Fix site-specific state freq usage in AliSim

StefanFlaumberg · StefanFlaumberg · commit cb977a7e8728 · 2025-06-21T19:51:13.000+03:00
diff --git a/simulator/alisimulatorheterogeneity.cpp b/simulator/alisimulatorheterogeneity.cpp
@@ -355,7 +355,8 @@ int AliSimulatorHeterogeneity::estimateStateFromOriginalTransMatrix(ModelSubst *
         #pragma omp critical
         #endif
         {
-            model->setStateFrequency(tmp_state_freqs);
+            model->getMixtureClass(model_component_index)->setStateFrequency(tmp_state_freqs);
+            model->getMixtureClass(model_component_index)->decomposeRateMatrix();
             // compute the transition matrix
             model->computeTransMatrix(combine_rate * branch_length * rate, trans_matrix, model_component_index, dad_state);
         }

Original file line number	Diff line number	Diff line change
`@@ -355,7 +355,8 @@ int AliSimulatorHeterogeneity::estimateStateFromOriginalTransMatrix(ModelSubst *`
`355`	`355`	`#pragma omp critical`
`356`	`356`	`#endif`
`357`	`357`	`{`
`358`		`- model->setStateFrequency(tmp_state_freqs);`
	`358`	`+ model->getMixtureClass(model_component_index)->setStateFrequency(tmp_state_freqs);`
	`359`	`+ model->getMixtureClass(model_component_index)->decomposeRateMatrix();`
`359`	`360`	`// compute the transition matrix`
`360`	`361`	`model->computeTransMatrix(combine_rate * branch_length * rate, trans_matrix, model_component_index, dad_state);`
`361`	`362`	`}`