Gene level parsimony option in protein association dialog (#2764)

- added gene level parsimony option in protein association dialog
* bumped schema to 23.12 for gene level parsimony
* fixed Skyline build system to copy vendor DLLs to both Debug and Release directories so vendor reader tests don't fail in Debug config
* removed MinPeptidesPerProtein test from TestHugeAssociateProteins because it's now hidden in the Refine -> Associate Proteins dialog
* greatly improved speed by using Nick's ReferenceValue for PeptideDocNodes
* fixed issues with cancellation in some parsimony calculations

Jamroot.jam

@@ -765,30 +765,39 @@ rule install-type ( properties * )
 }
 
 import string ;
+rule install-vendor-api-dependencies-to-locations ( locations + : properties * )
+{
+    local dependencies ;
+    if <toolset>msvc in $(properties) && <link>static in $(properties) && ! [ without-binary-msdata ]
+    {
+        for loc in $(locations)
+        {
+            local location = <location>$(loc) ;
+            if [ path.exists pwiz_aux/msrc/utility/vendor_api/ABI ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/ABI//install_pwiz_vendor_api_abi_dlls/$(location) ; }
+            if [ path.exists pwiz_aux/msrc/utility/vendor_api/ABI ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/ABI//install_pwiz_vendor_api_abi_sqlite/$(location) ; }
+            if [ path.exists pwiz_aux/msrc/utility/vendor_api/ABI/T2D ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/ABI/T2D//install_pwiz_vendor_api_abi_t2d/$(location) ; }
+            if [ path.exists pwiz_aux/msrc/utility/vendor_api/Agilent ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Agilent//install_pwiz_vendor_api_agilent/$(location) ; }
+            if [ path.exists pwiz_aux/msrc/utility/vendor_api/Bruker ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Bruker//install_pwiz_vendor_api_bruker/$(location) ; }
+    # wait for CCS<->DT support in Mobllion #         if [ path.exists pwiz_aux/msrc/utility/vendor_api/Mobilion ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Mobilion//install_pwiz_vendor_api_mbi/$(location) ; }
+            if [ path.exists pwiz_aux/msrc/utility/vendor_api/Shimadzu ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Shimadzu//install_pwiz_vendor_api_shimadzu/$(location) ; }
+            if [ path.exists pwiz_aux/msrc/utility/vendor_api/thermo ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/thermo//install_pwiz_vendor_api_thermo/$(location) ; }
+            if [ path.exists pwiz_aux/msrc/utility/vendor_api/UIMF ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/UIMF//install_pwiz_vendor_api_uimf/$(location) ; }
+            if [ path.exists pwiz_aux/msrc/utility/vendor_api/UNIFI ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/UNIFI//install_pwiz_vendor_api_unifi/$(location) ; }
+            if [ path.exists pwiz_aux/msrc/utility/vendor_api/Waters ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Waters//install_pwiz_vendor_api_waters/$(location) ; }
+            if <vendor-api-support>on in $(properties) { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_tools/prototype//ThermoRawMetaDumpInstall/$(location) ; }
+        }
+    }
+    return $(dependencies) ;
+}
+
 rule install-vendor-api-dependencies ( properties * )
 {
     properties = $(properties) [ vendor-api-support $(properties) ] ;
     local location = [ feature.get-values <location> : $(properties) ] ;
     if $(location) { location = [ string.join <location> [ path.make $(location[1]) ] ] ; }
     location ?= [ install-location $(properties) ] ;
 
-    local dependencies ;
-    if <toolset>msvc in $(properties) && <link>static in $(properties) && ! [ without-binary-msdata ]
-    {
-        if [ path.exists pwiz_aux/msrc/utility/vendor_api/ABI ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/ABI//install_pwiz_vendor_api_abi_dlls/$(location) ; }
-        if [ path.exists pwiz_aux/msrc/utility/vendor_api/ABI ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/ABI//install_pwiz_vendor_api_abi_sqlite/$(location) ; }
-        if [ path.exists pwiz_aux/msrc/utility/vendor_api/ABI/T2D ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/ABI/T2D//install_pwiz_vendor_api_abi_t2d/$(location) ; }
-        if [ path.exists pwiz_aux/msrc/utility/vendor_api/Agilent ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Agilent//install_pwiz_vendor_api_agilent/$(location) ; }
-        if [ path.exists pwiz_aux/msrc/utility/vendor_api/Bruker ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Bruker//install_pwiz_vendor_api_bruker/$(location) ; }
-# wait for CCS<->DT support in Mobllion #         if [ path.exists pwiz_aux/msrc/utility/vendor_api/Mobilion ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Mobilion//install_pwiz_vendor_api_mbi/$(location) ; }
-        if [ path.exists pwiz_aux/msrc/utility/vendor_api/Shimadzu ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Shimadzu//install_pwiz_vendor_api_shimadzu/$(location) ; }
-        if [ path.exists pwiz_aux/msrc/utility/vendor_api/thermo ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/thermo//install_pwiz_vendor_api_thermo/$(location) ; }
-        if [ path.exists pwiz_aux/msrc/utility/vendor_api/UIMF ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/UIMF//install_pwiz_vendor_api_uimf/$(location) ; }
-        if [ path.exists pwiz_aux/msrc/utility/vendor_api/UNIFI ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/UNIFI//install_pwiz_vendor_api_unifi/$(location) ; }
-        if [ path.exists pwiz_aux/msrc/utility/vendor_api/Waters ] { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_aux/msrc/utility/vendor_api/Waters//install_pwiz_vendor_api_waters/$(location) ; }
-        if <vendor-api-support>on in $(properties) { dependencies += <dependency>$(PWIZ_ROOT_PATH)/pwiz_tools/prototype//ThermoRawMetaDumpInstall/$(location) ; }
-    }
-    return $(dependencies) ;
+    return [ install-vendor-api-dependencies-to-locations $(location) : $(properties) ] ;
 }
 
