id="NeoFolder" Name="Neo">
            <Directory Id="NeoDataFolder" Name="Data" />
            <Directory Id="NeoTomlFilesFolder" Name="TomlFiles" />
          </Directory>
        </Directory>
      </Directory>
      <Directory Id="ProgramMenuFolder">
        <Directory Id="MetaMorpheusProgramMenuFolder" Name="MetaMorpheus">

        </Directory>
      </Directory>
      <Directory Id="LocalAppDataFolder">
        <Directory Id="MetaMorpheusAppFolder" Name="MetaMorpheus">
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            <Condition>OVERWRITEAPPDATA</Condition>
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            <File Id="settings.toml" Name="settings.toml" Source="$(var.GUI_TargetDir)settings.toml" />
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            <Condition>OVERWRITEAPPDATA</Condition>
            <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
            <File Id="GUIsettings.toml" Name="GUIsettings.toml" Source="$(var.GUI_TargetDir)GUIsettings.toml" />
          </Component>
          <Component Id="RemoveApp" Guid="a5443b89-65b0-4855-b521-e7bcc9c5a85c">
            <RemoveFolder Id="MetaMorpheusAppFolder" On="uninstall"/>
            <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
          </Component>
          <Directory Id="MetaAppDataFolder" Name="Data" />
          <Directory Id="MetaAppModsFolder" Name="Mods" />
          <Directory Id="NeoAppFolder" Name="Neo">
            <Directory Id="MetaAppNeoDataFolder" Name="Data" />
            <Directory Id="MetaAppNeoTomlFilesFolder" Name="TomlFiles" />
            <Component Id="RemoveNeo" Guid="af5ff12f-ef0c-4945-be30-36c00ea734e9">
              <RemoveFolder Id="NeoAppFolder" On="uninstall"/>
              <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
            </Component>
          </Directory>
        </Directory>
      </Directory>
    </Directory>

    <UI>
      <UIRef Id="WixUI_Mondo"/>
      <UIRef Id="newDlg"/>
      <UIRef Id="MyMaintenance"/>
      <Publish Dialog="WelcomeDlg" Control="Next" Event="NewDialog" Value="MetaSCDlg" Order="1">1</Publish>
      <Publish Dialog="MetaSCDlg" Control="Back" Event="NewDialog" Value="WelcomeDlg" Order="1">1</Publish>
      <Publish Dialog="MetaSCDlg" Control="Next" Event="NewDialog" Value="VerifyReadyDlg" Order="1">1</Publish>

      <Publish Dialog="VerifyReadyDlg" Control="Back" Event="NewDialog" Value="MetaSCDlg" Order="1">1</Publish>
      <Publish Dialog="MaintenanceWelcomeDlg" Control="Next" Event="NewDialog" Value="MyMaintenanceTypeDlg">1</Publish>
      <Publish Dialog="MyMaintenanceTypeDlg" Control="Back" Event="NewDialog" Value="MaintenanceWelcomeDlg" Order="1">1</Publish>
      <!--<Publish Dialog="MyMaintenanceTypeDlg" Control="Next" Event="NewDialog" Value="ExitDialog" Order="1">1</Publish>-->

      <Publish Dialog="ExitDialog"
        Control="Finish"
        Event="DoAction"
        Value="LaunchApplication">WIXUI_EXITDIALOGOPTIONALCHECKBOX = 1 and NOT Installed</Publish>

    </UI>


    <CustomAction Id='LaunchFile' FileKey='MetaMorpheusGUI.exe' ExeCommand='' Return="asyncNoWait" />
    <Property Id="OVERWRITEAPPDATA" Value="1" />
    <Property Id="WIXUI_MONDO" Value="INSTALLFOLDER" />
    <Property Id="WIXUI_EXITDIALOGOPTIONALCHECKBOXTEXT" Value="Launch MetaMorpheus" />
    <Property Id="WixShellExecTarget" Value="[#MetaMorpheusGUI.exe]" />
    <CustomAction Id="LaunchApplication" BinaryKey="WixCA" DllEntry="WixShellExec" Impersonate="yes" />

