CmdLine.h

#ifndef CMDLINE_H
#define CMDLINE_H

#include <climits>
#include "VerbosityLevels.h"

#ifdef _OPENMP
#include <omp.h>
#endif

/// The default maximum number of optimization steps.
///
static const unsigned int MAX_ITERATIONS = 10000;

/// Parse the command line flags.
///
///     @author Mario Valle - Swiss National Supercomputing Centre (CSCS)
///     @date 2010-12-22 (initial version)
///     @version 1.1
///
///
class CmdLine {

public:
  /// Constructor.
  ///
  /// Here are set the default values for the command line settable parameters
  ///
  CmdLine()
      : mDeltaValueForGradient(0.0), mRelativeError(1e-3), mTreeFile(NULL),
        mGeneFile(NULL), mGraphFile(NULL), mResultsFile(NULL),
        mVerboseLevel(VERBOSE_ONLY_RESULTS), mSeed(0), mBranchAll(false),
        // mBranchStart(UINT_MAX),
        // mBranchEnd(UINT_MAX),
        mExportComputedTimes(UINT_MAX), mComputeHypothesis(UINT_MAX),
        mOptimizationAlgo(22), mExtraDebug(0), mMaxIterations(MAX_ITERATIONS),
        mIgnoreFreq(false), mDoNotReduceForest(false),
        mBranchLengthsFromFile(false), mNoMaximization(false), mTrace(false),
#ifdef _OPENMP
        mNumThreads(omp_get_max_threads()/2 + 1 ), // to prevent possible false sharing
#else
        mNumThreads(1),
#endif
        mForceSerial(false), mBranchFromFile(false), mInitH0fromH1(false),
        mInitFromParams(false), mCleanData(false), mStopIfNotLRT(true),
        //		mCmdLineImpl(NULL),
        mFixedBranchLength(false), mCmdLineImpl(NULL)

  {
  }

  /// Destructor.
  ///
  ~CmdLine();

  /// Parse the command line.
  ///
  /// @param[in] aCnt Number of command line parameters (from main argc)
  /// @param[in] aVal Array of command line parameters (from main argv)
  ///
  /// @exception FastCodeMLFatal For invalid command line parameters.
  /// @exception FastCodeMLSuccess After showing help to exit the application
  ///
  void parseCmdLine(int aCnt, char **aVal);

public:
  double mDeltaValueForGradient; ///< The variable increment to compute gradient
                                 ///(zero means use a hardcoded default value)
  double mRelativeError;         ///< Relative error to stop maximization
  const char *mTreeFile;         ///< %Newick tree file name
  const char *mGeneFile;         ///< %Genes file name
  const char *mGraphFile; ///< If not null export the forest to this file in GML
  /// format to be visualized using R igraph package or
  /// yEd editor
  const char *mResultsFile;   ///< File to which the results should be written
  unsigned int mVerboseLevel; ///< Verbosity level. 0: no messages; 1: basic
  /// messages; 2: messages useful for debugging; 3:
  /// really annoying
  unsigned int mSeed; ///< Random number generator seed (0 means not set from
                      ///command line)
  bool mBranchAll;    ///< If it should consider all branches (internals plus
                      ///leaves) as foreground >
  // unsigned int	mBranchStart;			///< Compute from this branch. The
  // numbering starts at 0 (UINT_MAX means run all branches)
  // unsigned int	mBranchEnd;				///< Compute to this branch. The
  // numbering starts at 0 (UINT_MAX means run all branches). It is >=
  // mBranchStart
  unsigned int mExportComputedTimes; ///< If 0 or 1 the times exported are the
  /// computed ones in H0 or H1, otherwise
  ///(UINT_MAX) the one read from file
  unsigned int mComputeHypothesis; ///< If set to 0 compute only H0, if set to 1
  /// compute only H1, otherwise compute both
  unsigned int mOptimizationAlgo; ///< Select the optimization algorithm to use
  unsigned int mExtraDebug; ///< Extra debug parameter for development tests
  unsigned int
      mMaxIterations; ///< Maximum number of iterations for the maximization
  bool mIgnoreFreq; ///< Ignore the computed codon frequencies and set them all
  /// to 1/61
  bool mDoNotReduceForest; ///< If true do not reduce the forest merging common
  /// subtrees
  bool mBranchLengthsFromFile; ///< The initial value of the branch lengths is
  /// taken from the phylo tree file
  bool mNoMaximization; ///< Only the first step of the likelihood maximization
  /// is taken
  bool mTrace; ///< Trace the optimization steps
  unsigned int
      mNumThreads; ///< Number of threads (if 1 the parallelization is disabled)
  bool mForceSerial;    ///< Disable all parallelism
  bool mBranchFromFile; ///< Read the foreground branch to use from the phylo
  /// tree file (it is marked as #1)
  bool mInitH0fromH1; ///< If set starts the H0 computation from the H1 results
  bool mInitFromParams; ///< Initialize times from phylo tree and the other from
  /// values hardcoded or entered on the command line
  bool mCleanData; ///< Remove ambiguous or missing sites from the MSA (genes)
  bool mStopIfNotLRT; ///< Stop H0 maximization when LRT cannot be satisfied
  bool mFixedBranchLength; ///<fixed branch lengths

private:
  struct CmdLineImpl;
  CmdLineImpl *mCmdLineImpl; ///< Implementation so this structure could be used
  /// without other modules be aware of its internals
};

#endif