msasim 25.5.3__tar.gz → 25.9.4__tar.gz

{msasim-25.5.3/msasim.egg-info → msasim-25.9.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: msasim
-Version: 25.5.3
+Version: 25.9.4
 Summary: A fast MSA simulator
 Home-page: https://github.com/elyawy/Sailfish-backend
 Author: Elya Wygoda

{msasim-25.5.3 → msasim-25.9.4/msasim.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: msasim
-Version: 25.5.3
+Version: 25.9.4
 Summary: A fast MSA simulator
 Home-page: https://github.com/elyawy/Sailfish-backend
 Author: Elya Wygoda

{msasim-25.5.3 → msasim-25.9.4}/setup.py

@@ -9,7 +9,7 @@ from datetime import datetime
 now = datetime.now()
 
 
-__version__ = f"{now.year % 100}.{now.month+1}.3"
+__version__ = f"{now.year % 100}.{now.month+1}.4"
 
 # The main interface is through Pybind11Extension.
 # * You can add cxx_std=11/14/17, and then build_ext can be removed.

{msasim-25.5.3 → msasim-25.9.4}/src/modelFactory.cpp

@@ -92,14 +92,7 @@ std::shared_ptr<stochasticProcess> modelFactory::getStochasticProcess() {
     if (_state!=factoryState::COMPLETE) {
         std::cout << "Please set all the required model parameters.\n";
         // return;
-    }
-
-    alphabet *selectedAlphabet;
-    nucleotide nuc;
-    amino ami;
-    if (_alphabet==alphabetCode::NUCLEOTIDE) selectedAlphabet = &nuc;
-    if (_alphabet==alphabetCode::AMINOACID) selectedAlphabet = &ami;
-    
+    }    
 
     std::unique_ptr<replacementModel> repModel;
 
@@ -134,8 +127,9 @@ std::shared_ptr<stochasticProcess> modelFactory::getStochasticProcess() {
             repModel = std::make_unique<tamura92>(theta, TrTv);
             break;
         }
-        // case modelCode::WYANGMODEL:
-        //     repModel = &wYangModel();
+        case modelCode::WYANGMODEL:
+            throw std::runtime_error("Model not implemented: " + std::to_string(static_cast<int>(_model)));
+            break;
         case modelCode::CPREV45:
             repModel = std::make_unique<pupAll>(datMatrixHolder::cpREV45);
             break;
@@ -175,6 +169,9 @@ std::shared_ptr<stochasticProcess> modelFactory::getStochasticProcess() {
         case modelCode::EHO_HELIX:
             repModel = std::make_unique<pupAll>(datMatrixHolder::EHO_HELIX);
             break;
+        case modelCode::EHO_OTHER:
+            repModel = std::make_unique<pupAll>(datMatrixHolder::EHO_OTHER);
+            break;
         case modelCode::EX_EHO_BUR_EXT:
             repModel = std::make_unique<pupAll>(datMatrixHolder::EX_EHO_BUR_EXT);
             break;
@@ -226,11 +223,21 @@ std::shared_ptr<stochasticProcess> modelFactory::getStochasticProcess() {
 alphabet* modelFactory::getAlphabet() {
     if (_alphabet==alphabetCode::NULLCODE) {
         std::cout << "alphabet was not set! returning null pointer\n";
-        _alph = nullptr;
+        _alphPtr = nullptr;
     }
-    if (_alphabet==alphabetCode::NUCLEOTIDE) _alph = new nucleotide();
-    if (_alphabet==alphabetCode::AMINOACID) _alph = new amino();
-    return _alph;
+    // if (_alphabet==alphabetCode::NUCLEOTIDE) _alph = new nucleotide();
+    // if (_alphabet==alphabetCode::AMINOACID) _alph = new amino();
+    if (!_alphPtr) {
+        if (_alphabet == alphabetCode::NUCLEOTIDE) {
+            _alphPtr = std::make_unique<nucleotide>();
+        } else if (_alphabet == alphabetCode::AMINOACID) {
+            _alphPtr = std::make_unique<amino>();
+        } else {
+            return nullptr;
+        }
+    }
+    return _alphPtr.get();
+    // return _alph;
 }
 
 bool modelFactory::isModelValid() {
@@ -239,9 +246,6 @@ bool modelFactory::isModelValid() {
 
 
 
-modelFactory::~modelFactory()
-{
-    delete _alph;
-}
+modelFactory::~modelFactory() {}
 
 

{msasim-25.5.3 → msasim-25.9.4}/src/rateMatrixSim.cpp

@@ -108,7 +108,7 @@ void rateMatrixSim::generate_substitution_log(int seqLength) {
 	for (int h = 0; h < seqLength; h++)  {
 		int selectedRandomCategory = _rateSampler->drawSample() - 1;
 		_rateCategories[h] = selectedRandomCategory;
-		if (selectedRandomCategory == _sp->categories()) {
+		if (selectedRandomCategory >= _sp->categories()) {
 			ratesVec[h] = 0.0;
 			continue;
 		}
@@ -134,20 +134,21 @@ void rateMatrixSim::mutateSeqRecuresively(tree::nodeP currentNode, int seqLength
 		mutateSeqAlongBranch(node, seqLength);
 		if ((*_nodesToSave)[node->id()]) saveSequence(node->id(), node->name());
 		mutateSeqRecuresively(node, seqLength);
-
-		if (!_subManager.isEmpty(currentNode->id())) {
-			_subManager.undoSubs(currentNode->id(), _rootSequence, _rateCategories, _sp.get());
+		if (!_subManager.isEmpty(node->id())) {
+			_subManager.undoSubs(node->id(), _rootSequence, _rateCategories, _sp.get());
 		}
 	}
 }
 
 void rateMatrixSim::mutateSeqAlongBranch(tree::nodeP currentNode, int seqLength) {
 	const MDOUBLE distToFather = currentNode->dis2father();
-	if (distToFather > 0.5) {
-		mutateEntireSeq(currentNode, seqLength);
-	} else {
-		mutateSeqGillespie(currentNode, seqLength, distToFather);
-	}
+	mutateEntireSeq(currentNode, seqLength);
+	
+	// if (distToFather > 0.5) {
+	// 	mutateEntireSeq(currentNode, seqLength);
+	// } else {
+	// 	mutateSeqGillespie(currentNode, seqLength, distToFather);
+	// }
 	// testSumOfRates();
 }
 
@@ -252,7 +253,7 @@ std::unique_ptr<sequenceContainer> rateMatrixSim::getSequenceContainer() {
 	// 	myseqData->add(*std::move(_simulatedSequences[i]));
 	// }
 
-	return std::move(outputSequences);
+	return outputSequences;
 }