/dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
H A D | tracealign.c | 97 …ign_Seqs(ESL_SQ **sq, P7_TRACE **tr, int nseq, int M, int optflags, P7_HMM *hmm, ESL_MSA **ret_msa) in p7_tracealign_Seqs() 389 p7_tracealign_getMSAandStats(P7_HMM *hmm, ESL_SQ **sq, int N, ESL_MSA **ret_msa, float **ret_pp, f… in p7_tracealign_getMSAandStats() 603 …, int nseq, const int *matuse, const int *matmap, int M, int alen, int optflags, ESL_MSA **ret_msa) in make_digital_msa() 705 …, int nseq, const int *matuse, const int *matmap, int M, int alen, int optflags, ESL_MSA **ret_msa) in make_text_msa()
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H A D | hmmpgmd2msa.c | 75 …ESL_SQ *qsq, int *incl, int incl_size, int *excl, int excl_size, int excl_all, ESL_MSA **ret_msa) { in hmmpgmd2msa()
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H A D | p7_tophits.c | 1452 int optflags, ESL_MSA **ret_msa) in p7_tophits_Alignment()
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/dports/biology/hmmer/hmmer-3.3/src/ |
H A D | tracealign.c | 97 …ign_Seqs(ESL_SQ **sq, P7_TRACE **tr, int nseq, int M, int optflags, P7_HMM *hmm, ESL_MSA **ret_msa) in p7_tracealign_Seqs() 389 p7_tracealign_getMSAandStats(P7_HMM *hmm, ESL_SQ **sq, int N, ESL_MSA **ret_msa, float **ret_pp, f… in p7_tracealign_getMSAandStats() 603 …, int nseq, const int *matuse, const int *matmap, int M, int alen, int optflags, ESL_MSA **ret_msa) in make_digital_msa() 705 …, int nseq, const int *matuse, const int *matmap, int M, int alen, int optflags, ESL_MSA **ret_msa) in make_text_msa()
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H A D | hmmpgmd2msa.c | 75 …ESL_SQ *qsq, int *incl, int incl_size, int *excl, int excl_size, int excl_all, ESL_MSA **ret_msa) { in hmmpgmd2msa()
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H A D | p7_tophits.c | 1452 int optflags, ESL_MSA **ret_msa) in p7_tophits_Alignment()
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/dports/biology/infernal/infernal-1.1.3/easel/ |
H A D | esl_mpi.c | 862 …sa_MPIUnpack(const ESL_ALPHABET *abc, char *buf, int n, int *pos, MPI_Comm comm, ESL_MSA **ret_msa) in esl_msa_MPIUnpack() 952 …ource, int tag, MPI_Comm comm, const ESL_ALPHABET *abc, char **buf, int *nalloc, ESL_MSA **ret_msa) in esl_msa_MPIRecv()
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H A D | esl_msafile_selex.c | 234 esl_msafile_selex_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa) in esl_msafile_selex_Read() 536 selex_first_block(ESL_MSAFILE *afp, ESL_SELEX_BLOCK *b, ESL_MSA **ret_msa) in selex_first_block()
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H A D | esl_msafile_afa.c | 182 esl_msafile_afa_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa) in esl_msafile_afa_Read()
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H A D | esl_msafile_psiblast.c | 184 esl_msafile_psiblast_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa) in esl_msafile_psiblast_Read()
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H A D | esl_msafile.c | 997 esl_msafile_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa) in esl_msafile_Read()
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H A D | esl_msafile_a2m.c | 215 esl_msafile_a2m_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa) in esl_msafile_a2m_Read()
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H A D | esl_msafile_clustal.c | 188 esl_msafile_clustal_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa) in esl_msafile_clustal_Read()
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H A D | esl_msafile2.c | 352 …fp, ESL_ALPHABET *abc, int64_t known_alen, char *known_rf, char *known_ss_cons, ESL_MSA **ret_msa, in esl_msafile2_ReadInfoPfam()
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H A D | esl_sqio.c | 1375 convert_sq_to_msa(ESL_SQ *sq, ESL_MSA **ret_msa) in convert_sq_to_msa()
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/dports/biology/hmmer/hmmer-3.3/easel/ |
H A D | esl_mpi.c | 862 …sa_MPIUnpack(const ESL_ALPHABET *abc, char *buf, int n, int *pos, MPI_Comm comm, ESL_MSA **ret_msa) in esl_msa_MPIUnpack() 952 …ource, int tag, MPI_Comm comm, const ESL_ALPHABET *abc, char **buf, int *nalloc, ESL_MSA **ret_msa) in esl_msa_MPIRecv()
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H A D | esl_msafile_selex.c | 234 esl_msafile_selex_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa) in esl_msafile_selex_Read() 536 selex_first_block(ESL_MSAFILE *afp, ESL_SELEX_BLOCK *b, ESL_MSA **ret_msa) in selex_first_block()
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H A D | esl_msafile_afa.c | 182 esl_msafile_afa_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa) in esl_msafile_afa_Read()
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H A D | esl_msafile_psiblast.c | 184 esl_msafile_psiblast_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa) in esl_msafile_psiblast_Read()
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H A D | esl_msafile.c | 997 esl_msafile_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa) in esl_msafile_Read()
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H A D | esl_msafile_a2m.c | 215 esl_msafile_a2m_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa) in esl_msafile_a2m_Read()
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H A D | esl_msafile_clustal.c | 188 esl_msafile_clustal_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa) in esl_msafile_clustal_Read()
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H A D | esl_msafile2.c | 352 …fp, ESL_ALPHABET *abc, int64_t known_alen, char *known_rf, char *known_ss_cons, ESL_MSA **ret_msa, in esl_msafile2_ReadInfoPfam()
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H A D | esl_sqio.c | 1375 convert_sq_to_msa(ESL_SQ *sq, ESL_MSA **ret_msa) in convert_sq_to_msa()
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/dports/biology/infernal/infernal-1.1.3/src/ |
H A D | cp9_trace.c | 926 ESL_MSA **ret_msa) in CP9Traces2Alignment()
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