| /dports/biology/tRNAscan-SE/tRNAscan-SE-2.0/src/ |
| H A D | funcs.h | 21 extern int ViterbiScan(struct istate_s *icm, int statenum, char *seq, int window,
30 extern void PrintViterbiAMX(FILE *fp, struct istate_s *icm, int statenum,
34 extern void PrintICM(FILE *fp, struct cm_s *cm, struct istate_s *icm, int nstates);
58 extern int FastViterbiScan(struct istate_s *icm, int statenum, int *minb, int *maxb,
103 extern int RearrangeCM(struct cm_s *cm, double *rfreq, struct istate_s **ret_icm, int *ret_statenu…
146 extern int SmallViterbiAlign(struct istate_s *icm, int statenum, char *seq,
204 extern int ViterbiAlign(struct istate_s *cm, int statenum, char *seq,
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| H A D | model.c | 22 static void fill_state(struct istate_s *st, int nodeidx, int statetype, int offset);
25 static void copy_state_transitions(struct istate_s *st, double *tvec, int tflags);
178 struct istate_s **ret_icm, in RearrangeCM()
181 struct istate_s *icm; /* new int-lod states-based model */ in RearrangeCM()
182 struct istate_s *smallicm; /* streamlined (realloc'ed) icm */ in RearrangeCM()
194 …if ((icm = (struct istate_s *) calloc ((cm->nodes * STATETYPES), sizeof(struct istate_s))) == NULL) in RearrangeCM()
376 smallicm = (struct istate_s *) realloc (icm, y * sizeof(struct istate_s)); in RearrangeCM()
395 fill_state(struct istate_s *st, in fill_state()
413 copy_singlet_emissions(struct istate_s *st, double *emvec, double *rfreq) in copy_singlet_emissions()
433 copy_pairwise_emissions(struct istate_s *st, double *em, double *rfreq) in copy_pairwise_emissions()
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| H A D | dbviterbi.c | 42 static int allocate_mx(struct istate_s *icm, int statenum, int window,
44 static int init_mx (struct istate_s *icm, int statenum, int N,
46 static int recurse_mx (struct istate_s *icm, int statenum, char *seq, int seqlen,
66 ViterbiScan(struct istate_s *icm, int statenum, char *seq, int window, in ViterbiScan()
121 allocate_mx(struct istate_s *icm, in allocate_mx()
233 init_mx(struct istate_s *icm, /* integer model */ in init_mx()
321 recurse_mx(struct istate_s *icm, /* integer, state-form model */ in recurse_mx()
346 struct istate_s *st; /* state pointer: ptr at current state in icm */ in recurse_mx()
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| H A D | fast-dbviterbi.c | 48 static int allocate_mx(struct istate_s *icm, int statenum, int window,
50 static int init_mx (struct istate_s *icm, int statenum, int N,
52 static int recurse_mx (struct istate_s *icm, int statenum, int *minb, int *maxb,
76 FastViterbiScan(struct istate_s *icm, int statenum, int *minb, int *maxb, in FastViterbiScan()
133 allocate_mx(struct istate_s *icm, in allocate_mx()
245 init_mx(struct istate_s *icm, /* integer model */ in init_mx()
333 recurse_mx(struct istate_s *icm, /* integer, state-form model */ in recurse_mx()
360 struct istate_s *st; /* state pointer: ptr at current state in icm */ in recurse_mx()
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| H A D | smallviterbi.c | 91 static int allocate_mx(struct istate_s *icm,int statenum, int seqlen,
94 static int init_mx (struct istate_s *icm, int statenum, int N,
97 static int recurse_mx (struct istate_s *icm, int statenum, char *seq, int N,
100 static int trace_mx (struct istate_s *icm, char *seq, int N,
108 static void print_small_mx(FILE *fp, struct istate_s *icm, int statenum,
128 SmallViterbiAlign(struct istate_s *icm, in SmallViterbiAlign()
199 allocate_mx(struct istate_s *icm, in allocate_mx()
350 init_mx(struct istate_s *icm, /* integer model */ in init_mx()
451 recurse_mx(struct istate_s *icm, /* integer, state-form model */ in recurse_mx()
475 struct istate_s *st; /* state pointer: ptr at current state in icm */ in recurse_mx()
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| H A D | viterbi.c | 47 static int allocate_mx(struct istate_s *icm,int statenum, int seqlen,
49 static int init_mx(struct istate_s *icm, int statenum, int N, int ***amx, int ***bmx);
50 static int recurse_mx(struct istate_s *icm, int statenum, char *seq, int N, int ***amx, int ***bmx…
51 static int trace_mx(struct istate_s *icm, char *seq, int N,
71 ViterbiAlign(struct istate_s *icm, in ViterbiAlign()
145 allocate_mx(struct istate_s *icm, in allocate_mx()
250 init_mx(struct istate_s *icm, /* integer model */ in init_mx()
330 recurse_mx(struct istate_s *icm, /* integer, state-form model */ in recurse_mx()
349 struct istate_s *st; /* state pointer: ptr at current state in icm */ in recurse_mx()
471 trace_mx(struct istate_s *icm, /* the model to align */ in trace_mx()
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| H A D | debug.c | 87 struct istate_s *icm, /* integer model */ in PrintViterbiAMX()
172 PrintICM(FILE *fp, struct cm_s *cm, struct istate_s *icm, int nstates) in PrintICM()
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| H A D | mpcovels_main.c | 45 extern int MPViterbiScan(struct istate_s *fe_icm, int *fe_statenum,
74 struct istate_s *icm; /* integer log-odds model */ in main()
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| H A D | structs.h | 111 struct istate_s { struct
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| H A D | score_main.c | 62 struct istate_s *icm; /* integer log odds model */ in main()
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| H A D | align_main.c | 59 struct istate_s *icm; /* model, integer log odds form */ in main()
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| H A D | scan_main.c | 64 struct istate_s *icm; /* integer log-odds search model */ in main()
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| H A D | train_main.c | 58 struct istate_s *icm; /* model, integer log odds form */ in main()
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