  </Product>

  <!--Executables and libraries-->
  <Fragment>
    <ComponentGroup Id="ExecutablesAndLibrariesComponentGroup" Directory="MetaMorpheusInstallFolder">
      <Component Id="MetaMorpheusGUI.exe" Guid="63370d96-1880-40ab-8525-685ccf64326f">
        <File Id="MetaMorpheusGUI.exe" Name="MetaMorpheusGUI.exe" Source="$(var.GUI_TargetDir)MetaMorpheusGUI.exe" />
      </Component>
      <Component Id="app.manifest" Guid="d894958a-07c1-4078-9e0e-081a6cc29030">
        <File Id="app.manifest" Name="app.manifest" Source="$(var.GUI_TargetDir)app.manifest" />
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      <Component Id="src_TaskLayer.pdb" Guid="6ece566a-22ff-4208-bba2-ad0430eeee49">
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      <Component Id="src_UnmanagedThermoHelperLayer.dll" Guid="18bed74c-eedb-4efa-a6e3-1592ac7022e3">
        <File Id="src_UnmanagedThermoHelperLayer.dll" Name="UnmanagedThermoHelperLayer.dll" Source="$(var.GUI_TargetDir)UnmanagedThermoHelperLayer.dll" />
      </Component>
      <Component Id="src_Thermo.dll">
        <File Id="src_Thermo.dll" Name="Thermo.dll" Source="$(var.GUI_TargetDir)Thermo.dll" />
      </Component>
      <Component Id="src_Newtonsoft.Json.dll">
        <File Id="src_Newtonsoft.Json.dll" Name="Newtonsoft.Json.dll" Source="$(var.GUI_TargetDir)Newtonsoft.Json.dll" />
      </Component>
      <Component Id="src_UsefulProteomicsDatabases.dll" Guid="e7f76fbf-d21c-4e57-bed4-33f71822ee18">
        <File Id="src_UsefulProteomicsDatabases.dll" Name="UsefulProteomicsDatabases.dll" Source="$(var.GUI_TargetDir)UsefulProteomicsDatabases.dll" />
      </Component>
      <Component Id="src_TaskLayer.dll" Guid="7d468a75-d294-432e-bd59-8fcf1e254486">
        <File Id="src_TaskLayer.dll" Name="TaskLayer.dll" Source="$(var.GUI_TargetDir)TaskLayer.dll" />
      </Component>
      <Component Id="src_MetaMorpheusGUI.exe.config" Guid="929da846-1537-40ba-b615-2335b32cadb1">
        <File Id="src_MetaMorpheusGUI.exe.config" Name="MetaMorpheusGUI.exe.config" Source="$(var.GUI_TargetDir)MetaMorpheusGUI.exe.config" />
      </Component>
      <Component Id="src_Chemistry.dll" Guid="bd4869a2-82a3-4d52-97b7-888881ae1827">
        <File Id="src_Chemistry.dll" Name="Chemistry.dll" Source="$(var.GUI_TargetDir)Chemistry.dll" />
      </Component>
      <Component Id="src_EngineLayer.dll" Guid="ebfe6a93-fdc4-4cff-a510-ff516e532d50">
        <File Id="src_EngineLayer.dll" Name="EngineLayer.dll" Source="$(var.GUI_TargetDir)EngineLayer.dll" />
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      <Component Id="src_EngineLayer.pdb" Guid="8f9592a4-02b1-4462-a259-f7aa41d890a4">
        <File Id="src_EngineLayer.pdb" Name="EngineLayer.pdb" Source="$(var.GUI_TargetDir)EngineLayer.pdb" />
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      <Component Id="src_FlashLFQ.dll" Guid="69e33379-5301-49db-8913-4d777ed5a5f9">
        <File Id="src_FlashLFQ.dll" Name="FlashLFQ.dll" Source="$(var.GUI_TargetDir)FlashLFQ.dll" />
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      <Component Id="src_ManagedThermoHelperLayer.dll" Guid="5706aec2-8e67-4094-ac81-95cd9aa9a49e">
        <File Id="src_ManagedThermoHelperLayer.dll" Name="ManagedThermoHelperLayer.dll" Source="$(var.GUI_TargetDir)ManagedThermoHelperLayer.dll" />
      </Component>
      <Component Id="src_MassSpectrometry.dll" Guid="d6241678-3d48-4c7a-becf-9c1160fbe06b">
        <File Id="src_MassSpectrometry.dll" Name="MassSpectrometry.dll" Source="$(var.GUI_TargetDir)MassSpectrometry.dll" />
      </Component>
      <Component Id="src_MathNet.Numerics.dll" Guid="dea92905-719e-48e1-8a64-e845dca06dac">
        <File Id="src_MathNet.Numerics.dll" Name="MathNet.Numerics.dll" Source="$(var.GUI_TargetDir)MathNet.Numerics.dll" />
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      <Component Id="src_MetaMorpheusGUI.pdb" Guid="bf568e2b-42c1-4209-9f45-11a3af86110a">
        <File Id="src_MetaMorpheusGUI.pdb" Name="MetaMorpheusGUI.pdb" Source="$(var.GUI_TargetDir)MetaMorpheusGUI.pdb" />
      </Component>
      <Component Id="src_mzIdentML.dll" Guid="cb1200d2-2356-4664-8968-bff79c83eeac">
        <File Id="src_mzIdentML.dll" Name="mzIdentML.dll" Source="$(var.GUI_TargetDir)mzIdentML.dll" />
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      <Component Id="src_MzLibUtil.dll" Guid="9475fcb2-63bd-490c-8441-17a1760869ac">
        <File Id="src_MzLibUtil.dll" Name="MzLibUtil.dll" Source="$(var.GUI_TargetDir)MzLibUtil.dll" />
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      <Component Id="src_MzML.dll" Guid="40c12490-638a-41b9-9e0c-05e949236a5a">
        <File Id="src_MzML.dll" Name="MzML.dll" Source="$(var.GUI_TargetDir)MzML.dll" />
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      <Component Id="src_NetSerializer.dll" Guid="9eddc340-0dcb-415a-85f4-322f0eaeee4b">
        <File Id="src_NetSerializer.dll" Name="NetSerializer.dll" Source="$(var.GUI_TargetDir)NetSerializer.dll" />
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      <Component Id="src_Nett.dll" Guid="656c78ef-0234-4e45-957c-a6dd6fff044f">
        <File Id="src_Nett.dll" Name="Nett.dll" Source="$(var.GUI_TargetDir)Nett.dll" />
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      <Component Id="src_Nett.pdb" Guid="68030b29-c0fe-4287-9b7b-aa07f0cc153a">
        <File Id="src_Nett.pdb" Name="Nett.pdb" Source="$(var.GUI_TargetDir)Nett.pdb" />
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      <Component Id="src_SharpLearning.Metrics.dll" Guid="9ec3dd96-8228-49db-98e7-4288845b63a4">
        <File Id="src_SharpLearning.Metrics.dll" Name="SharpLearning.Metrics.dll" Source="$(var.GUI_TargetDir)SharpLearning.Metrics.dll" />
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        <File Id="src_SharpLearning.Optimization.dll" Name="SharpLearning.Optimization.dll" Source="$(var.GUI_TargetDir)SharpLearning.Optimization.dll" />
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      <Component Id="src_SharpLearning.GradientBoost.dll">
        <File Id="src_SharpLearning.GradientBoost.dll" Name="SharpLearning.GradientBoost.dll" Source="$(var.GUI_TargetDir)SharpLearning.GradientBoost.dll" />
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      <Component Id="src_System.Security.SecureString.dll" Guid="58b65b98-6752-4030-badc-ff30f2d160e3">
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    </ComponentGroup>
  </Fragment>

  <!--Build the App Mods folder-->
  <Fragment>
    <ComponentGroup Id="Appsrc_Mods_files" Directory="MetaAppModsFolder">
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      </Component>
      
      <!-- aListOfmods.txt -->
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        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
      </Component>
      
      <!-- detachers.txt -->
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        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_detachers.txt" Name="detachers.txt" Source="$(var.GUI_TargetDir)Mods\detachers.txt" />
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      <!-- fallOff.txt -->
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        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_fallOff.txt" Name="fallOff.txt" Source="$(var.GUI_TargetDir)Mods\fallOff.txt" />
      </Component>
      
