src/models/genephase6.dy

21   calc="GENOMIC_CDS_POT(target,j)"
23 …calc="query->gws->seg[i]->transition[GW_MATCH2MATCH] + query->gws->seg[i]->match[GENOMIC_CODON(tar…
26 …calc="query->gws->seg[i]->transition[GW_INSERT2MATCH] + query->gws->seg[i]->match[GENOMIC_CODON(ta…
29 …calc="query->gws->seg[i]->transition[GW_DELETE2MATCH] + query->gws->seg[i]->match[GENOMIC_CODON(ta…
32 …calc="query->gws->seg[i]->transition[GW_START2MATCH] + query->gws->seg[i]->match[GENOMIC_CODON(tar…
35 …calc="query->gws->seg[i]->transition[GW_START2MATCH] + query->gws->seg[i]->match[GENOMIC_CODON(tar…
39     calc="query->gws->seg[i]->match[GENOMIC_CODON(target,j)]+GENOMIC_3SS(target,j-3)"
43     calc="GENOMIC_3SS(target,j-2)"
47     calc="GENOMIC_3SS(target,j-1)"
54     calc="gp->transition[GP4_DELETE_1_BASE]"
58     calc="gp->transition[GP4_DELETE_2_BASE]"
62     calc="gp->transition[GP4_INSERT_1_BASE]"
66     calc="gp->transition[GP4_INSERT_2_BASE]"
74   calc="GENOMIC_CDS_POT(target,j)"
76 …calc="query->gws->seg[i]->transition[GW_MATCH2INSERT] + query->gws->seg[i]->insert[GENOMIC_CODON(t…
79 …calc="query->gws->seg[i]->transition[GW_INSERT2INSERT] + query->gws->seg[i]->insert[GENOMIC_CODON(…
82 …calc="query->gws->seg[i]->transition[GW_DELETE2INSERT] + query->gws->seg[i]->insert[GENOMIC_CODON(…
85 …calc="query->gws->seg[i]->transition[GW_START2INSERT] + query->gws->seg[i]->insert[GENOMIC_CODON(t…
91     calc="query->gws->seg[i]->match[GENOMIC_CODON(target,j)]+GENOMIC_3SS(target,j-3)"
95     calc="GENOMIC_3SS(target,j-2)"
99     calc="GENOMIC_3SS(target,j-1)"
107     calc="gp->transition[GP4_DELETE_1_BASE]"
111     calc="gp->transition[GP4_DELETE_2_BASE]"
119     calc="query->gws->seg[i]->transition[GW_MATCH2DELETE]"
122     calc="query->gws->seg[i]->transition[GW_INSERT2DELETE]"
125     calc="query->gws->seg[i]->transition[GW_DELETE2DELETE]"
135     calc="gp->intron[GENOMIC_BASE(target,j)]+GENOMIC_5SS(target,j-7)+query->phase[i]->intron_0"
139     calc="gp->intron[GENOMIC_BASE(target,j)]+GENOMIC_5SS(target,j-7)+query->phase[i]->insert_intron"
143     calc="gp->intron[GENOMIC_BASE(target,j)] + gp->transition[GP4_INTRON2INTRON]"
150     calc="gp->intron[GENOMIC_BASE(target,j)]+GENOMIC_5SS(target,j-7)+query->phase[i]->intron_1"
154     calc="gp->intron[GENOMIC_BASE(target,j)]+GENOMIC_5SS(target,j-7)+query->phase[i]->insert_intron"
158     calc="gp->intron[GENOMIC_BASE(target,j)] + gp->transition[GP4_INTRON2INTRON]"
165     calc="gp->intron[GENOMIC_BASE(target,j)]+GENOMIC_5SS(target,j-7)+query->phase[i]->intron_2"
169     calc="gp->intron[GENOMIC_BASE(target,j)]+GENOMIC_5SS(target,j-7)+query->phase[i]->insert_intron"
173     calc="gp->intron[GENOMIC_BASE(target,j)] + gp->transition[GP4_INTRON2INTRON]"
180     calc="0"
183     calc="query->gws->seg[i]->transition[GW_MATCH2END]"
186     calc="query->gws->seg[i]->transition[GW_INSERT2END]"
189     calc="query->gws->seg[i]->transition[GW_DELETE2END]"
192     calc="gp->transition[GP4_LOOP2LOOP]"
201     calc="0"
204     calc="general_model->stop->codon[GENOMIC_CODON(target,j)]"
211    calc="general_model->start->codon[GENOMIC_CODON(target,j)]"
214    calc="general_model->general->codon[GENOMIC_CODON(target,j)]"
217     calc="GENOMIC_3SS(target,j-3)"
221     calc="GENOMIC_3SS(target,j-2)"
225     calc="GENOMIC_3SS(target,j-1)"
233     calc="gp->intron[GENOMIC_BASE(target,j)]+GENOMIC_5SS(target,j)"
237     calc="gp->intron[GENOMIC_BASE(target,j)] + gp->transition[GP4_INTRON2INTRON]"
244     calc="gp->intron[GENOMIC_BASE(target,j)]+GENOMIC_5SS(target,j-7)"
248     calc="gp->intron[GENOMIC_BASE(target,j)] + gp->transition[GP4_INTRON2INTRON]"
255     calc="gp->intron[GENOMIC_BASE(target,j)]+GENOMIC_5SS(target,j-7)"
259     calc="gp->intron[GENOMIC_BASE(target,j)] + gp->transition[GP4_INTRON2INTRON]"
266    calc="query->gws->seg[i]->transition[GW_MATCH2END]"
269    calc="general_model->general->codon[GENOMIC_CODON(target,j)]"