| /dports/biology/wise/wise2.4.1/src/models/ |
| H A D | genewisemodel.dy | 29 GW_DELETE2DELETE,
622 out->transition[GW_DELETE2DELETE] = tsu->transition[TSM_DELETE2DELETE];
802 out->transition[GW_DELETE2DELETE] = Probability2Score(prev->transition[GW_DELETE2DELETE]);
811 out->transition[GW_DELETE2DELETE] = NEGI;
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| H A D | estquick3.dy | 89 calc="query->seg[i].transition[GW_DELETE2DELETE]"
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| H A D | genewisemodel.c | 663 out->transition[GW_DELETE2DELETE] = tsu->transition[TSM_DELETE2DELETE]; in GeneWiseSegment_from_ThreeStateUnit()
869 out->transition[GW_DELETE2DELETE] = Probability2Score(prev->transition[GW_DELETE2DELETE]); in GeneWiseScoreSegment_from_GeneWiseSegment()
878 out->transition[GW_DELETE2DELETE] = NEGI; in GeneWiseScoreSegment_from_GeneWiseSegment()
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| H A D | estslim3.dy | 86 calc="query->seg[i]->transition[GW_DELETE2DELETE]"
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| H A D | phasemodel.dy | 332 …out->gw->seg[i]->transition[GW_DELETE2DELETE] = (1.0 - ppp->marked_intron)*out->gw->seg[i]->transi…
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| H A D | estslimloop.dy | 92 calc="query->seg[i]->transition[GW_DELETE2DELETE]"
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| H A D | estquick3.c | 283 temp = SIG_1_0[DELETE] + mat->query->seg[i].transition[GW_DELETE2DELETE]; in calculate_shatter_EstQuick3()
805 … EstQuick3_VSMALL_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i].transition[GW_DELETE2DELETE]; in score_only_EstQuick3()
1122 pau->score = mat->query->seg[i].transition[GW_DELETE2DELETE] + (0); in recalculate_PackAln_EstQuick3()
1639 temp = cscore - (mat->query->seg[i].transition[GW_DELETE2DELETE]) - (0); in max_hidden_EstQuick3()
1973 … EstQuick3_HIDDEN_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i].transition[GW_DELETE2DELETE]; in calculate_hidden_EstQuick3()
2383 …Quick3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i].transition[GW_DELETE2DELETE]; in push_dc_at_merge_EstQuick3()
2549 …Quick3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i].transition[GW_DELETE2DELETE]; in follow_on_dc_EstQuick3()
2674 …Quick3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i].transition[GW_DELETE2DELETE]; in run_up_dc_EstQuick3()
3519 temp = cscore - (mat->query->seg[i].transition[GW_DELETE2DELETE]) - (0); in max_calc_EstQuick3()
3731 …mp = EstQuick3_EXPL_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i].transition[GW_DELETE2DELETE]; in calculate_EstQuick3()
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| H A D | genewisemodel.h | 29 GW_DELETE2DELETE, enumerator
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| H A D | gwlitemodel.dy | 124 seg->transition[GWL_DELETE2DELETE] = gwm->seg[i]->transition[GW_DELETE2DELETE];
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| H A D | estwise3.dy | 168 calc="query->seg[i]->transition[GW_DELETE2DELETE]"
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| H A D | estslim3.c | 307 temp = SIG_1_0[DELETE] + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in calculate_shatter_EstSlim3()
867 … EstSlim3_VSMALL_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in score_only_EstSlim3()
1210 pau->score = mat->query->seg[i]->transition[GW_DELETE2DELETE] + (0); in recalculate_PackAln_EstSlim3()
1756 temp = cscore - (mat->query->seg[i]->transition[GW_DELETE2DELETE]) - (0); in max_hidden_EstSlim3()
2137 … EstSlim3_HIDDEN_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in calculate_hidden_EstSlim3()
2587 …Slim3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in push_dc_at_merge_EstSlim3()
2767 …Slim3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in follow_on_dc_EstSlim3()
2902 …Slim3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in run_up_dc_EstSlim3()
3904 temp = cscore - (mat->query->seg[i]->transition[GW_DELETE2DELETE]) - (0); in max_calc_EstSlim3()
4179 …mp = EstSlim3_EXPL_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in calculate_EstSlim3()
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| H A D | estfrag3.dy | 183 calc="query->seg[i]->transition[GW_DELETE2DELETE]"
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| H A D | genewise4.dy | 116 calc="query->seg[i]->transition[GW_DELETE2DELETE]"
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| H A D | gwlite.dy | 118 calc="query->seg[i]->transition[GW_DELETE2DELETE]"
