C++ p7_CreateDefaultApp函数代码示例

int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go       = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_RANDOMNESS *rng      = esl_randomness_Create(esl_opt_GetInteger(go, "-s"));
  P7_COORDS2     *c2       = p7_coords2_Create(0, 0);
  P7_COORDS2_HASH *hash    = p7_coords2_hash_Create(0, 0, 0);
  int             L        = 20;
  int             maxseg   = 1;
  int             nsamples = 1000;
  int32_t        *wrk      = NULL;
  int32_t         keyidx;
  int             i;

  for (i = 0; i < nsamples; i++)
    {
      p7_coords2_Sample(rng, c2, maxseg, L, &wrk);
      p7_coords2_hash_Store(hash, c2, &keyidx);
      p7_coords2_Reuse(c2);
    }
  
  p7_coords2_hash_Dump(stdout, hash);

  if (wrk) free(wrk);
  p7_coords2_hash_Destroy(hash);
  p7_coords2_Destroy(c2);
  esl_randomness_Destroy(rng);
  esl_getopts_Destroy(go);
  return 0;
}

int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;

  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");
  p7_hmmfile_Close(hfp);

  esl_stopwatch_Start(w);
  while (N--)
    { /*                cfg   rng   bg    gm    om  */
      p7_Calibrate(hmm, NULL, NULL, NULL, NULL, NULL);
    }
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");

  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}

int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go   = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_RANDOMNESS *r    = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc  = NULL;
  P7_BG          *bg   = NULL;
  P7_HMM         *hmm  = NULL;
  P7_OPROFILE    *om   = NULL;
  int             M    = esl_opt_GetInteger(go, "-M");
  int             L    = esl_opt_GetInteger(go, "-L");
  
  fprintf(stderr, "## %s\n", argv[0]);
  fprintf(stderr, "#  rng seed = %" PRIu32 "\n", esl_randomness_GetSeed(r));

  /* Sample a random HMM and optimized profile, in amino acid alphabet.  */
  if ((abc = esl_alphabet_Create(eslAMINO))                    == NULL)  esl_fatal("failed to create alphabet");
  if ((bg = p7_bg_Create(abc))                                 == NULL)  esl_fatal("failed to create null model");
  if (( p7_oprofile_Sample(r, abc, bg, M, L, &hmm, NULL, &om)) != eslOK) esl_fatal("failed to sample HMM and profile");

  /* unit test(s) */
  utest_ReadWrite(hmm, om);

  p7_oprofile_Destroy(om);
  p7_hmm_Destroy(hmm);
  p7_bg_Destroy(bg);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);

  fprintf(stderr, "#  status = ok\n");
  return eslOK;
}

int
main(int argc, char **argv)
{
    ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
    char           *hmmfile = esl_opt_GetArg(go, 1);
    ESL_STOPWATCH  *w       = esl_stopwatch_Create();
    ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
    ESL_ALPHABET   *abc     = NULL;
    P7_HMMFILE     *hfp     = NULL;
    P7_HMM         *hmm     = NULL;
    P7_BG          *bg      = NULL;
    P7_PROFILE     *gm      = NULL;
    P7_GMX         *gx1     = NULL;
    P7_GMX         *gx2     = NULL;
    int             L       = esl_opt_GetInteger(go, "-L");
    int             N       = esl_opt_GetInteger(go, "-N");
    ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
    float           null2[p7_MAXCODE];
    int             i;
    float           fsc, bsc;
    double          Mcs;

    if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
    if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");

    bg = p7_bg_Create(abc);
    p7_bg_SetLength(bg, L);
    gm = p7_profile_Create(hmm->M, abc);
    p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
    gx1 = p7_gmx_Create(gm->M, L);
    gx2 = p7_gmx_Create(gm->M, L);

    esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
    p7_GForward (dsq, L, gm, gx1, &fsc);
    p7_GBackward(dsq, L, gm, gx2, &bsc);
    p7_GDecoding(gm, gx1, gx2, gx2);

    esl_stopwatch_Start(w);
    for (i = 0; i < N; i++)
        p7_GNull2_ByExpectation(gm, gx2, null2);
    esl_stopwatch_Stop(w);

