Fix NONREV protein model initialisation unintentionally converting rooted input tree (reported by Suha Naser)

Author: bqminh

model/modelmarkov.cpp

@@ -1526,7 +1526,7 @@ void ModelMarkov::readStateFreq(string str) throw(const char*) {
         state_freq[i] *= sum;
 }
 
-void ModelMarkov::readParameters(const char *file_name) {
+void ModelMarkov::readParameters(const char *file_name, bool adapt_tree) {
     if (!fileExists(file_name))
         outError("File not found ", file_name);
 
@@ -1538,9 +1538,9 @@ void ModelMarkov::readParameters(const char *file_name) {
         double d;
         in >> d;
         if (d < 0) {
-            setReversible(false);
+            setReversible(false, adapt_tree);
         } else
-            setReversible(true);
+            setReversible(true, adapt_tree);
         in.close();
     }
 	catch (...) {
@@ -1574,16 +1574,16 @@ void ModelMarkov::readParameters(const char *file_name) {
     }
 }
 
-void ModelMarkov::readParametersString(string &model_str) {
+void ModelMarkov::readParametersString(string &model_str, bool adapt_tree) {
 
     // if detect if reading full matrix or half matrix by the first entry
     int end_pos;
     double d = 0.0;
     d = convert_double(model_str.c_str(), end_pos);
     if (d < 0) {
-        setReversible(false);
+        setReversible(false, adapt_tree);
     } else
-        setReversible(true);
+        setReversible(true, adapt_tree);
 
 	try {
 		stringstream in(model_str);

model/modelmarkov.h

@@ -170,13 +170,13 @@ class ModelMarkov : public ModelSubst, public EigenDecomposition
 		read model parameters from a file
 		@param file_name file containing rate matrix and state frequencies
 	*/
-	void readParameters(const char *file_name);
+	void readParameters(const char *file_name, bool adapt_tree = true);
 
 	/**
 		read model parameters from a string
 		@param model_str string containing rate matrix and state frequencies
 	*/
-	void readParametersString(string &model_str);
+	void readParametersString(string &model_str, bool adapt_tree = true);
 
 	/**
 		compute the transition probability matrix.

model/modelprotein.cpp

@@ -780,10 +780,10 @@ void ModelProtein::init(const char *model_name, string model_params, StateFreqTy
         if (Params::getInstance().model_name_init) {
             nxs_model = models_block->findModel(Params::getInstance().model_name_init);
             if (nxs_model) {
-                readParametersString(nxs_model->description);
+                readParametersString(nxs_model->description, false);
             } else {
                 // initialize with custom model file
-                readParameters(Params::getInstance().model_name_init);
+                readParameters(Params::getInstance().model_name_init, false);
             }
             rescaleRates(rates, getNumRateEntries());
             if (!isReversible())
@@ -792,7 +792,7 @@ void ModelProtein::init(const char *model_name, string model_params, StateFreqTy
             // initialize rate matrix with LG
             nxs_model = models_block->findModel("LG");
             ASSERT(nxs_model);
-            readParametersString(nxs_model->description);
+            readParametersString(nxs_model->description, false);
             rescaleRates(rates, getNumRateEntries());
         }
         // 2018-05-08 bug fix: GTR20 rates are not optimized
@@ -807,10 +807,10 @@ void ModelProtein::init(const char *model_name, string model_params, StateFreqTy
         if (Params::getInstance().model_name_init) {
             nxs_model = models_block->findModel(Params::getInstance().model_name_init);
             if (nxs_model) {
-                readParametersString(nxs_model->description);
+                readParametersString(nxs_model->description, false);
             } else {
                 // initialize with custom model file
-                readParameters(Params::getInstance().model_name_init);
+                readParameters(Params::getInstance().model_name_init, false);
             }
             rescaleRates(rates, getNumRateEntries());
             if (isReversible())
@@ -819,7 +819,7 @@ void ModelProtein::init(const char *model_name, string model_params, StateFreqTy
             // initialize rate matrix with LG
             nxs_model = models_block->findModel("LG");
             ASSERT(nxs_model);
-            readParametersString(nxs_model->description);
+            readParametersString(nxs_model->description, false);
             rescaleRates(rates, getNumRateEntries());
             setReversible(false);
         }