Gh93 Maternal Deposition work (#104)

Adding MaternalDeposition functionality to the vector genetics model. For details, please see https://github.com/EMOD-Hub/EMOD/issues/93

Author: stitova-idm

Eradication/GeneticProbabilityConfig.cpp

@@ -59,7 +59,7 @@ namespace Kernel
 
             jsonConfigurable::ConstrainedString species_name;
             species_name.constraint_param = &r_species_name_set;
-            species_name.constraints = "<configuration>:Vector_Species_Params.Name";
+            species_name.constraints = m_pSpeciesCollection->SPECIES_NAME_CONSTRAINTS;
 
             initConfigTypeMap( "Species", &species_name, Insecticide_Species_Name_DESC_TEXT );
 
@@ -76,15 +76,12 @@ namespace Kernel
         // --- Now that we have the species parameters, we can make sure
         // --- that the alleles entered are valid.
         // -------------------------------------------------------------
-        const char* constraint_schema = "<configuration>:Vector_Species_Params.Genes.*";
-
         std::set<std::string> allowed_values = m_pVectorSpeciesParameters->genes.GetDefinedAlleleNames();
         allowed_values.insert( "*" );
-
         float probability = 0.0;
         std::vector<std::vector<std::string>> combo_strings;
 
-        initConfigTypeMap( "Allele_Combinations", &combo_strings, ACPC_Allele_Combinations_DESC_TEXT, constraint_schema, allowed_values );
+        initConfigTypeMap( "Allele_Combinations", &combo_strings, ACPC_Allele_Combinations_DESC_TEXT, "Vector_Species_Params[X].Genes", allowed_values );
         initConfigTypeMap( "Probability",         &probability,   ACPC_Probability_DESC_TEXT, 0.0f, 1.0f, 0.0f );
 
         bool is_configured = JsonConfigurable::Configure( inputJson );

Eradication/Insecticides.cpp

@@ -48,7 +48,7 @@ namespace Kernel
 
         jsonConfigurable::ConstrainedString species_name;
         species_name.constraint_param = &r_species_name_set;
-        species_name.constraints = "<configuration>:Vector_Species_Params.Name";
+        species_name.constraints = m_pSpeciesCollection->SPECIES_NAME_CONSTRAINTS;
 
         initConfigTypeMap( "Species", &species_name, Insecticide_Species_Name_DESC_TEXT );
 
@@ -66,7 +66,7 @@ namespace Kernel
             allowed_values = r_species_params.genes.GetDefinedAlleleNames();
         }
         allowed_values.insert( "*" );
-        const char* constraint_schema = "<configuration>:Vector_Species_Params.Genes.*";
+        const char* constraint_schema = "Vector_Species_Params[X].Genes";
 
         std::vector<std::vector<std::string>> combo_strings;
         float modifier_larval = 1.0f;
@@ -360,7 +360,7 @@ namespace Kernel
             // because insecticides has the real thing.
             this->constraint_param = &(p_vp->insecticides.GetInsecticideNames());
         }
-        this->constraints = "<configuration>:Insecticides.Name";
+        this->constraints = "Insecticides[X].Name";
     }
 
     InsecticideName::InsecticideName( const InsecticideName& rMaster )

Eradication/MigrationInfoVector.cpp

@@ -42,7 +42,7 @@ namespace Kernel
 
     bool MigrationMetadataVector::Configure( const Configuration* config )
     {
-        const char* constraint_schema = "<configuration>:Vector_Species_Params.Genes.*";
+        const char* constraint_schema = "Vector_Species_Params[X].Genes";
         std::set<std::string> allowed_values = m_pGenes->GetDefinedAlleleNames();
         allowed_values.insert( "*" );
 

