Commit a6eaa3d7 authored by akalantz's avatar akalantz
Browse files

Version added in the help message - few dispalay changes

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@7157 95c5a404-1f88-0410-a6b0-c3f062b6f34a
parent 223c0749
......@@ -6,6 +6,9 @@
#include "simpleopt/SimpleOpt.h"
#include "Exceptions.h"
#include "ParseParameters.h"
extern const char* version;
/// Implementation of the CmdLine class.
///
......@@ -250,7 +253,8 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal)
break;
default:
case OPT_HELP:
case OPT_HELP:
std::cout <<std::endl<<"------------------"<< std::endl<<"FastCodeML V"<<version<<std::endl<<"------------------"<<std::endl;
std::cout << "Usage:" << std::endl;
std::cout << " " << usage_msg << std::endl << std::endl;
mCmdLineImpl->showHelp(parser_options);
......@@ -390,11 +394,13 @@ void CmdLine::parseCmdLine(int aCnt, char **aVal)
switch(args.FileCount())
{
case 0:
std::cout << "Missing NEWICK TREE file" << std::endl;
std::cout << "Missing NEWICK TREE file" << std::endl;
std::cout <<std::endl<<"------------------"<< std::endl<<"FastCodeML V"<<version<<std::endl<<"------------------"<<std::endl;
// Falltrough
case 1:
std::cout << "Missing PHYLIP CODON ALIGNMENT file" << std::endl << std::endl;
std::cout << "Missing PHYLIP CODON ALIGNMENT file" << std::endl << std::endl;
std::cout <<std::endl<<"------------------"<< std::endl<<"FastCodeML V"<<version<<std::endl<<"------------------"<<std::endl;
std::cout << "Usage:" << std::endl;
std::cout << " " << usage_msg << std::endl << std::endl;
mCmdLineImpl->showHelp(parser_options);
......
......@@ -26,7 +26,7 @@
#include "BranchSiteModel.h"
#include "ParseParameters.h"
#include "VerbosityLevels.h"
#include "WriteResults.h"
#include "WriteResults.h"
#ifndef VTRACE
#ifdef _OPENMP
......@@ -49,13 +49,15 @@
///
/// @param[in] aRgc Number of command line parameters
/// @param[in] aRgv Command line parameters
///
///
const char* version="1.1.0";
int main(int aRgc, char **aRgv)
{
try
{
const char* version="1.1.0";
#ifdef USE_MKL_VML
// If used, intitialize the MKL VML library
vmlSetMode(VML_HA|VML_DOUBLE_CONSISTENT);
......@@ -106,8 +108,8 @@ int main(int aRgc, char **aRgv)
#ifdef USE_MPI
// Shutdown messages from all MPI processes except the master
if(!hlc.isMaster()) cmd.mVerboseLevel = VERBOSE_NONE;
#endif
//<<"* * * * * * * * * * *"<<
#endif
std::cout <<std::endl<<"------------------"<< std::endl<<"FastCodeML V"<<version<<std::endl<<"------------------"<<std::endl;
// Write out command line parameters (if not quiet i.e. if verbose level > 0)
if(cmd.mVerboseLevel >= VERBOSE_INFO_OUTPUT)
......@@ -639,7 +641,10 @@ Usage:
Don't stop H0 maximization even if it cannot satisfy LRT (default: stop)
-mi --max-iterations (required argument)
Maximum number of iterations for the maximizer (default: 10000)
Maximum number of iterations for the maximizer (default: 10000)
-bl --branch-lengths-fixed (no argument)
The length of the brances is fixed
@endverbatim
*/
......
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