some changes in command line option comments as well as final printed

trees

CmdLine.cpp

@@ -182,7 +182,7 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal) {
       // configuration parameters
 
       {OPT_SEED, "-s", SO_REQ_SEP,
-       "Random number generator seed (0 < seed < 1000000000)"},
+       "Random number generator seed (0 < seed < 1000000000, seed=0 -> random seed)"},
       {OPT_SEED, "--seed", SO_REQ_SEP, ""},
       {OPT_NUM_THREADS, "-nt", SO_REQ_SEP,
        "Number of threads (1 for non parallel execution)"},
@@ -242,10 +242,10 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal) {
       // initialization parameters
 
       {OPT_TIMES_FROM_FILE, "-l", SO_NONE,
-       "Initial branch lengths from tree file"},
+       "Initial branch lengths from tree file (otherwise random initial branch lengths)"},
       {OPT_TIMES_FROM_FILE, "--blengths-from-file", SO_NONE, ""},
       {OPT_BRANCH_LENGTH, "-bl", SO_NONE,
-       "The length of the branches is fixed"},
+       "Initial branch lengths from tree file and fixed"},
       {OPT_BRANCH_LENGTH, "--branch-lengths-fixed", SO_NONE, ""},
       {OPT_BRANCH_ALL, "-ba", SO_NONE,
        "Do for all branches as foreground branch (including leaves)"},
@@ -255,7 +255,7 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal) {
                                          "in the phylo tree"},
       {OPT_COMP_TIMES, "--export-comp-times", SO_REQ_SEP, ""},
       {OPT_INIT_PARAM, "-p", SO_REQ_SEP, "Pass initialization parameter in the "
-                                         "form: P=value (P: w0, k, p0, p1, w2) "
+                                         "form (otherwise random): P=value (P: w0, k, p0, p1, w2) "
                                          "-> e.g. -p w0=1.1 -p p0=2.1 ..."},
       {OPT_INIT_PARAM, "--init-param", SO_REQ_SEP, ""},
       {OPT_INIT_DEFAULT, "-ic", SO_NONE,

Newick.cpp

@@ -304,7 +304,7 @@ int Newick::printTreeAnnotated(std::ostream &aOut, TreeNode *aNode, int aBranch,
 
 int Newick::printTreeAnnotatedWithEstLens(std::ostream &aOut, TreeNode *aNode,
                                           int aBranch, bool wLeaves,
-                                          std::vector<double> *mVar) const {
+                                          std::vector<double> *mVar, bool bNumber) const {
   TreeNode *m;
   unsigned int idx;
   int branch_idx = aBranch;
@@ -312,10 +312,10 @@ int Newick::printTreeAnnotatedWithEstLens(std::ostream &aOut, TreeNode *aNode,
   // Special case for the root
   if (!aNode) {
     if (wLeaves)
-      aOut << "Annotated Newick Tree (*N marks the branch N)" << std::endl;
+      aOut << "Annotated Newick Tree (*N marks the branch N)" << std::endl << std::endl;
     else
       aOut << "Annotated Newick Tree (*N marks the internal branch N)"
-           << std::endl;
+           << std::endl << std::endl;
     aOut << '(';
     for (idx = 0; (m = mTreeRoot.getChild(idx)) != NULL; ++idx) {
       if (idx > 0)
@@ -333,7 +333,7 @@ int Newick::printTreeAnnotatedWithEstLens(std::ostream &aOut, TreeNode *aNode,
       branch_idx = aBranch + 1;
     aNode->printNodeWoutLen();
     std::cout << std::setprecision(6) << ":" << (*mVar)[aBranch];
-    if (wLeaves)
+    if (wLeaves and bNumber)
       aOut << '*' << aBranch;
   } else {
     branch_idx = aBranch + 1;
@@ -347,7 +347,7 @@ int Newick::printTreeAnnotatedWithEstLens(std::ostream &aOut, TreeNode *aNode,
     aOut << ')';
     aNode->printNodeWoutLen();
     std::cout << std::setprecision(6) << ":" << (*mVar)[aBranch];
-    aOut << '*' << aBranch;
+    if (bNumber) aOut << '*' << aBranch;
   }
 
   return branch_idx;

Newick.h

@@ -86,7 +86,7 @@ public:
   virtual int
   printTreeAnnotatedWithEstLens(std::ostream &aOut, TreeNode *aNode = NULL,
                                 int aInternalBranch = 0, bool wLeaves = false,
-                                std::vector<double> *mVar = NULL) const;
+                                std::vector<double> *mVar = NULL, bool bNumber=true) const;
 
 private:
   /// Load a phylo tree definition from a Newick formatted string.

fast.cpp

@@ -635,6 +635,8 @@ int main(int aRgc, char **aRgv) {
 						std::cout << std::endl << "H1 Final ";
 					tree.printTreeAnnotatedWithEstLens(std::cout, NULL, 0, true,
 							&mVar);
+					tree.printTreeAnnotatedWithEstLens(std::cout, NULL, 0, true,
+							&mVar, false);
 				}
 				// tree.printTreeAnnotatedWithEstLens(std::cout, NULL, 0, true,
 				// &h1.getVariables());
@@ -869,6 +871,8 @@ int main(int aRgc, char **aRgv) {
 							std::cout << std::endl << "H1 Final ";
 						tree.printTreeAnnotatedWithEstLens(std::cout, NULL, 0,
 								true, &mVar);
+						tree.printTreeAnnotatedWithEstLens(std::cout, NULL, 0,
+														true, &mVar, false);
 					}
 				}
 			}