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| H A D | estloop3.dy | 169 calc="query->seg[i]->transition[GW_DELETE2DELETE]"
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| H A D | geneloop6.dy | 125 calc="query->seg[i]->transition[GW_DELETE2DELETE]"
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| H A D | genewise6.dy | 124 calc="query->seg[i]->transition[GW_DELETE2DELETE]"
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| H A D | pseudowise7.dy | 98 calc="query->seg[i]->transition[GW_DELETE2DELETE]"
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| H A D | estslimloop.c | 336 temp = SIG_1_0[DELETE] + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in calculate_shatter_EstSlimLoop3()
985 …SlimLoop3_VSMALL_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in score_only_EstSlimLoop3()
1397 pau->score = mat->query->seg[i]->transition[GW_DELETE2DELETE] + (0); in recalculate_PackAln_EstSlimLoop3()
1997 temp = cscore - (mat->query->seg[i]->transition[GW_DELETE2DELETE]) - (0); in max_hidden_EstSlimLoop3()
2440 …SlimLoop3_HIDDEN_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in calculate_hidden_EstSlimLoop3()
2890 …Loop3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in push_dc_at_merge_EstSlimLoop3()
3070 …Loop3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in follow_on_dc_EstSlimLoop3()
3205 …Loop3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in run_up_dc_EstSlimLoop3()
4437 temp = cscore - (mat->query->seg[i]->transition[GW_DELETE2DELETE]) - (0); in max_calc_EstSlimLoop3()
4819 … EstSlimLoop3_EXPL_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in calculate_EstSlimLoop3()
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| H A D | phasemodel.c | 291 …out->gw->seg[i]->transition[GW_DELETE2DELETE] = (1.0 - ppp->marked_intron)*out->gw->seg[i]->transi… in GenePhaseModel_from_ThreeStateModel()
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| H A D | genestretch6.dy | 129 calc="query->seg[i]->transition[GW_DELETE2DELETE]"
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| H A D | genephase6.dy | 125 calc="query->gws->seg[i]->transition[GW_DELETE2DELETE]"
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| H A D | gwlitemodel.c | 69 seg->transition[GWL_DELETE2DELETE] = gwm->seg[i]->transition[GW_DELETE2DELETE]; in GwLite_from_GeneWise()
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| H A D | estfrag3.c | 435 temp = SIG_1_0[DELETE] + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in calculate_shatter_EstFrag3()
894 … EstFrag3_VSMALL_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in score_only_EstFrag3()
1329 pau->score = mat->query->seg[i]->transition[GW_DELETE2DELETE] + (0); in recalculate_PackAln_EstFrag3()
2104 temp = cscore - (mat->query->seg[i]->transition[GW_DELETE2DELETE]) - (0); in max_hidden_EstFrag3()
2617 … EstFrag3_HIDDEN_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in calculate_hidden_EstFrag3()
3467 …Frag3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in push_dc_at_merge_EstFrag3()
3787 …Frag3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in follow_on_dc_EstFrag3()
4022 …Frag3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in run_up_dc_EstFrag3()
5605 temp = cscore - (mat->query->seg[i]->transition[GW_DELETE2DELETE]) - (0); in max_calc_EstFrag3()
6014 …mp = EstFrag3_EXPL_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in calculate_EstFrag3()
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| H A D | estwise3.c | 415 temp = SIG_1_0[DELETE] + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in calculate_shatter_EstWise3()
1075 … EstWise3_VSMALL_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in score_only_EstWise3()
1498 pau->score = mat->query->seg[i]->transition[GW_DELETE2DELETE] + (0); in recalculate_PackAln_EstWise3()
2264 temp = cscore - (mat->query->seg[i]->transition[GW_DELETE2DELETE]) - (0); in max_hidden_EstWise3()
2765 … EstWise3_HIDDEN_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in calculate_hidden_EstWise3()
3615 …Wise3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in push_dc_at_merge_EstWise3()
3935 …Wise3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in follow_on_dc_EstWise3()
4170 …Wise3_DC_SHADOW_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in run_up_dc_EstWise3()
5692 temp = cscore - (mat->query->seg[i]->transition[GW_DELETE2DELETE]) - (0); in max_calc_EstWise3()
6067 …mp = EstWise3_EXPL_MATRIX(mat,i-1,j-0,DELETE) + mat->query->seg[i]->transition[GW_DELETE2DELETE]; in calculate_EstWise3()
[all …]
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