    Mcs  = (double) N * (double) L * (double) gm->M * 1e-6 / w->user;
    esl_stopwatch_Display(stdout, w, "# CPU time: ");
    printf("# M    = %d\n", gm->M);
    printf("# %.1f Mc/s\n", Mcs);

    free(dsq);
    p7_gmx_Destroy(gx1);
    p7_gmx_Destroy(gx2);
    p7_profile_Destroy(gm);
    p7_bg_Destroy(bg);
    p7_hmm_Destroy(hmm);
    p7_hmmfile_Close(hfp);
    esl_alphabet_Destroy(abc);
    esl_stopwatch_Destroy(w);
    esl_randomness_Destroy(r);
    esl_getopts_Destroy(go);
    return 0;
}

int 
main(int argc, char **argv)
{
  char           *msg  = "p7_gmx unit test driver failed";
  ESL_GETOPTS    *go   = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_RANDOMNESS *r    = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc  = esl_alphabet_Create(eslAMINO);
  P7_BG          *bg   = p7_bg_Create(abc);
  P7_HMM         *hmm  = NULL;
  P7_PROFILE     *gm   = NULL;
  int             M    = esl_opt_GetInteger(go, "-M");
  int             L    = esl_opt_GetInteger(go, "-L");
  float           tol  = esl_opt_GetReal   (go, "-t");

  p7_FLogsumInit();

  if (p7_hmm_Sample(r, M, abc, &hmm)                != eslOK) esl_fatal(msg);
  if ((gm = p7_profile_Create(hmm->M, abc))         == NULL)  esl_fatal(msg);
  if (p7_bg_SetLength(bg, L)                        != eslOK) esl_fatal(msg);
  if (p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL) != eslOK) esl_fatal(msg);

  utest_GrowTo();
  utest_Compare(r, gm, bg, L, tol);

  esl_getopts_Destroy(go);
  esl_randomness_Destroy(r);
  esl_alphabet_Destroy(abc);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_profile_Destroy(gm);
  return eslOK;
}

int 
main(int argc, char **argv)
{
  ESL_GETOPTS   *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_STOPWATCH *w       = esl_stopwatch_Create();
  char          *hmmfile = esl_opt_GetArg(go, 1);
  P7_HMMCACHE   *hcache  = NULL;
  char           errbuf[eslERRBUFSIZE];
  size_t         tot_mem;
  int            status;

  esl_stopwatch_Start(w);

  status = p7_hmmcache_Open(hmmfile, &hcache, errbuf);
  if      (status == eslENOTFOUND) p7_Fail("Failed to read %s\n  %s\n",           hmmfile, errbuf);
  else if (status == eslEFORMAT)   p7_Fail("Failed to parse %s\n  %s\n",          hmmfile, errbuf);
  else if (status == eslEINCOMPAT) p7_Fail("Mixed profile types in %s\n  %s\n",   hmmfile, errbuf);
  else if (status != eslOK)        p7_Fail("Failed to cache %s: error code %d\n", hmmfile, status);

  p7_hmmcache_SetNumericNames(hcache);
  tot_mem = p7_hmmcache_Sizeof(hcache);

  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("models     = %d\n",          hcache->n);
  printf("tot memory = %" PRIu64 "\n", (uint64_t) tot_mem);
  
  p7_hmmcache_Close(hcache);
  esl_getopts_Destroy(go);
  esl_stopwatch_Destroy(w);
  return 0;
}

int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go       = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_RANDOMNESS *rng      = esl_randomness_Create(esl_opt_GetInteger(go, "-s"));
  P7_ANCHORS     *anch     = p7_anchors_Create();
  P7_ANCHORHASH  *ah       = p7_anchorhash_Create();
  int             L        = 400;
  int             M        = 200;
  int             maxD     = 50;
  int             nsamples = 1000;
  int32_t         keyidx;
  int             s;

  for (s = 0; s < nsamples; s++)
    {
      p7_anchors_Sample(rng, L, M, maxD, anch);
      p7_anchorhash_Store(ah, anch, 0, &keyidx);
      p7_anchors_Reuse(anch);
    }
  
  p7_anchorhash_Dump(stdout, ah);

  p7_anchorhash_Destroy(ah);
  p7_anchors_Destroy(anch);
  esl_randomness_Destroy(rng);
  esl_getopts_Destroy(go);
  return 0;
}

int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go       = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_RANDOMNESS *rng      = NULL;
  int             stalling = esl_opt_GetBoolean(go, "--stall");
  int             my_rank;
  int             nproc;