      <!-- glyco.txt -->
      <Component Id="Appsrc_Mods_glyco.txt" Guid="1707b26b-070e-46d5-9632-f1bc8bf4d281">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_glyco.txt" Name="glyco.txt" Source="$(var.GUI_TargetDir)Mods\glyco.txt" />
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      <!-- missing.txt -->
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        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_missing.txt" Name="missing.txt" Source="$(var.GUI_TargetDir)Mods\missing.txt" />
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      <!-- Mods.txt -->
      <Component Id="Appsrc_Mods_Mods.txt" Guid="9be193e3-266c-4c1d-9973-341f0a5d108a">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_Mods.txt" Name="Mods.txt" Source="$(var.GUI_TargetDir)Mods\Mods.txt" />
      </Component>
      
      <!-- substitutions.txt -->
      <Component Id="Appsrc_Mods_substitutions.txt" Guid="f108606b-f9eb-4c3c-893b-7ec33c88a1d1">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_substitutions.txt" Name="substitutions.txt" Source="$(var.GUI_TargetDir)Mods\substitutions.txt" />
      </Component>
      
      <!-- surfactants.txt -->
      <Component Id="Appsrc_Mods_surfactants.txt" Guid="937d6734-a4c0-469a-b070-64bf5de84b13">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_surfactants.txt" Name="surfactants.txt" Source="$(var.GUI_TargetDir)Mods\surfactants.txt" />
      </Component>
      
      <!-- tmt.txt -->
      <Component Id="Appsrc_Mods_tmt.txt" Guid="f064b7a0-c650-4a40-8a9f-301cc6cb946e">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_tmt.txt" Name="tmt.txt" Source="$(var.GUI_TargetDir)Mods\tmt.txt" />
      </Component>
      
      <!-- Crosslink.txt -->
      <Component Id="Appsrc_Mods_Crosslink.txt" Guid="172f7116-4772-4f3b-a48b-b1e98a48b73d">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_Crosslink.txt" Name="Crosslink.txt" Source="$(var.GUI_TargetDir)Mods\Crosslink.txt" />
      </Component>
      
      <!-- RNA.txt -->
      <Component Id="Appsrc_Mods_RNA.txt" Guid="99f09cd8-fbe1-454d-8cb3-9cc46de33515">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_RNA.txt" Name="RNA.txt" Source="$(var.GUI_TargetDir)Mods\RNA.txt" />
      </Component>
      
      <!--<Component Id="Appsrc_Mods_CommonArtifacts.txt" Guid="36555bef-88bf-4e06-87c7-ff2b196d1d0a">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_CommonArtifacts.txt" Name="CommonArtifacts.txt" Source="$(var.GUI_TargetDir)Mods\CommonArtifacts.txt" />
      </Component>
      <Component Id="Appsrc_Mods_CommonBiological.txt" Guid="e6ec148f-5dc6-46d4-9ecf-272d3c553fdd">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_CommonBiological.txt" Name="CommonBiological.txt" Source="$(var.GUI_TargetDir)Mods\CommonBiological.txt" />
      </Component>
      <Component Id="Appsrc_Mods_RareMods.txt" Guid="668ab900-9aa3-4efe-9644-976bc2e658b8">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_RareMods.txt" Name="RareMods.txt" Source="$(var.GUI_TargetDir)Mods\RareMods.txt" />
      </Component>-->
    </ComponentGroup>
  </Fragment>

  <!--Builds the App Data folder-->
  <Fragment>
    <ComponentGroup Id="Appsrc_Data_files" Directory="MetaAppDataFolder">
      <Component Id="RemoveData" Guid="80dd5110-5563-499a-93ee-652e351c64f9">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RemoveFolder Id="MetaAppDataFolder" On="both"/>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
      </Component>
      <Component Id="Appsrc_Data_combos.txt" Guid="e16d25a3-d773-4a7f-9252-63d737c2c7ba">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Data_combos.txt" Name="combos.txt" Source="$(var.GUI_TargetDir)Data\combos.txt" />
      </Component>
      <Component Id="Appsrc_Data_PSI_MOD.obo.xml" Guid="348109bd-4645-448e-b272-19a126e4c3cf">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Data_PSI_MOD.obo.xml" Name="PSI-MOD.obo.xml" Source="$(var.GUI_TargetDir)Data\PSI-MOD.obo.xml" />
      </Component>
      <Component Id="Appsrc_Data_ptmlist.txt" Guid="ea6237f4-9acd-4660-a4e8-831b7aab8c39">
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <Condition>OVERWRITEAPPDATA</Condition>
        <File ReadOnly="no" Id="Appsrc_Data_ptmlist.txt" Name="ptmlist.txt" Source="$(var.GUI_TargetDir)Data\ptmlist.txt" />
      </Component>
      <Component Id="Appsrc_Data_unimod.xml" Guid="cb7b6d9e-3eb0-47ac-857f-7a0009d95619">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Data_unimod.xml" Name="unimod.xml" Source="$(var.GUI_TargetDir)Data\unimod.xml" />
      </Component>
      <Component Id="Appsrc_Data_elements.dat" Guid="5ba496cc-8b84-4d25-a410-b2274718ebf9">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Data_elements.dat" Name="elements.dat" Source="$(var.GUI_TargetDir)Data\elements.dat" />
      </Component>
      <Component Id="Appsrc_Data_proteases.tsv" Guid="fd26b186-64bd-49b7-b8ee-638efef79e03">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Data_proteases.tsv" Name="proteases.tsv" Source="$(var.GUI_TargetDir)Data\proteases.tsv" />
      </Component>
    </ComponentGroup>
  </Fragment><commit_msg>fix installer issue that caused metamorpheus to not open (#1288) (#1289)<commit_after><?xml version="1.0" encoding="UTF-8"?>
<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi">

  <!--Shorthand way of getting the install directory-->
  <?define GUI_TargetDir=$(var.GUI.TargetDir)?>

  <!--Product compiles into an msi file. Only one can be present.-->
  <!--Version needs to be replaced automatically-->
  <Product Id="*" Name="MetaMorpheus" Language="1033" Version="!(bind.FileVersion.MetaMorpheusGUI.exe)" Manufacturer="Smith Group" UpgradeCode="438ad6ff-f027-423a-ab0b-c73384c0e2e5">

