output rtt distance and date in verbose mode

tothuhien · Oct 9, 2020 · 49846df · 49846df
1 parent 62ad74a
commit 49846df
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Showing 6 changed files with 35 additions and 5 deletions.
diff --git a/bin/lsd2_mac b/bin/lsd2_mac
diff --git a/src/confidence_interval.cpp b/src/confidence_interval.cpp
@@ -495,7 +495,21 @@ void output(double br,int y, InputOutputStream *io, Pr* pr,Node** nodes,ostream&
             pr->resultMessage.push_back(oss.str());
         }
     }
-
+    //Write input trees out after all pre-process steps (collapse branches, remove outgroups, rooting, remove outliers etc)
+    if (pr->verbose){
+        std::ostringstream oss;
+        oss<<"- Evolution distance & date of each node:\n";
+        oss<<"Node  Branch_length Branch_elapsed_time   RttDistance NodeDate\n";
+        double* r2t = rtt(pr,nodes);
+        for (int i=0;i<=pr->nbBranches;i++){
+            if (i<pr->nbINodes) oss<<"node_"<<i<<"   ";
+            else oss<<nodes[i]->L<<"    ";
+            if (i==0) oss<<"NA  NA  ";
+            else oss<<nodes[i]->B<<" "<<pr->rho*(nodes[i]->D-nodes[nodes[i]->P]->D)<<"   ";
+            oss<<r2t[i]<<"    "<<nodes[i]->D<<"\n";
+        }
+        pr->resultMessage.push_back(oss.str());
+    }
     //Replace branche length by time-scaled lengths
     if (pr->ratePartition.size()==0){
         for (int i=1;i<=pr->nbBranches;i++){

diff --git a/src/options.cpp b/src/options.cpp
@@ -25,7 +25,7 @@ Pr* getOptions( int argc, char** argv )
 
 Pr* getCommandLine( int argc, char** argv)
 {
-    const string VERSION="v.1.9.5";
+    const string VERSION="v.1.9.6";
     Pr* opt = new Pr();
     int c;
     string s;
@@ -356,7 +356,7 @@ Pr* getInterface()
 
 void printInterface(ostream& in, Pr* opt)
 {
-    const string VERSION = "v.1.9.5";
+    const string VERSION = "v.1.9.6";
 
     in<<"\nLEAST-SQUARE METHODS TO ESTIMATE RATES AND DATES - "<<VERSION<<" \n\n";
     in<<"\nInput files:\n";
@@ -513,7 +513,7 @@ void printHelp( void )
     const string BOLD = "\033[00;01m";
     const string LINE = "\033[00;04m";
     const string FLAT = "\033[00;00m";
-    const string VERSION = "v.1.9.5";
+    const string VERSION = "v.1.9.6";
 
     cout<<BOLD<<"LSD: LEAST-SQUARES METHODS TO ESTIMATE RATES AND DATES - "<<VERSION<<"\n\n";
     cout<<BOLD<<"DESCRIPTION\n"

diff --git a/src/readData.cpp b/src/readData.cpp
@@ -447,7 +447,7 @@ void extrait_outgroup(InputOutputStream *io, Pr* pr, bool useBootstrapTree){
                 w << newick(p_r, p_r,pr, nodes_new,nbTips).c_str();
             }
             if ((nbTips+outgroups.size()) != (pr->nbBranches+1 - pr->nbINodes)){
-                cerr<<"Error: The outgroups do not form a monophyletic in the tree "<<y+1<<endl;
+                cerr<<"The outgroups do not form a monophyletic in the tree "<<y+1<<endl;
                 exit(EXIT_FAILURE);
             }
             if (!pr->removeOutgroup) {

diff --git a/src/utils.cpp b/src/utils.cpp
@@ -3305,3 +3305,17 @@ bool checkTopology(Pr* pr,Node** nodes1, Node** nodes2){
     }
     return true;
 }*/
+
+double* rtt(Pr* pr,Node** nodes){
+    double* r2t = new double[pr->nbBranches+1];
+    for (int i=0;i<=pr->nbBranches;i++){
+        double r=0;
+        int j=i;
+        while (j!=0){
+            r+=nodes[j]->B;
+            j=nodes[j]->P;
+        }
+        r2t[i]=r;
+    }
+    return r2t;
+}
diff --git a/src/utils.h b/src/utils.h
@@ -322,4 +322,6 @@ void adjustDateToYM(Date*& date,int m1,int d1,int m2,int d2);
 
 bool checkTopology(Pr* pr,Node** nodes1, Node** nodes2);
 
+double* rtt(Pr* pr,Node** nodes);
+
 #endif
Original file line number	Diff line number	Diff line change
Expand Up		@@ -322,4 +322,6 @@ void adjustDateToYM(Date*& date,int m1,int d1,int m2,int d2);

		bool checkTopology(Pr* pr,Node nodes1, Node nodes2);

		double* rtt(Pr* pr,Node** nodes);

		#endif