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Searched refs:cmfp (Results 1 – 25 of 55) sorted by relevance

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/dports/biology/infernal/infernal-1.1.3/src/
H A Dcm_file.c234 if (cmfp != NULL) cm_file_Close(cmfp); in cm_file_OpenBuffer()
387 if (!cmfp->do_stdin && !cmfp->do_gzip) { in open_engine()
399 cmfp->hfp->f = cmfp->f; in open_engine()
402 cmfp->hfp->do_gzip = cmfp->do_gzip; in open_engine()
403 cmfp->hfp->do_stdin = cmfp->do_stdin; in open_engine()
405 cmfp->hfp->is_pressed = cmfp->is_pressed; in open_engine()
485 if (cmfp != NULL) cm_file_Close(cmfp); in open_engine()
506 if (cmfp->do_gzip && cmfp->f != NULL) { in cm_file_Close()
519 if (!cmfp->do_gzip && !cmfp->do_stdin && cmfp->f != NULL) fclose(cmfp->f); in cm_file_Close()
520 if (cmfp->ffp != NULL) fclose(cmfp->ffp); in cm_file_Close()
[all …]
H A Dcmfetch.c64 static void create_ssi_index(ESL_GETOPTS *go, CM_FILE *cmfp);
124 status = cm_file_Open(cmfile, NULL, FALSE, &cmfp, errbuf); in main()
133 if (cmfp->is_pressed && esl_opt_GetBoolean(go, "--index")) { in main()
156 onefetch(go, ofp, keyname, cmfp); in main()
161 cm_file_Close(cmfp); in main()
171 create_ssi_index(ESL_GETOPTS *go, CM_FILE *cmfp) in create_ssi_index() argument
265 if (cmfp->ssi != NULL) { onefetch(go, ofp, key, cmfp); ncm++; } in multifetch()
268 if (cmfp->ssi == NULL) in multifetch()
306 if (cmfp->ssi != NULL) in onefetch()
308 status = cm_file_PositionByKey(cmfp, key); in onefetch()
[all …]
H A Dcmconvert.c46 CM_FILE *cmfp = NULL; in main() local
61 …status = cm_file_Open(cmfile, NULL, TRUE, &cmfp, errbuf); /* TRUE says: allow CM file to be in v1.… in main()
72 while ((status = cm_file_Read(cmfp, TRUE, &abc, &cm)) == eslOK) in main()
74 if(cmfp->format == CM_FILE_1 || esl_opt_GetBoolean(go, "--mlhmm")) { in main()
102 …us == eslEFORMAT) cm_Fail("bad file format in CM file %s\n%s", cmfile, cmfp->errbuf); in main()
103 …us == eslEINCOMPAT) cm_Fail("CM file %s contains different alphabets\n%s", cmfile, cmfp->errbuf); in main()
104 …us != eslEOF) cm_Fail("Unexpected error in reading CMs from %s\n%s", cmfile, cmfp->errbuf); in main()
106 cm_file_Close(cmfp); in main()
H A Dcmscan.c500 cm_file_Close(cmfp); in serial_master()
637 cm_file_Close(cmfp); in serial_master()
1409 pli->cmfp = cmfp; /* for four-stage input, pipeline needs <cmfp> */ in mpi_master()
1477 cm_file_Close(cmfp); in mpi_master()
1730 cm_file_Close(cmfp); in mpi_worker()
1787 pli->cmfp = cmfp; /* for four-stage input, pipeline needs <cmfp> */ in mpi_worker()
1954 cm_file_Close(cmfp); in mpi_worker()
2510 cmfp->ssi->nsecondary = 0; in read_glocal_list_file()
2536 if(cmfp->ssi != NULL) cmfp->ssi->nsecondary = save_nsecondary; in read_glocal_list_file()
2598 cmfp->ssi->nsecondary = 0; in read_clan_info_file()
[all …]
H A Dtrcyk.c23 CM_FILE *cmfp; in main() local
44 cmfp = NULL; in main()
60 if((status = cm_file_Open(cmfile, NULL, FALSE, &cmfp, errbuf)) != eslOK) in main()
62 if ((status = cm_file_Read(cmfp, TRUE, &abc, &cm)) != eslOK) in main()
66 cm_file_Close(cmfp); in main()
H A Dcmpress.c55 CM_FILE *cmfp = NULL; in main() local
71 status = cm_file_OpenNoDB(cmfile, NULL, FALSE, &cmfp, errbuf); in main()
76 …if (cmfp->do_stdin || cmfp->do_gzip) cm_Fail("CM file %s must be a normal file, not gzipped or a s… in main()
80 …if (esl_newssi_AddFile(dbf->nssi, cmfp->fname, 0, &fh) != eslOK) /* 0 = format code (CMs don't hav… in main()
