From 89eaf9de52984349c89011e64e54b7f6f3c2da3e Mon Sep 17 00:00:00 2001
From: Theo Pannetier <theo@pannetier.nl>
Date: Wed, 3 Jul 2024 17:30:46 +0100
Subject: [PATCH] progress on test for #35

---
 Individual.cpp                | 12 +++--
 Individual.h                  |  1 +
 SpeciesTrait.cpp              |  7 ++-
 unit_tests/testIndividual.cpp | 83 +++++++++++++++++++++++++++++++++++
 4 files changed, 99 insertions(+), 4 deletions(-)

diff --git a/Individual.cpp b/Individual.cpp
index 3d09b7e..79a501f 100644
--- a/Individual.cpp
+++ b/Individual.cpp
@@ -188,9 +188,9 @@ void Individual::inherit(Species* pSpecies, const Individual* mother) {
 	set<unsigned int> recomPositions; //not used here cos haploid but need it for inherit function, not ideal 
 	int startingChromosome = 0;
 
-	const auto& mumTraits = getTraitTypes();
+	const auto& motherTraits = getTraitTypes();
 
-	for (auto const& trait : mumTraits)
+	for (auto const& trait : motherTraits)
 	{
 		const auto motherTrait = mother->getTrait(trait);
 		auto newTrait = motherTrait->clone(); // shallow copy, pointer to species trait initialised and empty sequence
@@ -1591,11 +1591,17 @@ Cell* Individual::getCurrCell() const {
 	return pCurrCell;
 }
 
-
 void Individual::setInitAngle(const float angle) {
 	auto pCRW = dynamic_cast<crwData*>(pTrfrData.get());
 	pCRW->prevdrn = angle;
 }
 
+// Force mutations to trigger for all traits
+void Individual::triggerMutations() {
+	for (auto const& [trType, indTrait] : spTraitTable) {
+		indTrait->mutate();
+	}
+}
+
 #endif // RSDEBUG
 
diff --git a/Individual.h b/Individual.h
index c6378ab..3d29cb7 100644
--- a/Individual.h
+++ b/Individual.h
@@ -349,6 +349,7 @@ class Individual {
 	void insertIndDispTrait(TraitType trType, DispersalTrait tr) {
 		spTraitTable.insert(make_pair(trType, make_unique<DispersalTrait>(tr)));
 	};
+	void triggerMutations();
 #endif
 
 private:
diff --git a/SpeciesTrait.cpp b/SpeciesTrait.cpp
index 05b1abd..b222335 100644
--- a/SpeciesTrait.cpp
+++ b/SpeciesTrait.cpp
@@ -51,7 +51,12 @@ SpeciesTrait::SpeciesTrait(
 		switch (paramType)
 		{
 		case MIN: case MAX: case MEAN:
-			if (!isValidTraitVal(paramVal))
+			if (
+				(trType == NEUTRAL || trType == GENETIC_LOAD || trType == GENETIC_LOAD1 ||
+				trType == GENETIC_LOAD2 || trType == GENETIC_LOAD3 || trType == GENETIC_LOAD4 || trType == GENETIC_LOAD5)
+				&& !isValidTraitVal(paramVal)
+				// dispersal traits are cumulative so no value is invalid
+				)
 				throw logic_error("Invalid parameter value: mutation parameter " + to_string(paramType) + " must have a valid value for trait" + to_string(traitType) + ".");
 			break;
 		case SD: case SHAPE: case SCALE:
diff --git a/unit_tests/testIndividual.cpp b/unit_tests/testIndividual.cpp
index 0a0d621..c4a7f90 100644
--- a/unit_tests/testIndividual.cpp
+++ b/unit_tests/testIndividual.cpp
@@ -598,6 +598,89 @@ void testIndividual() {
 		assert(countRecombineTogetherAB > countRecombineTogetherAC);
 		assert(35 < countRecombineTogetherCD && countRecombineTogetherCD < 65);
 	}
+
+	// Traits can be sex-specific
+	{
+		Patch* pPatch = new Patch(0, 0);
+		Cell* pCell = new Cell(0, 0, (intptr)pPatch, 0);
+
+		const int genomeSz = 6;
+		Species* pSpecies = new Species();
+		pSpecies->setGeneticParameters(
+			set<int>{genomeSz - 1}, // one chromosome
+			genomeSz,
+			0.0, // no recombination
+			set<int>{}, "none", set<int>{}, 0 // no output so no sampling
+		);
+		emigRules emig;
+		emig.indVar = true; 
+		emig.sexDep = true;
+		emig.densDep = false;
+		pSpecies->setEmigRules(emig);
+
+		// Create species trait
+		//// Shared params
+		const map<GenParamType, float> initParams{
+			// all values are 1
+			pair<GenParamType, float>{GenParamType::MIN, 1.0},
+			pair<GenParamType, float>{GenParamType::MAX, 1.0}
+		};
+		const map<GenParamType, float> mutationParams{
+			// reduction of emigration probability
+			pair<GenParamType, float>{GenParamType::MIN, -0.5},
+			pair<GenParamType, float>{GenParamType::MAX, -0.25}
+		};
+		const bool isDiploid{ true };
+
+		//// Sex-specific params
+		const set<int> maleGenePositions = { 0, 2, 4 };
+		const set<int> femaleGenePositions = { 1, 3, 5 };
+		const float maleMutationRate = 0.0;
+		const float femaleMutationRate = 1.0;
+
+		SpeciesTrait* spTrM = new SpeciesTrait(
+			TraitType::E_D0_M,
+			sex_t::MAL,
+			maleGenePositions,
+			ExpressionType::AVERAGE,
+			// Set all initial alleles values to 1
+			DistributionType::UNIFORM, initParams,
+			DistributionType::NONE, initParams, // no dominance, params are ignored
+			true, // isInherited
+			maleMutationRate, // does not mutate
+			DistributionType::UNIFORM, mutationParams, // not used
+			isDiploid ? 2 : 1
+		);
+
+		pSpecies->addTrait(TraitType::E_D0_M, *spTrM);
+
+		SpeciesTrait* spTrF = new SpeciesTrait(
+			TraitType::E_D0_F,
+			sex_t::FEM,
+			femaleGenePositions,
+			ExpressionType::AVERAGE,
+			// Set all initial alleles values to 1
+			DistributionType::UNIFORM, initParams,
+			DistributionType::NONE, initParams, // no dominance, params are ignored
+			true, // isInherited
+			femaleMutationRate, // does not mutate
+			DistributionType::UNIFORM, mutationParams, // not used
+			isDiploid ? 2 : 1
+		);
+		pSpecies->addTrait(TraitType::E_D0_F, *spTrF);
+
+		Individual indFemale = Individual(pCell, pPatch, 0, 0, 0, 0.0, false, 0);
+		Individual indMale = Individual(pCell, pPatch, 0, 0, 0, 1.0, false, 0);
+		indFemale.setUpGenes(pSpecies, 1.0);
+		indMale.setUpGenes(pSpecies, 1.0);
+		indFemale.triggerMutations();
+		indMale.triggerMutations();
+
+		emigTraits femaleEmig = indFemale.getIndEmigTraits();
+		emigTraits maleEmig = indMale.getIndEmigTraits();
+		assert(femaleEmig.d0 != 1.0);
+		assert(maleEmig.d0 == 1.0);
+	}
 }
 
 #endif //RSDEBUG
\ No newline at end of file