    <!--Properties about the package to be placed in the Summary Information Stream.-->
    <!--These are visible from COM through the IStream interface, and these properties can be seen on the package in Explorer.-->
    <Package Id="*" InstallerVersion="500" Compressed="yes" InstallScope="perMachine" Platform="x64"/>
    <MajorUpgrade AllowSameVersionUpgrades="yes" Schedule="afterInstallValidate" DowngradeErrorMessage="A newer version of MetaMorpheus is already installed."/>

    <Condition Message="This application is only supported on Windows 7 or higher.">
      <![CDATA[Installed OR (VersionNT >= 601)]]>
    </Condition>

    <Condition Message="This application requires 64-bit windows">
      <![CDATA[Installed OR VersionNT64]]>
    </Condition>

    <MediaTemplate EmbedCab="yes"/>



    <!--A feature for the Feature table. Features are the smallest installable unit.-->
    <Feature Id="ProductFeature" Level="1">

      <!-- ComponentGroupRef creates a reference to a ComponentGroup in another Fragment-->
      <ComponentGroupRef Id="ExecutablesAndLibrariesComponentGroup" />
      <!--ComponentRef creates a reference to a Component element in another Fragment-->
      <ComponentRef Id="MetaMorpheusProgramMenuFolderComponent"/>
      <!--App Data Section-->

      <ComponentGroupRef Id="Appsrc_Mods_files"/>
      <ComponentGroupRef Id="Appsrc_Data_files"/>
      <ComponentGroupRef Id="Appsrc_NeoData_files" />
      <ComponentGroupRef Id="Appsrc_NeoTomlFiles_files" />
      <ComponentGroupRef Id="Appsrc_ProteolyticDigestion_files" />
      <ComponentRef Id="RemoveNeo"/>
      <ComponentRef Id="MetaAppsettings.toml"/>
      <ComponentRef Id="MetaAppGUIsettings.toml"/>
      <ComponentRef Id="RemoveApp"/>
      <ComponentRef Id="DesktopShortcut"/>
    </Feature>

    <Directory Id="TARGETDIR" Name="SourceDir">
      <!--Desktop Shortcut Installation-->
      <Directory Id="DesktopFolder" Name="Desktop">
        <Component Id="DesktopShortcut" Guid="ef1fd292-b162-4990-80cb-cd2a0c839d4b">
          <Condition>INSTALLDESKTOPSHORTCUT</Condition>
          <RegistryKey Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Action="createAndRemoveOnUninstall">
            <RegistryValue Name="MetaMorpheusDeskTop" Value="1" Type="integer" KeyPath="yes"/>
          </RegistryKey>
          <Shortcut Id="AppDeskTopSC" Name="MetaMorpheus" Description="Shortcut to App" Target="[#MetaMorpheusGUI.exe]" WorkingDirectory="MetaMorpheusInstallFolder" />
        </Component>
      </Directory>

      <Directory Id="ProgramFiles64Folder">
        <Directory Id="MetaMorpheusInstallFolder" Name="MetaMorpheus">
          <Directory Id="DataFolder" Name="Data" />
          <Directory Id="ModsFolder" Name="Mods" />
          <Directory Id="ProteolyticDigestionFolder" Name="ProteolyticDigestion" />
          <Directory Id="NeoFolder" Name="Neo">
            <Directory Id="NeoDataFolder" Name="Data" />
            <Directory Id="NeoTomlFilesFolder" Name="TomlFiles" />
          </Directory>
        </Directory>
      </Directory>
      <Directory Id="ProgramMenuFolder">
        <Directory Id="MetaMorpheusProgramMenuFolder" Name="MetaMorpheus">

        </Directory>
      </Directory>
      <Directory Id="LocalAppDataFolder">
        <Directory Id="MetaMorpheusAppFolder" Name="MetaMorpheus">
          <Component Id="MetaAppsettings.toml" Guid="1d8da0c2-5b44-4fe4-a581-1fc526346313">
            <Condition>OVERWRITEAPPDATA</Condition>
            <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
            <File Id="settings.toml" Name="settings.toml" Source="$(var.GUI_TargetDir)settings.toml" />
          </Component>
          <Component Id="MetaAppGUIsettings.toml" Guid="9b60d7a4-a764-4ba1-8903-1733fc70618a">
            <Condition>OVERWRITEAPPDATA</Condition>
            <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
            <File Id="GUIsettings.toml" Name="GUIsettings.toml" Source="$(var.GUI_TargetDir)GUIsettings.toml" />
          </Component>
          <Component Id="RemoveApp" Guid="a5443b89-65b0-4855-b521-e7bcc9c5a85c">
            <RemoveFolder Id="MetaMorpheusAppFolder" On="uninstall"/>
            <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
          </Component>
          <Directory Id="MetaAppDataFolder" Name="Data" />
          <Directory Id="MetaAppModsFolder" Name="Mods" />
          <Directory Id="MetaAppProteolyticDigestionFolder" Name="ProteolyticDigestion" />
          <Directory Id="NeoAppFolder" Name="Neo">
            <Directory Id="MetaAppNeoDataFolder" Name="Data" />
            <Directory Id="MetaAppNeoTomlFilesFolder" Name="TomlFiles" />
            <Component Id="RemoveNeo" Guid="af5ff12f-ef0c-4945-be30-36c00ea734e9">
              <RemoveFolder Id="NeoAppFolder" On="uninstall"/>
              <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
            </Component>
          </Directory>
        </Directory>
      </Directory>
    </Directory>

    <UI>
      <UIRef Id="WixUI_Mondo"/>
      <UIRef Id="newDlg"/>
      <UIRef Id="MyMaintenance"/>
      <Publish Dialog="WelcomeDlg" Control="Next" Event="NewDialog" Value="MetaSCDlg" Order="1">1</Publish>
      <Publish Dialog="MetaSCDlg" Control="Back" Event="NewDialog" Value="WelcomeDlg" Order="1">1</Publish>
      <Publish Dialog="MetaSCDlg" Control="Next" Event="NewDialog" Value="VerifyReadyDlg" Order="1">1</Publish>

      <Publish Dialog="VerifyReadyDlg" Control="Back" Event="NewDialog" Value="MetaSCDlg" Order="1">1</Publish>
      <Publish Dialog="MaintenanceWelcomeDlg" Control="Next" Event="NewDialog" Value="MyMaintenanceTypeDlg">1</Publish>
      <Publish Dialog="MyMaintenanceTypeDlg" Control="Back" Event="NewDialog" Value="MaintenanceWelcomeDlg" Order="1">1</Publish>
      <!--<Publish Dialog="MyMaintenanceTypeDlg" Control="Next" Event="NewDialog" Value="ExitDialog" Order="1">1</Publish>-->

