Commit dd310797 authored by mvalle's avatar mvalle
Browse files

Changed option --times-from-file to --lenghts-from-file

Changed gene file to alignment file.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5470 95c5a404-1f88-0410-a6b0-c3f062b6f34a
parent ee5c527a
......@@ -159,7 +159,7 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal)
{ OPT_NOT_REDUCE, "-nr", SO_NONE, "Do not reduce forest by merging common subtrees" },
{ OPT_NOT_REDUCE, "--no-reduce", SO_NONE, "" },
{ OPT_TIMES_FROM_FILE, "-l", SO_NONE, "Initial branch lengths from tree file" },
{ OPT_TIMES_FROM_FILE, "--times-from-file", SO_NONE, "" },
{ OPT_TIMES_FROM_FILE, "--lengths-from-file", SO_NONE, "" },
{ OPT_ONE_STEP, "-o", SO_NONE, "Only the initial step is performed (no maximization)" },
{ OPT_ONE_STEP, "--initial-step", SO_NONE, "" },
{ OPT_COMP_TIMES, "-c", SO_REQ_SEP, "Export the computed times from H0 if 0, H1 if 1, otherwise the one read in the phylo tree" },
......@@ -196,7 +196,7 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal)
};
// Setup the usage string
const char* usage_msg = "FastCodeML [options] tree_file gene_file";
const char* usage_msg = "FastCodeML [options] tree_file alignment_file";
// Declare our options parser, pass in the arguments from main as well as our array of valid options.
CSimpleOpt args(aCnt, aVal, parser_options, SO_O_NOSLASH);
......@@ -347,7 +347,7 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal)
// Falltrough
case 1:
std::cout << "Missing GENE file" << std::endl << std::endl;
std::cout << "Missing PHYLIP CODON ALIGNMENT file" << std::endl << std::endl;
std::cout << "Usage:" << std::endl;
std::cout << " " << usage_msg << std::endl << std::endl;
mCmdLineImpl->showHelp(parser_options);
......
......@@ -11,7 +11,7 @@ static const int N = 61;
static const int N64 = 64;
/// Max number of possible tree traversals for each cycle (4).
/// This is also the number of codon classes
/// This is also the number of codon classes.
///
static const int Nt = 4;
......
......@@ -141,7 +141,7 @@ public:
///
TreeNode* getChild(unsigned int aIdx) const
{
if(aIdx >= mChildrenList.size()) return NULL;
if(aIdx >= static_cast<unsigned int>(mChildrenList.size())) return NULL;
return mChildrenList[aIdx];
}
......
......@@ -516,7 +516,7 @@ Usage:
-nr --no-reduce (no argument)
Do not reduce forest by merging common subtrees
-l --times-from-file (no argument)
-l --lenghts-from-file (no argument)
Initial branch lengths from tree file
-o --initial-step (no argument)
......
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