  /* The startup sequence below is designed in part to facilitate debugging.
   * To debug an MPI program, you start it with 'mpirun' as usual, but 
   * with the --stall flag; this causes all processes to start, but then
   * wait for the developer to attach gdb's to each running process.
   * Example:
   *      mpirun -n 2 ./p7_hmm_mpi_utest --stall
   *      [pid's <pid0> and <pid1> are reported for processes 0 and 1]
   *   in one terminal window:
   *      gdb ./p7_hmm_mpi_utest <pid0>
   *        [set desired breakpoint in the master]
   *        set stalling=0
   *        c
   *   and similarly in a second terminal window, for worker <pid1>.
   *   
   * Additionally, we want to show the rng seed. This is so we can diagnose
   * failures that are rare; we can re-run the unit test until we see it fail,
   * get the rng seed, then reproduce exactly that failure.
   */ 
  MPI_Init(&argc, &argv);
  MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);
  MPI_Comm_size(MPI_COMM_WORLD, &nproc);
  if (my_rank == 0) {
    rng = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
    fprintf(stderr, "## %s\n", argv[0]);
    fprintf(stderr, "#  rng seed  = %" PRIu32 "\n", esl_randomness_GetSeed(rng));
    fprintf(stderr, "#  MPI nproc = %d\n", nproc);
  }
#ifdef HAVE_GETPID
  /* To debug an MPI program, you attach gdb's to each process, already running;
   * for this, you need the pid of each process. Provide the pid's to help the
   * developer.
   */
  fprintf(stderr, "#    %6d = %d\n", my_rank, getpid()); 
#endif
  /* This infinite loop waits on the developer to attach gdb's to each process.
   * In each gdb, developer may set a better breakpoint, then does "set stalling=0"
   * and "continue" to release the waiting process from this stall point.
   */
  while (stalling);	

  utest_SendRecv(rng, my_rank, nproc);
  
  if (my_rank == 0) {
    fprintf(stderr, "#  status = ok\n");
    esl_randomness_Destroy(rng);
  }

  MPI_Finalize();
  esl_getopts_Destroy(go);
  exit(0); /* success */
}

int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go    = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_RANDOMNESS *r    = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc  = NULL;
  P7_HMM         *hmm  = NULL;
  P7_PROFILE     *gm   = NULL;
  P7_BG          *bg   = NULL;
  int             M    = 100;
  int             L    = 200;
  int             nseq = 20;
  char            errbuf[eslERRBUFSIZE];

  if ((abc = esl_alphabet_Create(eslAMINO))         == NULL)  esl_fatal("failed to create alphabet");
  if (p7_hmm_Sample(r, M, abc, &hmm)                != eslOK) esl_fatal("failed to sample an HMM");
  if ((bg = p7_bg_Create(abc))                      == NULL)  esl_fatal("failed to create null model");
  if ((gm = p7_profile_Create(hmm->M, abc))         == NULL)  esl_fatal("failed to create profile");
  if (p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL)    != eslOK) esl_fatal("failed to config profile");
  if (p7_hmm_Validate    (hmm, errbuf, 0.0001)      != eslOK) esl_fatal("whoops, HMM is bad!: %s", errbuf);
  if (p7_profile_Validate(gm,  errbuf, 0.0001)      != eslOK) esl_fatal("whoops, profile is bad!: %s", errbuf);

  utest_basic  (go);
  utest_viterbi(go, r, abc, bg, gm, nseq, L);

  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}

int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  int             i;
 
  /* Read one HMM from <hmmfile> */
  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");
  p7_hmmfile_Close(hfp);

  bg = p7_bg_Create(abc);

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    p7_bg_SetFilterByHMM(bg, hmm);
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");

  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}

int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_RANDOMNESS *rng     = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  char           *hmmfile = esl_opt_GetArg(go, 1);
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_TRACE       *tr      = p7_trace_Create();
  ESL_SQ         *sq      = NULL;
  char            errbuf[eslERRBUFSIZE];
  int             i;
  int             status;

  status = p7_hmmfile_OpenE(hmmfile, NULL, &hfp, errbuf);
  if      (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
  else if (status == eslEFORMAT)   p7_Fail("File format problem in trying to open HMM file %s.\n%s\n",                hmmfile, errbuf);
  else if (status != eslOK)        p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n",                       status, hmmfile, errbuf);  

  status = p7_hmmfile_Read(hfp, &abc, &hmm);
  if      (status == eslEFORMAT)   p7_Fail("Bad file format in HMM file %s:\n%s\n",          hfp->fname, hfp->errbuf);
  else if (status == eslEINCOMPAT) p7_Fail("HMM in %s is not in the expected %s alphabet\n", hfp->fname, esl_abc_DecodeType(abc->type));
  else if (status == eslEOF)       p7_Fail("Empty HMM file %s? No HMM data found.\n",        hfp->fname);
  else if (status != eslOK)        p7_Fail("Unexpected error in reading HMMs from %s\n",     hfp->fname);

  p7_hmmfile_Close(hfp);

  bg = p7_bg_Create(abc);                p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);   p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  sq = esl_sq_CreateDigital(abc);