      <Publish Dialog="ExitDialog"
        Control="Finish"
        Event="DoAction"
        Value="LaunchApplication">WIXUI_EXITDIALOGOPTIONALCHECKBOX = 1 and NOT Installed</Publish>

    </UI>


    <CustomAction Id='LaunchFile' FileKey='MetaMorpheusGUI.exe' ExeCommand='' Return="asyncNoWait" />
    <Property Id="OVERWRITEAPPDATA" Value="1" />
    <Property Id="WIXUI_MONDO" Value="INSTALLFOLDER" />
    <Property Id="WIXUI_EXITDIALOGOPTIONALCHECKBOXTEXT" Value="Launch MetaMorpheus" />
    <Property Id="WixShellExecTarget" Value="[#MetaMorpheusGUI.exe]" />
    <CustomAction Id="LaunchApplication" BinaryKey="WixCA" DllEntry="WixShellExec" Impersonate="yes" />

  </Product>

  <!--Executables and libraries-->
  <Fragment>
    <ComponentGroup Id="ExecutablesAndLibrariesComponentGroup" Directory="MetaMorpheusInstallFolder">
      <Component Id="MetaMorpheusGUI.exe" Guid="63370d96-1880-40ab-8525-685ccf64326f">
        <File Id="MetaMorpheusGUI.exe" Name="MetaMorpheusGUI.exe" Source="$(var.GUI_TargetDir)MetaMorpheusGUI.exe" />
      </Component>
      <Component Id="app.manifest" Guid="d894958a-07c1-4078-9e0e-081a6cc29030">
        <File Id="app.manifest" Name="app.manifest" Source="$(var.GUI_TargetDir)app.manifest" />
      </Component>
      <Component Id="src_TaskLayer.pdb" Guid="6ece566a-22ff-4208-bba2-ad0430eeee49">
        <File Id="src_TaskLayer.pdb" Name="TaskLayer.pdb" Source="$(var.GUI_TargetDir)TaskLayer.pdb" />
      </Component>
      <Component Id="src_UnmanagedThermoHelperLayer.dll" Guid="18bed74c-eedb-4efa-a6e3-1592ac7022e3">
        <File Id="src_UnmanagedThermoHelperLayer.dll" Name="UnmanagedThermoHelperLayer.dll" Source="$(var.GUI_TargetDir)UnmanagedThermoHelperLayer.dll" />
      </Component>
      <Component Id="Chromatography.dll">
        <File Id="src_Chromatography.dll" Name="Chromatography.dll" Source="$(var.GUI_TargetDir)Chromatography.dll" />
      </Component>
      <Component Id="src_Thermo.dll">
        <File Id="src_Thermo.dll" Name="Thermo.dll" Source="$(var.GUI_TargetDir)Thermo.dll" />
      </Component>
      <Component Id="src_Newtonsoft.Json.dll">
        <File Id="src_Newtonsoft.Json.dll" Name="Newtonsoft.Json.dll" Source="$(var.GUI_TargetDir)Newtonsoft.Json.dll" />
      </Component>
      <Component Id="src_UsefulProteomicsDatabases.dll" Guid="e7f76fbf-d21c-4e57-bed4-33f71822ee18">
        <File Id="src_UsefulProteomicsDatabases.dll" Name="UsefulProteomicsDatabases.dll" Source="$(var.GUI_TargetDir)UsefulProteomicsDatabases.dll" />
      </Component>
      <Component Id="src_TaskLayer.dll" Guid="7d468a75-d294-432e-bd59-8fcf1e254486">
        <File Id="src_TaskLayer.dll" Name="TaskLayer.dll" Source="$(var.GUI_TargetDir)TaskLayer.dll" />
      </Component>
      <Component Id="src_MetaMorpheusGUI.exe.config" Guid="929da846-1537-40ba-b615-2335b32cadb1">
        <File Id="src_MetaMorpheusGUI.exe.config" Name="MetaMorpheusGUI.exe.config" Source="$(var.GUI_TargetDir)MetaMorpheusGUI.exe.config" />
      </Component>
      <Component Id="src_Chemistry.dll" Guid="bd4869a2-82a3-4d52-97b7-888881ae1827">
        <File Id="src_Chemistry.dll" Name="Chemistry.dll" Source="$(var.GUI_TargetDir)Chemistry.dll" />
      </Component>
      <Component Id="src_EngineLayer.dll" Guid="ebfe6a93-fdc4-4cff-a510-ff516e532d50">
        <File Id="src_EngineLayer.dll" Name="EngineLayer.dll" Source="$(var.GUI_TargetDir)EngineLayer.dll" />
      </Component>
      <Component Id="src_EngineLayer.pdb" Guid="8f9592a4-02b1-4462-a259-f7aa41d890a4">
        <File Id="src_EngineLayer.pdb" Name="EngineLayer.pdb" Source="$(var.GUI_TargetDir)EngineLayer.pdb" />
      </Component>
      <Component Id="src_FlashLFQ.dll" Guid="69e33379-5301-49db-8913-4d777ed5a5f9">
        <File Id="src_FlashLFQ.dll" Name="FlashLFQ.dll" Source="$(var.GUI_TargetDir)FlashLFQ.dll" />
      </Component>
      <Component Id="src_ManagedThermoHelperLayer.dll" Guid="5706aec2-8e67-4094-ac81-95cd9aa9a49e">
        <File Id="src_ManagedThermoHelperLayer.dll" Name="ManagedThermoHelperLayer.dll" Source="$(var.GUI_TargetDir)ManagedThermoHelperLayer.dll" />
      </Component>
      <Component Id="src_MassSpectrometry.dll" Guid="d6241678-3d48-4c7a-becf-9c1160fbe06b">
        <File Id="src_MassSpectrometry.dll" Name="MassSpectrometry.dll" Source="$(var.GUI_TargetDir)MassSpectrometry.dll" />
      </Component>
      <Component Id="src_MathNet.Numerics.dll" Guid="dea92905-719e-48e1-8a64-e845dca06dac">
        <File Id="src_MathNet.Numerics.dll" Name="MathNet.Numerics.dll" Source="$(var.GUI_TargetDir)MathNet.Numerics.dll" />
      </Component>
      <Component Id="src_MetaMorpheusGUI.pdb" Guid="bf568e2b-42c1-4209-9f45-11a3af86110a">
        <File Id="src_MetaMorpheusGUI.pdb" Name="MetaMorpheusGUI.pdb" Source="$(var.GUI_TargetDir)MetaMorpheusGUI.pdb" />
      </Component>
      <Component Id="src_mzIdentML.dll" Guid="cb1200d2-2356-4664-8968-bff79c83eeac">
        <File Id="src_mzIdentML.dll" Name="mzIdentML.dll" Source="$(var.GUI_TargetDir)mzIdentML.dll" />
      </Component>
      <Component Id="src_MzLibUtil.dll" Guid="9475fcb2-63bd-490c-8441-17a1760869ac">
        <File Id="src_MzLibUtil.dll" Name="MzLibUtil.dll" Source="$(var.GUI_TargetDir)MzLibUtil.dll" />
      </Component>
      <Component Id="src_MzML.dll" Guid="40c12490-638a-41b9-9e0c-05e949236a5a">
        <File Id="src_MzML.dll" Name="MzML.dll" Source="$(var.GUI_TargetDir)MzML.dll" />
      </Component>
      <Component Id="src_NetSerializer.dll" Guid="9eddc340-0dcb-415a-85f4-322f0eaeee4b">
        <File Id="src_NetSerializer.dll" Name="NetSerializer.dll" Source="$(var.GUI_TargetDir)NetSerializer.dll" />
      </Component>
      <Component Id="src_Nett.dll" Guid="656c78ef-0234-4e45-957c-a6dd6fff044f">
        <File Id="src_Nett.dll" Name="Nett.dll" Source="$(var.GUI_TargetDir)Nett.dll" />
      </Component>
      <Component Id="src_Nett.pdb" Guid="68030b29-c0fe-4287-9b7b-aa07f0cc153a">
        <File Id="src_Nett.pdb" Name="Nett.pdb" Source="$(var.GUI_TargetDir)Nett.pdb" />
      </Component>
      <Component Id="src_pepXML.dll" Guid="9a086709-4b5d-4711-aec0-9a8a9ba7b886">
        <File Id="src_pepXML.dll" Name="pepXML.dll" Source="$(var.GUI_TargetDir)pepXML.dll" />
      </Component>
      <Component Id="src_Proteomics.dll" Guid="e0bd6f66-afa5-49fa-a17c-2a24164f600d">
