Merge remote-tracking branch 'origin/gtr_optim' into opt_mix_model

gtroptim_flags.txt

@@ -0,0 +1,31 @@
+--link-exchange-rates
+	This flag indicates to the program that you want to optimize a single rate
+	matrix that's linked between every class. It triggers the optimizeLinkedSubst
+	method within the ModelMixture class which utilizes BFGS to optimize the
+	model parameters. 
+
+--rates-file
+	Tells the program to generate a .ratemat file that includes the linked
+	exchange rate matrix, assuming the above option is used.
+
+--gtr20-model
+	Which model should be used as the starting point when optimizing with
+	GTR20. Comes with an associated value: POISSON, or LG.
+	By default, it uses POISSON. (previously it defaulted to LG)
+
+--reset-method
+	Defines the behavior of the Optimization::restartParameters routine.
+	Comes with an associated value: const, or rand. Default: const.
+	"const" is the new behavior that we have defined wherein the rate matrix
+	values are all multiplied by a constant value if one or more values goes
+	over the boundary. "rand" is the previous behavior wherein all values
+	are multiplied by random_double() * (upper[i] - lower[i])/3 + lower[i].
+
+--guess-multiplier
+	Very closely related to the above option, if the reset method is "const",
+	then this controls the constant value by which to multiply each value
+	(hereby referred to as "c"). If parameters are detected to go over the
+	upper boundary, then every parameter is multiplied by c, if the result isn't
+	also under the lower boundary. Conversely, if parameters are detected to go
+	under the lower boundary, then every parameter is multiplied by 1/c, if the
+	result isn't also over the upper boundary. 

main/phyloanalysis.cpp

@@ -588,6 +588,33 @@ void reportRate(ostream &out, PhyloTree &tree) {
                 " of the portion of the Gamma distribution falling in the category." << endl;
         }
     }
+    //output ratemat to iqtree file -JD
+    if(Params::getInstance().optimize_linked_gtr) { 
+        string fname = Params::getInstance().out_prefix;
+        fname += ".ratemat";
+        ifstream f(fname.c_str());
+        if(f.good()) {
+            out << endl << "Rate matrix:" << endl;
+            cout << endl << "Rate matrix:" << endl;
+            string data;
+            getline(f,data);
+            size_t last = 0;
+            size_t next = 0;
+            while ((next = data.find(" ", last)) != string::npos) { 
+                string outline = data.substr(last, next-last) + " ";
+                out << outline;   
+                cout << outline;
+                last = next + 1; 
+            } 
+            out << data.substr(last) << endl;
+            cout << data.substr(last) << endl;
+            if(!Params::getInstance().rates_file) { //delete ratemat files if not using flag to keep them
+                remove(fname.c_str());
+                remove((fname+"_init").c_str());
+            }
+        }
+        f.close();
+    }
     out << endl;
 }