 rule install-identdata-dependencies ( properties * )

pwiz_tools/Skyline/CommandArgUsage.resx

@@ -1018,4 +1018,7 @@ Useful in sample mixtures including multiple species.</value>
   <data name="_verbose_errors" xml:space="preserve">
     <value>Adds additional information to the program output in the case of an error, that may be helpful to Skyline developers.</value>
   </data>
+  <data name="_associate_proteins_gene_level_parsimony" xml:space="preserve">
+    <value>Associate peptides with genes (or gene groups) instead of proteins, and apply parsimony options to that association.</value>
+  </data>
 </root>

pwiz_tools/Skyline/CommandArgs.cs

@@ -1399,6 +1399,8 @@ public bool ImportingSearch
 
         public static readonly Argument ARG_AP_GROUP_PROTEINS = new Argument(@"associate-proteins-group-proteins",
             (c, p) => c.AssociateProteinsGroupProteins = p.IsNameOnly || bool.Parse(p.Value));
+        public static readonly Argument ARG_AP_GENE_LEVEL = new Argument(@"associate-proteins-gene-level-parsimony",
+            (c, p) => c.AssociateProteinsGeneLevelParsimony = p.IsNameOnly || bool.Parse(p.Value));
         public static readonly Argument ARG_AP_SHARED_PEPTIDES = DocArgument.FromEnumType<SharedPeptides>(@"associate-proteins-shared-peptides",
             (c, p) => c.AssociateProteinsSharedPeptides = p);
         public static readonly Argument ARG_AP_MINIMAL_LIST = new Argument(@"associate-proteins-minimal-protein-list",
@@ -1409,16 +1411,18 @@ public bool ImportingSearch
             (c, p) => c.AssociateProteinsMinPeptidesPerProtein = p.ValueInt) { WrapValue = true };
 
         private static readonly ArgumentGroup GROUP_ASSOCIATE_PROTEINS = new ArgumentGroup(() => Resources.CommandLine_AssociateProteins_Associating_peptides_with_proteins, false,
-            ARG_AP_GROUP_PROTEINS, ARG_AP_SHARED_PEPTIDES, ARG_AP_MINIMAL_LIST, ARG_AP_MIN_PEPTIDES, ARG_AP_REMOVE_SUBSETS)
+            ARG_AP_GROUP_PROTEINS, ARG_AP_GENE_LEVEL, ARG_AP_SHARED_PEPTIDES, ARG_AP_MINIMAL_LIST, ARG_AP_MIN_PEPTIDES, ARG_AP_REMOVE_SUBSETS)
             { LeftColumnWidth = 45 };
 
         public bool? AssociateProteinsGroupProteins { get; private set; }
+        public bool? AssociateProteinsGeneLevelParsimony { get; private set; }
         public bool? AssociateProteinsFindMinimalProteinList { get; private set; }
         public bool? AssociateProteinsRemoveSubsetProteins { get; private set; }
         public SharedPeptides? AssociateProteinsSharedPeptides { get; private set; }
         public int? AssociateProteinsMinPeptidesPerProtein { get; private set; }
         public bool AssociatingProteins => AssociateProteinsFindMinimalProteinList.HasValue ||
                                            AssociateProteinsGroupProteins.HasValue ||
+                                           AssociateProteinsGeneLevelParsimony.HasValue ||
                                            AssociateProteinsMinPeptidesPerProtein.HasValue ||
                                            AssociateProteinsRemoveSubsetProteins.HasValue ||
                                            AssociateProteinsSharedPeptides.HasValue;

pwiz_tools/Skyline/CommandLine.cs

@@ -2189,6 +2189,7 @@ private bool AssociateProteins(CommandArgs commandArgs)
                 var proteinAssociation = new ProteinAssociation(Document, progressMonitor);
                 proteinAssociation.UseFastaFile(fastaPath, DigestProteinToPeptides, progressMonitor);
                 proteinAssociation.ApplyParsimonyOptions(commandArgs.AssociateProteinsGroupProteins.GetValueOrDefault(),
+                    commandArgs.AssociateProteinsGeneLevelParsimony.GetValueOrDefault(),
                     commandArgs.AssociateProteinsFindMinimalProteinList.GetValueOrDefault(),
                     commandArgs.AssociateProteinsRemoveSubsetProteins.GetValueOrDefault(),
                     commandArgs.AssociateProteinsSharedPeptides.GetValueOrDefault(),