        <File Id="src_Proteomics.dll" Name="Proteomics.dll" Source="$(var.GUI_TargetDir)Proteomics.dll" />
      </Component>
      <Component Id="src_SharpLearning.Common.Interfaces.dll" Guid="62b8e7de-7965-4942-9e5b-9449c5ab7deb">
        <File Id="src_SharpLearning.Common.Interfaces.dll" Name="SharpLearning.Common.Interfaces.dll" Source="$(var.GUI_TargetDir)SharpLearning.Common.Interfaces.dll" />
      </Component>
      <Component Id="src_SharpLearning.Containers.dll" Guid="6bdbf050-26d7-4e11-b378-d71055ecba80">
        <File Id="src_SharpLearning.Containers.dll" Name="SharpLearning.Containers.dll" Source="$(var.GUI_TargetDir)SharpLearning.Containers.dll" />
      </Component>
      <Component Id="src_SharpLearning.CrossValidation.dll" Guid="da2245c7-362d-4a90-9408-a671e210896a">
        <File Id="src_SharpLearning.CrossValidation.dll" Name="SharpLearning.CrossValidation.dll" Source="$(var.GUI_TargetDir)SharpLearning.CrossValidation.dll" />
      </Component>
      <Component Id="src_SharpLearning.DecisionTrees.dll" Guid="b3c202a8-795d-4198-b927-0fcd02d8ae05">
        <File Id="src_SharpLearning.DecisionTrees.dll" Name="SharpLearning.DecisionTrees.dll" Source="$(var.GUI_TargetDir)SharpLearning.DecisionTrees.dll" />
      </Component>
      <Component Id="src_SharpLearning.InputOutput.dll" Guid="357e6a45-5852-474d-aceb-e05942958ae6">
        <File Id="src_SharpLearning.InputOutput.dll" Name="SharpLearning.InputOutput.dll" Source="$(var.GUI_TargetDir)SharpLearning.InputOutput.dll" />
      </Component>
      <Component Id="src_SharpLearning.Metrics.dll" Guid="9ec3dd96-8228-49db-98e7-4288845b63a4">
        <File Id="src_SharpLearning.Metrics.dll" Name="SharpLearning.Metrics.dll" Source="$(var.GUI_TargetDir)SharpLearning.Metrics.dll" />
      </Component>
      <Component Id="src_SharpLearning.RandomForest.dll" Guid="f86fdc0c-6a23-4e4f-803b-0012aaa418e7">
        <File Id="src_SharpLearning.RandomForest.dll" Name="SharpLearning.RandomForest.dll" Source="$(var.GUI_TargetDir)SharpLearning.RandomForest.dll" />
      </Component>
      <Component Id="src_SharpLearning.Optimization.dll">
        <File Id="src_SharpLearning.Optimization.dll" Name="SharpLearning.Optimization.dll" Source="$(var.GUI_TargetDir)SharpLearning.Optimization.dll" />
      </Component>
      <Component Id="src_SharpLearning.GradientBoost.dll">
        <File Id="src_SharpLearning.GradientBoost.dll" Name="SharpLearning.GradientBoost.dll" Source="$(var.GUI_TargetDir)SharpLearning.GradientBoost.dll" />
      </Component>
      <Component Id="src_Spectra.dll" Guid="280ccb7f-a4f8-4df7-9f88-6cf6fa9bc15b">
        <File Id="src_Spectra.dll" Name="Spectra.dll" Source="$(var.GUI_TargetDir)Spectra.dll" />
      </Component>
      <Component Id="src_Mgf.dll">
        <File Id="src_Mgf.dll" Name="Mgf.dll" Source="$(var.GUI_TargetDir)Mgf.dll" />
      </Component>
      <Component Id="src_System.Data.Common.dll" Guid="795499dd-11a0-4132-8e33-c1f64bd11c51">
        <File Id="src_System.Data.Common.dll" Name="System.Data.Common.dll" Source="$(var.GUI_TargetDir)System.Data.Common.dll" />
      </Component>
      <Component Id="src_System.Diagnostics.StackTrace.dll" Guid="727eb4a0-a11d-4948-b8d0-403b96de69c4">
        <File Id="src_System.Diagnostics.StackTrace.dll" Name="System.Diagnostics.StackTrace.dll" Source="$(var.GUI_TargetDir)System.Diagnostics.StackTrace.dll" />
      </Component>
      <Component Id="src_System.Diagnostics.Tracing.dll" Guid="7e43f9df-4a1c-4f02-99f7-d7f5aa8c63f1">
        <File Id="src_System.Diagnostics.Tracing.dll" Name="System.Diagnostics.Tracing.dll" Source="$(var.GUI_TargetDir)System.Diagnostics.Tracing.dll" />
      </Component>
      <Component Id="src_System.Globalization.Extensions.dll" Guid="12b04d22-78d4-4cf3-b2a5-92d2ca9eb504">
        <File Id="src_System.Globalization.Extensions.dll" Name="System.Globalization.Extensions.dll" Source="$(var.GUI_TargetDir)System.Globalization.Extensions.dll" />
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      <Component Id="src_System.IO.Compression.dll" Guid="5d786beb-ae3e-4a9e-9496-189ddb307903">
        <File Id="src_System.IO.Compression.dll" Name="System.IO.Compression.dll" Source="$(var.GUI_TargetDir)System.IO.Compression.dll" />
      </Component>
      <Component Id="src_System.Net.Http.dll" Guid="480e547f-a7d7-4f57-a9a3-4ddb448faddf">
        <File Id="src_System.Net.Http.dll" Name="System.Net.Http.dll" Source="$(var.GUI_TargetDir)System.Net.Http.dll" />
      </Component>
      <Component Id="src_System.Net.Sockets.dll" Guid="340d9c4a-dc96-4ddf-8813-d071f92581cb">
        <File Id="src_System.Net.Sockets.dll" Name="System.Net.Sockets.dll" Source="$(var.GUI_TargetDir)System.Net.Sockets.dll" />
      </Component>
      <Component Id="src_System.Runtime.Serialization.Primitives.dll" Guid="561a0d2f-182d-42f4-9e0c-81e4f81650c6">
        <File Id="src_System.Runtime.Serialization.Primitives.dll" Name="System.Runtime.Serialization.Primitives.dll" Source="$(var.GUI_TargetDir)System.Runtime.Serialization.Primitives.dll" />
      </Component>
      <Component Id="src_System.Security.Cryptography.Algorithms.dll" Guid="af07a661-d962-48e2-8ca4-96f40f167ee7">
        <File Id="src_System.Security.Cryptography.Algorithms.dll" Name="System.Security.Cryptography.Algorithms.dll" Source="$(var.GUI_TargetDir)System.Security.Cryptography.Algorithms.dll" />
      </Component>
      <Component Id="src_System.Security.SecureString.dll" Guid="58b65b98-6752-4030-badc-ff30f2d160e3">
        <File Id="src_System.Security.SecureString.dll" Name="System.Security.SecureString.dll" Source="$(var.GUI_TargetDir)System.Security.SecureString.dll" />
      </Component>
      <Component Id="src_System.Threading.Overlapped.dll" Guid="252a5ba3-10e0-41ac-8fb3-af9a955ea71a">
        <File Id="src_System.Threading.Overlapped.dll" Name="System.Threading.Overlapped.dll" Source="$(var.GUI_TargetDir)System.Threading.Overlapped.dll" />
      </Component>
      <Component Id="src_System.Xml.XPath.XDocument.dll" Guid="70f63556-f331-4c08-ac9f-3515dacbf0e9">
        <File Id="src_System.Xml.XPath.XDocument.dll" Name="System.Xml.XPath.XDocument.dll" Source="$(var.GUI_TargetDir)System.Xml.XPath.XDocument.dll" />
      </Component>
    </ComponentGroup>
  </Fragment>