81 ESL_XFAIL(status, errbuf, "Failed to add CM file %s to new SSI index\n", cmfp->fname); in main()
86 while ((status = cm_file_Read(cmfp, TRUE, &abc, &cm)) == eslOK) in main()
144 cm_file_Close(cmfp); in main()
152 cm_file_Close(cmfp); in main()
H A Dcp9-test.c49 CM_FILE *cmfp; /* open CM file for reading */ in main() local
79 …if ((status = cm_file_Open(cmfile, NULL, FALSE, &(cmfp), errbuf)) != eslOK) cm_Fail("Failed to ope… in main()
80 if ((cm_file_Read(cmfp, TRUE, &abc, &cm)) != eslOK) cm_Fail("Failed to read CM"); in main()
81 cm_file_Close(cmfp); in main()
H A Dcmstat.c69 CM_FILE *cmfp; /* open input CM file stream */ in main() local
118 status = cm_file_Open(cmfile, NULL, FALSE, &cmfp, errbuf); in main()
185 while ((status = cm_file_Read(cmfp, TRUE, &abc, &cm)) != eslEOF) in main()
188 else if (status != eslOK) cm_Fail(cmfp->errbuf); in main()
198 if(cmfp->ssi != NULL) { in main()
200 status = cm_file_PositionByKey(cmfp, key); in main()
205 while ((status = cm_file_Read(cmfp, TRUE, &abc, &cm)) != eslEOF) in main()
208 if(cm == NULL) cm_Fail(cmfp->errbuf); in main()
219 cm_Fail(cmfp->errbuf); /* cm_file_Read() returned an error, die. */ in main()
228 cm_file_Close(cmfp); in main()
H A Dbandcyk-montecarlo-test.c54 CM_FILE *cmfp; /* open CM file for reading */ in main() local
86 …if ((status = cm_file_Open(cmfile, NULL, FALSE, &(cmfp), errbuf)) != eslOK) cm_Fail("Failed to ope… in main()
87 if ((cm_file_Read(cmfp, TRUE, &abc, &cm)) != eslOK) cm_Fail("Failed to read CM"); in main()
88 cm_file_Close(cmfp); in main()
H A Dbandcyk-truncation-test.c66 CM_FILE *cmfp; /* open CM file for reading */ in main() local
98 …if ((status = cm_file_Open(cmfile, NULL, FALSE, &(cmfp), errbuf)) != eslOK) cm_Fail("Failed to ope… in main()
99 if ((cm_file_Read(cmfp, TRUE, &abc, &cm)) != eslOK) cm_Fail("Failed to read CM"); in main()
100 cm_file_Close(cmfp); in main()
H A Dtruncyk_check.c40 CM_FILE *cmfp; /* open CM file for reading */ in main() local
98 if((status = cm_file_Open(cmfile, NULL, FALSE, &cmfp, errbuf)) != eslOK) in main()
100 if ((status = cm_file_Read(cmfp, TRUE, &abc, &cm)) != eslOK) in main()
218 cm_file_Close(cmfp); in main()
H A Dsub_cm-test.c56 CM_FILE *cmfp; /* open CM file for reading */ in main() local
148 …if ((status = cm_file_Open(cmfile, NULL, FALSE, &(cmfp), errbuf)) != eslOK) cm_Fail("Failed to ope… in main()
149 if ((cm_file_Read(cmfp, TRUE, &abc, &cm)) != eslOK) cm_Fail("Failed to read CM"); in main()
150 cm_file_Close(cmfp); in main()
H A Dcmsim.c78 CM_FILE *cmfp; /* open input CM file stream */ member
159 cfg.cmfp = NULL; /* opened in init_cfg() */ in main()
174 if (cfg.cmfp != NULL) cm_file_Close(cfg.cmfp); in main()
210 …if((status = cm_file_Open(cfg->cmfile, NULL, FALSE, &(cfg->cmfp), errbuf)) != eslOK) return status; in init_cfg()
274 while ((status = cm_file_Read(cfg->cmfp, TRUE, &(cfg->abc), &cm)) == eslOK) in master()
373 if(status != eslEOF) cm_Fail(cfg->cmfp->errbuf); in master()
/dports/biology/tRNAscan-SE/tRNAscan-SE-2.0/src/
H A Dtrain_main.c55 FILE *cmfp; /* OUTPUT: fp to cvfile */ in main() local
379 if ((cmfp = fopen(cmfile, "w")) == NULL) in main()
382 if (do_flatformat && ! WriteCM(cmfp, cm)) in main()
384 else if (! WriteBinaryCM(cmfp, cm)) in main()
386 fclose(cmfp); in main()
H A Dbuild_main.c55 FILE *cmfp; /* OUTPUT: fp to cmfile */ in main() local
293 if ((cmfp = fopen(cmfile, "w")) == NULL) in main()
295 if (! WriteCM(cmfp, cm)) in main()
297 fclose(cmfp); in main()