Eradication/ParasiteGenetics.cpp

@@ -815,8 +815,8 @@ namespace Kernel
         if( m_VarGeneRandomnessType != VarGeneRandomnessType::FIXED_NEIGHBORHOOD )
         {
             std::stringstream ss;
-            ss << "It is invalid for <config>.Parasite_Genetics.Var_Gene_Randomness_Type != FIXED_NEIGHBORHOOD and\n"
-               << "<campaign>.OutbreakIndividualMalariaGenetics.Create_Nucleotide_Sequence_From = NUCLEOTIDE_SEQUENCE.";
+            ss << "It is invalid for 'Parasite_Genetics.Var_Gene_Randomness_Type' != 'FIXED_NEIGHBORHOOD' and\n"
+                << "'OutbreakIndividualMalariaGenetics.Create_Nucleotide_Sequence_From' = 'NUCLEOTIDE_SEQUENCE'.";
             throw GeneralConfigurationException( __FILE__, __LINE__, __FUNCTION__, ss.str().c_str() );
         }
 
@@ -868,8 +868,8 @@ namespace Kernel
             std::stringstream ss;
             ss << "Invalid number of frequency sets in '" << pParamNameAlleleFreq << "'.\n";
             ss << "'" << pParamNameAlleleFreq << "' has " << sizeAlleleFreq << "\n";
-            ss << "and '<config>." << pParamNameLocations << "' has " << sizeLocations << ".\n";
-            ss << "There should be one set for each location defined in '<config>." << pParamNameLocations << "'.";
+            ss << "and '" << pParamNameLocations << "' has " << sizeLocations << ".\n";
+            ss << "There should be one set for each location defined in '" << pParamNameLocations << "'.";
             throw GeneralConfigurationException( __FILE__, __LINE__, __FUNCTION__, ss.str().c_str() );
         }
 
@@ -1219,7 +1219,7 @@ namespace Kernel
             ss << "It has " << rString.length() << " characters and ";
             if( isReportParameter )
             {
-                ss << "<config." << pLocationsParameterName << ">";
+                ss << "'" << pLocationsParameterName << "'";
             }
             else
             {

Eradication/SConscript_coreLib

@@ -169,6 +169,7 @@ else:
                             "VectorSpeciesReport.cpp",
                             "VectorTraitModifiers.cpp",
                             "VectorSurveillanceEventCoordinator.cpp",
+                            "VectorMaternalDeposition.cpp",
                             "Climate.cpp",
                             "ClimateByData.cpp",
                             "ClimateConstant.cpp",

Eradication/VectorFertilizer.cpp

@@ -4,6 +4,7 @@
 #include "VectorGene.h"
 #include "VectorGeneDriver.h"
 #include "VectorTraitModifiers.h"
+#include "VectorMaternalDeposition.h"
 #include "RANDOM.h"
 #include "Exceptions.h"
 #include "Log.h"
@@ -17,6 +18,7 @@ namespace Kernel
         : m_pGenes( nullptr )
         , m_pTraitModifiers( nullptr )
         , m_pGeneDrivers( nullptr )
+        , m_pMaternalDepositions( nullptr )
     {
     }
 
@@ -26,11 +28,13 @@ namespace Kernel
 
     void VectorFertilizer::Initialize( const VectorGeneCollection* pGenes,
                                        const VectorTraitModifiers* pTraitModifiers,
-                                       const VectorGeneDriverCollection* pGeneDrivers )
+                                       const VectorGeneDriverCollection* pGeneDrivers,
+                                       const VectorMaternalDepositionCollection* pMaternalDepositions )
     {
         m_pGenes = pGenes;
         m_pTraitModifiers = pTraitModifiers;
         m_pGeneDrivers = pGeneDrivers;
+        m_pMaternalDepositions = pMaternalDepositions;
     }
 
     InitialGenomeData VectorFertilizer::DetermineInitialGenomeData( RANDOMBASE* pRNG, uint32_t total )
@@ -144,6 +148,13 @@ namespace Kernel
         GermlineMutation( gametes_female );
         GermlineMutation( gametes_male   );
 