  <!--Build the App Mods folder-->
  <Fragment>
    <ComponentGroup Id="Appsrc_Mods_files" Directory="MetaAppModsFolder">
      <Component Id="RemoveMods" Guid="284c0784-2183-4f80-af61-56cadeb800bf">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RemoveFolder Id="MetaAppModsFolder" On="both"/>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
      </Component>

      <!-- aListOfmods.txt -->
      <Component Id="Appsrc_Mods_aListOfmods.txt" Guid="0aa9b5ed-b47d-4a78-93b1-49ebc104d011">
        <File ReadOnly="no" Id="Appsrc_Mods_aListOfmods.txt" Name="aListOfmods.txt" Source="$(var.GUI_TargetDir)Mods\aListOfmods.txt" />
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
      </Component>

      <!-- detachers.txt -->
      <Component Id="Appsrc_Mods_detachers.txt" Guid="9224cf63-edb0-4e30-83c2-b10fff7af13e">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_detachers.txt" Name="detachers.txt" Source="$(var.GUI_TargetDir)Mods\detachers.txt" />
      </Component>

      <!-- fallOff.txt -->
      <Component Id="Appsrc_Mods_fallOff.txt" Guid="233836d8-d981-4ea9-a8fc-f62cdbc7b01a">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_fallOff.txt" Name="fallOff.txt" Source="$(var.GUI_TargetDir)Mods\fallOff.txt" />
      </Component>

      <!-- glyco.txt -->
      <Component Id="Appsrc_Mods_glyco.txt" Guid="1707b26b-070e-46d5-9632-f1bc8bf4d281">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_glyco.txt" Name="glyco.txt" Source="$(var.GUI_TargetDir)Mods\glyco.txt" />
      </Component>

      <!-- missing.txt -->
      <Component Id="Appsrc_Mods_missing.txt" Guid="0f659a4e-3ea9-4d3a-9a0f-65cda1015b01">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_missing.txt" Name="missing.txt" Source="$(var.GUI_TargetDir)Mods\missing.txt" />
      </Component>

      <!-- Mods.txt -->
      <Component Id="Appsrc_Mods_Mods.txt" Guid="9be193e3-266c-4c1d-9973-341f0a5d108a">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_Mods.txt" Name="Mods.txt" Source="$(var.GUI_TargetDir)Mods\Mods.txt" />
      </Component>

