| /dports/biology/tRNAscan-SE/tRNAscan-SE-2.0/src/ |
| H A D | viterbi.c | 185 if (icm[y].statetype == uBEGIN_ST) in allocate_mx()
296 else if (icm[y].statetype == uDEL_ST || icm[y].statetype == uBEGIN_ST) in init_mx()
312 if (icm[y].statetype == uBEGIN_ST) in init_mx()
380 case uBEGIN_ST: in recurse_mx()
431 if (st->statetype == uBEGIN_ST) in recurse_mx()
498 curr_tr = AttachTrace(tr, NULL, 0, N-1, 0, uBEGIN_ST); in trace_mx()
539 PushTracestack(dolist, AttachTrace(curr_tr, NULL, i-1, j-1, icm[y].tmx[1], uBEGIN_ST)); in trace_mx()
554 icm[y].tmx[1], uBEGIN_ST)); in trace_mx()
556 icm[y].tmx[0], uBEGIN_ST)); in trace_mx()
574 case uBEGIN_ST: in trace_mx()
[all …]
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| H A D | model.c | 226 tflags = uBEGIN_ST; in RearrangeCM()
259 fflags = uBEGIN_ST; in RearrangeCM()
264 fflags = uBEGIN_ST | uINSL_ST; in RearrangeCM()
270 fflags = uBEGIN_ST | uINSL_ST | uINSR_ST; in RearrangeCM()
299 else if (fflags & uBEGIN_ST) in RearrangeCM()
467 tflags & uBEGIN_ST || tflags & uEND_ST) in copy_state_transitions()
567 fflags = uBEGIN_ST; in MakePCM()
572 fflags = uBEGIN_ST | uINSL_ST; in MakePCM()
578 fflags = uBEGIN_ST | uINSL_ST | uINSR_ST; in MakePCM()
601 else if (fflags & uBEGIN_ST) in MakePCM()
[all …]
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| H A D | dbviterbi.c | 164 if (icm[y].statetype == uBEGIN_ST) in allocate_mx()
286 else if (icm[y].statetype == uDEL_ST || icm[y].statetype == uBEGIN_ST) in init_mx()
302 if (icm[y].statetype == uBEGIN_ST) in init_mx()
373 case uBEGIN_ST: in recurse_mx()
425 if (st->statetype == uBEGIN_ST) in recurse_mx()
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| H A D | fast-dbviterbi.c | 176 if (icm[y].statetype == uBEGIN_ST) in allocate_mx()
298 else if (icm[y].statetype == uDEL_ST || icm[y].statetype == uBEGIN_ST) in init_mx()
314 if (icm[y].statetype == uBEGIN_ST) in init_mx()
386 case uBEGIN_ST: in recurse_mx()
437 if (st->statetype == uBEGIN_ST) in recurse_mx()
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| H A D | emit.c | 91 pick_transit(cm, 0, uBEGIN_ST, &newidx, &newtype); in EmitSequence()
110 Push_m2ali(emstack, cm->nd[oldidx].nxt2, uBEGIN_ST, newafter); in EmitSequence()
112 Push_m2ali(emstack, cm->nd[oldidx].nxt, uBEGIN_ST, oldafter); in EmitSequence()
227 pick_best_transit(cm, 0, uBEGIN_ST, &newidx, &newtype); in EmitBestSequence()
246 Push_m2ali(stack, cm->nd[oldidx].nxt2, uBEGIN_ST, new); in EmitBestSequence()
248 Push_m2ali(stack, cm->nd[oldidx].nxt, uBEGIN_ST, curr); in EmitBestSequence()
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| H A D | align.c | 82 Push_m2ali(stack, cm->nd[oldidx].nxt2, uBEGIN_ST, newafter); in create_master()
85 Push_m2ali(stack, cm->nd[oldidx].nxt, uBEGIN_ST, oldafter); in create_master()
92 Push_m2ali(stack, cm->nd[oldidx].nxt, uBEGIN_ST, oldafter); in create_master()
100 Push_m2ali(stack, cm->nd[oldidx].nxt, uBEGIN_ST, newafter); in create_master()
169 case uBEGIN_ST: in Trace2ali()
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| H A D | smallviterbi.c | 252 if (icm[y].statetype == uBEGIN_ST || icm[y].statetype == uBIFURC_ST) in allocate_mx()
263 if (icm[y].statetype == uBEGIN_ST) in allocate_mx()
418 else if (icm[y].statetype == uDEL_ST || icm[y].statetype == uBEGIN_ST) in init_mx()
434 if (icm[y].statetype == uBEGIN_ST || in init_mx()
511 case uBEGIN_ST: in recurse_mx()
573 if (st->statetype == uBEGIN_ST) in recurse_mx()
773 if (icm[y].statetype == uBEGIN_ST) in print_small_mx()
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| H A D | lengthdist.c | 72 case uBEGIN_ST: in LengthDistribution()
93 case uBEGIN_ST: in LengthDistribution()
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| H A D | modelmaking.c | 155 PushTracestack(tr_stack, AttachTrace(tr, pool, -1, -1, 0, uBEGIN_ST)); in Transmogrify()
213 case BEGINL_NODE: curr_tr->type = uBEGIN_ST; break; in Transmogrify()
216 curr_tr->type = uBEGIN_ST; in Transmogrify()
228 curr_tr->type = uBEGIN_ST; in Transmogrify()
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| H A D | konings.c | 69 case uBEGIN_ST: in Align2kh()
137 case uBEGIN_ST: in PrintAliLandscape()
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| H A D | structs.c | 45 case uBEGIN_ST: return BEGIN_ST; in StatetypeIndex()
76 case BEGINR_NODE: return uBEGIN_ST; in UniqueStatetype()
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| H A D | structs.h | 67 #define uBEGIN_ST (1<<6) macro
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| H A D | debug.c | 30 case uBEGIN_ST: return "uBEGIN_ST"; in UstatetypeName()
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| H A D | trace.c | 61 new->type = uBEGIN_ST; in InitTrace()
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