+        // -------------------------------------------------------------------------
+        // --- Pre-calculating allele changes due to maternal deposition of Cas9
+        // -------------------------------------------------------------------------
+
+        DoMaternalDepostion( rFemale, gametes_female );
+        DoMaternalDepostion( rFemale, gametes_male );
+
         // -------------------------------------------------------------------------
         // --- Now that we have the gametes from each parent and the probability of
         // --- that gamete generate the possible genomes (i.e. fertilized eggs).
@@ -487,6 +498,23 @@ namespace Kernel
         return gppv;
     }
 
+    void VectorFertilizer::DoMaternalDepostion( const VectorGenome& rMomGenome, GameteProbPairVector_t& rGametes ) const
+    {
+        if( ( m_pGeneDrivers == nullptr ) || ( m_pGeneDrivers->Size() == 0 ) ||
+            ( m_pMaternalDepositions == nullptr) || ( m_pMaternalDepositions->Size() == 0) )
+        {
+            return;
+        }
+        else
+        {
+            m_pMaternalDepositions->DoMaternalDeposition( rMomGenome, rGametes );
+            return;
+        }
+
+    }
+
+
+
     void VectorFertilizer::AdjustForNonFertileEggs( GenomeProbPairVector_t& rPossibilities ) const
     {
         for( auto& r_gpp : rPossibilities )

Eradication/VectorFertilizer.h

@@ -9,6 +9,7 @@ namespace Kernel
     class VectorGeneCollection;
     class VectorTraitModifiers;
     class VectorGeneDriverCollection;
+    class VectorMaternalDepositionCollection;
 
     struct MatedGenomeCount
     {
@@ -31,7 +32,8 @@ namespace Kernel
 
         void Initialize( const VectorGeneCollection* pGenes,
                          const VectorTraitModifiers* pTraitModifiers,
-                         const VectorGeneDriverCollection* pGeneDrivers );
+                         const VectorGeneDriverCollection* pGeneDrivers,
+                         const VectorMaternalDepositionCollection* pMaternalDepositions );
 
         InitialGenomeData DetermineInitialGenomeData( RANDOMBASE* pRNG, uint32_t total );
 
@@ -63,12 +65,14 @@ namespace Kernel
                                               const VectorGenome& rGenome );
 
         void GermlineMutation( GameteProbPairVector_t& rGametes );
-
+        void DoMaternalDepostion( const VectorGenome& rMomGenome, GameteProbPairVector_t& rGametes ) const;
         void AdjustForNonFertileEggs( GenomeProbPairVector_t& rPossibilities ) const;
 
+
     private:
         const VectorGeneCollection*       m_pGenes;
         const VectorTraitModifiers*       m_pTraitModifiers;
         const VectorGeneDriverCollection* m_pGeneDrivers;
+        const VectorMaternalDepositionCollection* m_pMaternalDepositions;
     };
 }

Eradication/VectorGene.cpp

@@ -32,11 +32,11 @@ namespace Kernel
     {
         jsonConfigurable::ConstrainedString tmp_from;
         tmp_from.constraint_param = m_pAlleleNameSet;
-        tmp_from.constraints = "<configuration>:Genes.Alleles.Name";
+        tmp_from.constraints = "Genes[X].Alleles[X].Name";
 
         jsonConfigurable::ConstrainedString tmp_to;
         tmp_to.constraint_param = m_pAlleleNameSet;
-        tmp_to.constraints = "<configuration>:Genes.Alleles.Name";
+        tmp_to.constraints = "Genes[X].Alleles[X].Name";
 
         initConfigTypeMap( "Mutate_From",             &tmp_from,    VAM_Mutate_From_DESC_TEXT,             std::string("") );
         initConfigTypeMap( "Mutate_To",               &tmp_to,      VAM_Mutate_To_DESC_TEXT,               std::string("") );

Eradication/VectorGene.h

@@ -170,6 +170,7 @@ namespace Kernel
 
         // IVectorGenomeNames
         virtual std::string GetGenomeName( const VectorGenome& rGenome ) const override; 
+        static constexpr const char* GENE_CONSTRAINTS = "Vector_Species_Params[X].Genes";
 
     protected:
         virtual VectorGene* CreateObject() override;