      <!-- substitutions.txt -->
      <Component Id="Appsrc_Mods_substitutions.txt" Guid="f108606b-f9eb-4c3c-893b-7ec33c88a1d1">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_substitutions.txt" Name="substitutions.txt" Source="$(var.GUI_TargetDir)Mods\substitutions.txt" />
      </Component>

      <!-- surfactants.txt -->
      <Component Id="Appsrc_Mods_surfactants.txt" Guid="937d6734-a4c0-469a-b070-64bf5de84b13">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_surfactants.txt" Name="surfactants.txt" Source="$(var.GUI_TargetDir)Mods\surfactants.txt" />
      </Component>

      <!-- tmt.txt -->
      <Component Id="Appsrc_Mods_tmt.txt" Guid="f064b7a0-c650-4a40-8a9f-301cc6cb946e">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_tmt.txt" Name="tmt.txt" Source="$(var.GUI_TargetDir)Mods\tmt.txt" />
      </Component>

      <!-- Crosslink.txt -->
      <Component Id="Appsrc_Mods_Crosslink.txt" Guid="172f7116-4772-4f3b-a48b-b1e98a48b73d">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_Crosslink.txt" Name="Crosslink.txt" Source="$(var.GUI_TargetDir)Mods\Crosslink.txt" />
      </Component>

      <!-- RNA.txt -->
      <Component Id="Appsrc_Mods_RNA.txt" Guid="99f09cd8-fbe1-454d-8cb3-9cc46de33515">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_RNA.txt" Name="RNA.txt" Source="$(var.GUI_TargetDir)Mods\RNA.txt" />
      </Component>

      <!--<Component Id="Appsrc_Mods_CommonArtifacts.txt" Guid="36555bef-88bf-4e06-87c7-ff2b196d1d0a">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_CommonArtifacts.txt" Name="CommonArtifacts.txt" Source="$(var.GUI_TargetDir)Mods\CommonArtifacts.txt" />
      </Component>
      <Component Id="Appsrc_Mods_CommonBiological.txt" Guid="e6ec148f-5dc6-46d4-9ecf-272d3c553fdd">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_CommonBiological.txt" Name="CommonBiological.txt" Source="$(var.GUI_TargetDir)Mods\CommonBiological.txt" />
      </Component>
      <Component Id="Appsrc_Mods_RareMods.txt" Guid="668ab900-9aa3-4efe-9644-976bc2e658b8">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Mods_RareMods.txt" Name="RareMods.txt" Source="$(var.GUI_TargetDir)Mods\RareMods.txt" />
      </Component>-->
    </ComponentGroup>
  </Fragment>

  <!--Builds the App Data folder-->
  <Fragment>
    <ComponentGroup Id="Appsrc_Data_files" Directory="MetaAppDataFolder">
      <Component Id="RemoveData" Guid="80dd5110-5563-499a-93ee-652e351c64f9">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RemoveFolder Id="MetaAppDataFolder" On="both"/>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
      </Component>
      <Component Id="Appsrc_Data_combos.txt" Guid="e16d25a3-d773-4a7f-9252-63d737c2c7ba">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Data_combos.txt" Name="combos.txt" Source="$(var.GUI_TargetDir)Data\combos.txt" />
      </Component>
      <Component Id="Appsrc_Data_PSI_MOD.obo.xml" Guid="348109bd-4645-448e-b272-19a126e4c3cf">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Data_PSI_MOD.obo.xml" Name="PSI-MOD.obo.xml" Source="$(var.GUI_TargetDir)Data\PSI-MOD.obo.xml" />
      </Component>
      <Component Id="Appsrc_Data_ptmlist.txt" Guid="ea6237f4-9acd-4660-a4e8-831b7aab8c39">
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <Condition>OVERWRITEAPPDATA</Condition>
        <File ReadOnly="no" Id="Appsrc_Data_ptmlist.txt" Name="ptmlist.txt" Source="$(var.GUI_TargetDir)Data\ptmlist.txt" />
      </Component>
      <Component Id="Appsrc_Data_unimod.xml" Guid="cb7b6d9e-3eb0-47ac-857f-7a0009d95619">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Data_unimod.xml" Name="unimod.xml" Source="$(var.GUI_TargetDir)Data\unimod.xml" />
      </Component>
      <Component Id="Appsrc_Data_elements.dat" Guid="5ba496cc-8b84-4d25-a410-b2274718ebf9">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Data_elements.dat" Name="elements.dat" Source="$(var.GUI_TargetDir)Data\elements.dat" />
      </Component>
      <Component Id="Appsrc_Data_proteases.tsv" Guid="fd26b186-64bd-49b7-b8ee-638efef79e03">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_Data_proteases.tsv" Name="proteases.tsv" Source="$(var.GUI_TargetDir)Data\proteases.tsv" />
      </Component>
    </ComponentGroup>
  </Fragment>

  <!--Builds the App Neo\ProteolyticDigestion folder-->
  <Fragment>
    <ComponentGroup Id="Appsrc_ProteolyticDigestion_files" Directory="MetaAppProteolyticDigestionFolder">
      <Component Id="RemoveProteolyticDigestion">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RemoveFolder Id="MetaAppProteolyticDigestionFolder" On="both"/>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
      </Component>
      <Component Id="Appsrc_ProteolyticDigestion_proteases.tsv" Guid="A3AF0FEB-59EE-4207-9BDB-3B285D1E720E">
        <Condition>OVERWRITEAPPDATA</Condition>
        <RegistryValue Root="HKCU" Key="Software\SmithGroup\MetaMorpheus" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        <File ReadOnly="no" Id="Appsrc_ProteolyticDigestion_proteases.tsv" Name="proteases.tsv" Source="$(var.GUI_TargetDir)ProteolyticDigestion\proteases.tsv" />
      </Component>
    </ComponentGroup>
  </Fragment>
{'fraction_non_alphanumeric': 0.1548800873332651, 'fraction_numerical': 0.05214409988742196, 'mean_word_length': 4.391980134277568, 'pattern_counts': {'":': 0, '<': 874, '<?xml version=': 2, '>': 876, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 20}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6247895', 'n_tokens_mistral': 22842, 'n_tokens_neox': 20038, 'n_words': 2462}