Commit 57979c06 authored by omid's avatar omid
Browse files

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

trees
parent c0b2d7bb
......@@ -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,
......
......@@ -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;
......
......@@ -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.
......
......@@ -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);
}
}
}
......
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