  for (i = 0; i < N; i++)
    {
      p7_ProfileEmit(rng, hmm, gm, bg, sq, tr);
      esl_sq_FormatName(sq, "%s-sample%d", hmm->name, i);
      esl_sqio_Write(stdout, sq, eslSQFILE_FASTA, FALSE);

      if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) esl_fatal(errbuf);

      esl_sq_Reuse(sq);
      p7_trace_Reuse(tr);
    }      

  esl_sq_Destroy(sq);
  p7_trace_Destroy(tr);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(rng);
  esl_getopts_Destroy(go);
  return 0;
}

int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go       = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_RANDOMNESS *r        = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  int             N        = esl_opt_GetInteger(go, "-N");
  P7_TOPHITS     *h1       = NULL;
  P7_TOPHITS     *h2       = NULL;
  P7_TOPHITS     *h3       = NULL;
  char            name[]   = "not_unique_name";
  char            acc[]    = "not_unique_acc";
  char            desc[]   = "Test description for the purposes of making the test driver allocate space";
  double          key;
  int             i;

  fprintf(stderr, "## %s\n", argv[0]);
  fprintf(stderr, "#  rng seed = %" PRIu32 "\n", esl_randomness_GetSeed(r));

  h1 = p7_tophits_Create(p7_TOPHITS_DEFAULT_INIT_ALLOC);
  h2 = p7_tophits_Create(p7_TOPHITS_DEFAULT_INIT_ALLOC);
  h3 = p7_tophits_Create(p7_TOPHITS_DEFAULT_INIT_ALLOC);
  
  for (i = 0; i < N; i++) 
  {
      key = esl_random(r);
      tophits_Add(h1, name, acc, desc, key);
      key = 10.0 * esl_random(r);
      tophits_Add(h2, name, acc, desc, key);
      key = 0.1 * esl_random(r);
      tophits_Add(h3, name, acc, desc, key);
  }
  tophits_Add(h1, "last",  NULL, NULL, -1.0);
  tophits_Add(h1, "first", NULL, NULL, 20.0);

  p7_tophits_SortBySortkey(h1);
  if (strcmp(h1->hit[0]->name,   "first") != 0) esl_fatal("sort failed (top is %s = %f)", h1->hit[0]->name,   h1->hit[0]->sortkey);
  if (strcmp(h1->hit[N+1]->name, "last")  != 0) esl_fatal("sort failed (last is %s = %f)", h1->hit[N+1]->name, h1->hit[N+1]->sortkey);

  p7_tophits_Merge(h1, h2);
  if (strcmp(h1->hit[0]->name,     "first") != 0) esl_fatal("after merge 1, sort failed (top is %s = %f)", h1->hit[0]->name,     h1->hit[0]->sortkey);
  if (strcmp(h1->hit[2*N+1]->name, "last")  != 0) esl_fatal("after merge 1, sort failed (last is %s = %f)", h1->hit[2*N+1]->name, h1->hit[2*N+1]->sortkey);

  p7_tophits_Merge(h3, h1);
  if (strcmp(h3->hit[0]->name,     "first") != 0) esl_fatal("after merge 2, sort failed (top is %s = %f)", h3->hit[0]->name,     h3->hit[0]->sortkey);
  if (strcmp(h3->hit[3*N+1]->name, "last")  != 0) esl_fatal("after merge 2, sort failed (last is %s = %f)", h3->hit[3*N+1]->name,     h3->hit[3*N+1]->sortkey);
  
  if (p7_tophits_GetMaxNameLength(h3) != strlen(name)) esl_fatal("GetMaxNameLength() failed");

  p7_tophits_Destroy(h1);
  p7_tophits_Destroy(h2);
  p7_tophits_Destroy(h3);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);

  fprintf(stderr, "#  status = ok\n");
  return eslOK;
}

int
main(int argc, char **argv)
{
  ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);

  fprintf(stderr, "## %s\n", argv[0]);

  utest_Compare();

  fprintf(stderr, "#  status = ok\n");

  esl_getopts_Destroy(go);
  return 0;
}

int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go   = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);

  fprintf(stderr, "## %s\n", argv[0]);

  utest_normalization(go);

  esl_getopts_Destroy(go);

  fprintf(stderr, "#  status = ok\n");
  exit(0); /* success */
}

int
main(int argc, char **argv)
{
  ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);

  utest_alphabet_config(eslAMINO);
  utest_alphabet_config(eslDNA);
  utest_alphabet_config(eslRNA);
  utest_alphabet_config(eslCOINS);
  utest_alphabet_config(eslDICE);

  esl_getopts_Destroy(go);
  return 0;
}