profillic-hmmer.hpp

/**
 * \file profillic-hmmer.hpp
 * \brief Minor modifications necessary to compile profillic mods in c++
 * \details
 * Had to change hmmer3/easel/esl_msa.h, where keyword "new" was being used as an 
 * argument name in a predeclaration for esl_msa_Copy (..).  It now reads:
 * \code
 * extern int      esl_msa_Copy (const ESL_MSA *msa, ESL_MSA *_new);
 * \endcode
 */
#ifndef __GALOSH_PROFILLICHMMER_HPP__
#define __GALOSH_PROFILLICHMMER_HPP__

// HMMoC-BFloat-Algebra:
#include "Algebra.hpp"

/// TAH 2/12 solving some circular reference problems by forward declaring DynamicProgramming
namespace galosh {
template <typename ResidueType,
          typename ProbabilityType,
          typename ScoreType,
          typename MatrixValueType>
class DynamicProgramming;

template <typename ResidueType,
        typename ProbabilityType,
        typename ScoreType,
        typename MatrixValueType>
class AlignmentProfileAccessor;

}


// Galosh:
#include "Profile.hpp"
using galosh::ProfileTreeRoot;

/* ////////////// For profillic-hmmer ////////////////////////////////// */
// Stuff we needed to modify in order to compile it in c++:
// NOTE I had to change hmmer3/easel/esl_msa.h, where keyword "new" was being used as an argument name in a predeclaration for esl_msa_Copy (..).  It now reads:
//extern int      esl_msa_Copy (const ESL_MSA *msa, ESL_MSA *_new);
#define ESL_ALLOC_CPP(arg_type, p, size) do {            \
    if ( ( (p) = ( static_cast<arg_type *>( malloc(size)) ) ) == NULL) { \
       status = eslEMEM;\
       esl_exception(eslEMEM, FALSE, __FILE__, __LINE__, "malloc of size %d failed", size); \
       goto ERROR;\
     }} while (0)
#define ESL_RALLOC_CPP(arg_type, p, tmp, newsize) do {           \
    if ((p) == NULL) { \
      (tmp) = ( static_cast<arg_type *>( malloc(newsize) ) );           \
    } else             { (tmp) = static_cast<arg_type *>(realloc((p), (newsize))); } \
     if ((tmp) != NULL) (p) = static_cast<arg_type *>(tmp);\
     else {\
       status = eslEMEM;\
       esl_exception(eslEMEM, FALSE, __FILE__, __LINE__, "realloc for size %d failed", newsize);\
       goto ERROR;\
     }} while (0)

#define ESL_REALLOC_CPP(arg_type, p, newsize) do {       \
     void *esltmpp;\
     if ((p) == NULL) { (esltmpp) = static_cast<arg_type *>( malloc(newsize) );         } \
     else             { (esltmpp) = static_cast<arg_type *>( realloc((p), (newsize)) ); } \
     if ((esltmpp) != NULL) (p) = static_cast<arg_type *>(esltmpp);\
     else {\
       status = eslEMEM;\
       esl_exception(eslEMEM, FALSE, __FILE__, __LINE__, "realloc for size %d failed", newsize);\
       goto ERROR;\
     }} while (0)
//
/* ////////////// End profillic-hmmer ////////////////////////////////// */

#endif // __GALOSH_PROFILLICHMMER_HPP__