/dports/biology/infernal/infernal-1.1.3/src/impl_sse/
H A Dsse_cmsearch.c74 CM_FILE *cmfp; /* open input CM file stream */ in main() local
127 status = cm_file_Open(cmfile, NULL, FALSE, &cmfp, errbuf); in main()
131 status = cm_file_Read(cmfp, TRUE, &abc, &cm); in main()
132 if(status != eslOK) cm_Fail(cmfp->errbuf); in main()
133 status = cm_file_Read(cmfp, TRUE, &abc, NULL); in main()
134 if(status != eslEOF) cm_Fail("CM file %s does not contain just one CM\n", cmfp->fname); in main()
135 cm_file_Close(cmfp); in main()
/dports/devel/tinygo/tinygo-0.14.1/llvm-project/clang/test/SemaCXX/
H A Dbuiltins.cpp70 MemFnType mfp, ConstMemFnType cmfp, int (&Arr)[5]) { in test_builtin_launder_diags() argument
75 …__builtin_launder(cmfp); // expected-error {{non-pointer argument to '__builtin_launder' is not al… in test_builtin_launder_diags()
/dports/devel/llvm11/llvm-11.0.1.src/tools/clang/test/SemaCXX/
H A Dbuiltins.cpp69 MemFnType mfp, ConstMemFnType cmfp, int (&Arr)[5]) { in test_builtin_launder_diags() argument
74 …__builtin_launder(cmfp); // expected-error {{non-pointer argument to '__builtin_launder' is not al… in test_builtin_launder_diags()
/dports/devel/llvm90/llvm-9.0.1.src/tools/clang/test/SemaCXX/
H A Dbuiltins.cpp70 MemFnType mfp, ConstMemFnType cmfp, int (&Arr)[5]) { in test_builtin_launder_diags() argument
75 …__builtin_launder(cmfp); // expected-error {{non-pointer argument to '__builtin_launder' is not al… in test_builtin_launder_diags()
/dports/devel/llvm-cheri/llvm-project-37c49ff00e3eadce5d8703fdc4497f28458c64a8/clang/test/SemaCXX/
H A Dbuiltins.cpp69 MemFnType mfp, ConstMemFnType cmfp, int (&Arr)[5]) { in test_builtin_launder_diags() argument
74 …__builtin_launder(cmfp); // expected-error {{non-pointer argument to '__builtin_launder' is not al… in test_builtin_launder_diags()
/dports/devel/llvm10/llvm-10.0.1.src/tools/clang/test/SemaCXX/
H A Dbuiltins.cpp70 MemFnType mfp, ConstMemFnType cmfp, int (&Arr)[5]) { in test_builtin_launder_diags() argument
75 …__builtin_launder(cmfp); // expected-error {{non-pointer argument to '__builtin_launder' is not al… in test_builtin_launder_diags()
/dports/devel/llvm80/llvm-8.0.1.src/tools/clang/test/SemaCXX/
H A Dbuiltins.cpp70 MemFnType mfp, ConstMemFnType cmfp, int (&Arr)[5]) { in test_builtin_launder_diags() argument
75 …__builtin_launder(cmfp); // expected-error {{non-pointer argument to '__builtin_launder' is not al… in test_builtin_launder_diags()
/dports/www/chromium-legacy/chromium-88.0.4324.182/third_party/llvm/clang/test/SemaCXX/
H A Dbuiltins.cpp69 MemFnType mfp, ConstMemFnType cmfp, int (&Arr)[5]) { in test_builtin_launder_diags() argument
74 …__builtin_launder(cmfp); // expected-error {{non-pointer argument to '__builtin_launder' is not al… in test_builtin_launder_diags()
/dports/devel/wasi-libcxx/llvm-project-13.0.1.src/clang/test/SemaCXX/
H A Dbuiltins.cpp69 MemFnType mfp, ConstMemFnType cmfp, int (&Arr)[5]) { in test_builtin_launder_diags() argument
74 …__builtin_launder(cmfp); // expected-error {{non-pointer argument to '__builtin_launder' is not al… in test_builtin_launder_diags()
/dports/devel/llvm12/llvm-project-12.0.1.src/clang/test/SemaCXX/
H A Dbuiltins.cpp69 MemFnType mfp, ConstMemFnType cmfp, int (&Arr)[5]) { in test_builtin_launder_diags() argument
74 …__builtin_launder(cmfp); // expected-error {{non-pointer argument to '__builtin_launder' is not al… in test_builtin_launder_diags()

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