| /dports/biology/wise/wise2.4.1/src/models/ |
| H A D | genewisemodel.dy | 25 GW_INSERT2DELETE,
617 out->transition[GW_INSERT2DELETE] = tsu->transition[TSM_INSERT2DELETE] * factor;
801 out->transition[GW_INSERT2DELETE] = Probability2Score(prev->transition[GW_INSERT2DELETE]);
810 out->transition[GW_INSERT2DELETE] = NEGI;
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| H A D | genewisemodel.c | 658 out->transition[GW_INSERT2DELETE] = tsu->transition[TSM_INSERT2DELETE] * factor; in GeneWiseSegment_from_ThreeStateUnit()
868 out->transition[GW_INSERT2DELETE] = Probability2Score(prev->transition[GW_INSERT2DELETE]); in GeneWiseScoreSegment_from_GeneWiseSegment()
877 out->transition[GW_INSERT2DELETE] = NEGI; in GeneWiseScoreSegment_from_GeneWiseSegment()
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| H A D | estslim3.dy | 83 calc="query->seg[i]->transition[GW_INSERT2DELETE]"
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| H A D | estslimloop.dy | 89 calc="query->seg[i]->transition[GW_INSERT2DELETE]"
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| H A D | genewisemodel.h | 25 GW_INSERT2DELETE, enumerator
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| H A D | gwlitemodel.dy | 119 seg->transition[GWL_INSERT2DELETE] = gwm->seg[i]->transition[GW_INSERT2DELETE];
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| H A D | estwise3.dy | 165 calc="query->seg[i]->transition[GW_INSERT2DELETE]"
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| H A D | estslim3.c | 302 temp = SIG_1_0[INSERT] + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_shatter_EstSlim3()
862 … EstSlim3_VSMALL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in score_only_EstSlim3()
1206 pau->score = mat->query->seg[i]->transition[GW_INSERT2DELETE] + (0); in recalculate_PackAln_EstSlim3()
1767 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_hidden_EstSlim3()
2132 … EstSlim3_HIDDEN_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_hidden_EstSlim3()
2567 …Slim3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in push_dc_at_merge_EstSlim3()
2760 …Slim3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in follow_on_dc_EstSlim3()
2897 …Slim3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in run_up_dc_EstSlim3()
3915 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_calc_EstSlim3()
4174 …mp = EstSlim3_EXPL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_EstSlim3()
[all …]
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| H A D | estfrag3.dy | 180 calc="query->seg[i]->transition[GW_INSERT2DELETE]"
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| H A D | genewise4.dy | 113 calc="query->seg[i]->transition[GW_INSERT2DELETE]"
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| H A D | estloop3.dy | 166 calc="query->seg[i]->transition[GW_INSERT2DELETE]"
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| H A D | geneloop6.dy | 122 calc="query->seg[i]->transition[GW_INSERT2DELETE]"
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| H A D | genewise6.dy | 121 calc="query->seg[i]->transition[GW_INSERT2DELETE]"
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| H A D | pseudowise7.dy | 95 calc="query->seg[i]->transition[GW_INSERT2DELETE]"
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| H A D | estslimloop.c | 331 temp = SIG_1_0[INSERT] + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_shatter_EstSlimLoop3()
980 …SlimLoop3_VSMALL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in score_only_EstSlimLoop3()
1393 pau->score = mat->query->seg[i]->transition[GW_INSERT2DELETE] + (0); in recalculate_PackAln_EstSlimLoop3()
2008 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_hidden_EstSlimLoop3()
2435 …SlimLoop3_HIDDEN_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_hidden_EstSlimLoop3()
2870 …Loop3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in push_dc_at_merge_EstSlimLoop3()
3063 …Loop3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in follow_on_dc_EstSlimLoop3()
3200 …Loop3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in run_up_dc_EstSlimLoop3()
4448 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_calc_EstSlimLoop3()
4814 … EstSlimLoop3_EXPL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_EstSlimLoop3()
[all …]
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| H A D | genestretch6.dy | 126 calc="query->seg[i]->transition[GW_INSERT2DELETE]"
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| H A D | genephase6.dy | 122 calc="query->gws->seg[i]->transition[GW_INSERT2DELETE]"
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| H A D | gwlitemodel.c | 64 seg->transition[GWL_INSERT2DELETE] = gwm->seg[i]->transition[GW_INSERT2DELETE]; in GwLite_from_GeneWise()
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| H A D | estfrag3.c | 430 temp = SIG_1_0[INSERT] + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_shatter_EstFrag3()
889 … EstFrag3_VSMALL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in score_only_EstFrag3()
1325 pau->score = mat->query->seg[i]->transition[GW_INSERT2DELETE] + (0); in recalculate_PackAln_EstFrag3()
2115 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_hidden_EstFrag3()
2612 … EstFrag3_HIDDEN_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_hidden_EstFrag3()
3447 …Frag3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in push_dc_at_merge_EstFrag3()
3780 …Frag3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in follow_on_dc_EstFrag3()
4017 …Frag3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in run_up_dc_EstFrag3()
5616 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_calc_EstFrag3()
6009 …mp = EstFrag3_EXPL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_EstFrag3()
[all …]
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| H A D | estwise3.c | 410 temp = SIG_1_0[INSERT] + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_shatter_EstWise3()
1070 … EstWise3_VSMALL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in score_only_EstWise3()
1494 pau->score = mat->query->seg[i]->transition[GW_INSERT2DELETE] + (0); in recalculate_PackAln_EstWise3()
2275 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_hidden_EstWise3()
2760 … EstWise3_HIDDEN_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_hidden_EstWise3()
3595 …Wise3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in push_dc_at_merge_EstWise3()
3928 …Wise3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in follow_on_dc_EstWise3()
4165 …Wise3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in run_up_dc_EstWise3()
5703 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_calc_EstWise3()
6062 …mp = EstWise3_EXPL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_EstWise3()
[all …]
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| H A D | genewise4.c | 343 temp = SIG_1_0[INSERT] + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_shatter_GeneWise4()
960 … GeneWise4_VSMALL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in score_only_GeneWise4()
1364 pau->score = mat->query->seg[i]->transition[GW_INSERT2DELETE] + (0); in recalculate_PackAln_GeneWise4()
2010 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_hidden_GeneWise4()
2502 … GeneWise4_HIDDEN_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_hidden_GeneWise4()
3105 …eWise4_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in push_dc_at_merge_GeneWise4()
3482 …eWise4_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in follow_on_dc_GeneWise4()
3711 …eWise4_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in run_up_dc_GeneWise4()
5002 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_calc_GeneWise4()
5336 … GeneWise4_EXPL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_GeneWise4()
[all …]
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| H A D | estloop3.c | 434 temp = SIG_1_0[INSERT] + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_shatter_EstLoop3()
1178 … EstLoop3_VSMALL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in score_only_EstLoop3()
1667 pau->score = mat->query->seg[i]->transition[GW_INSERT2DELETE] + (0); in recalculate_PackAln_EstLoop3()
2501 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_hidden_EstLoop3()
3037 … EstLoop3_HIDDEN_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_hidden_EstLoop3()
3872 …Loop3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in push_dc_at_merge_EstLoop3()
4205 …Loop3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in follow_on_dc_EstLoop3()
4442 …Loop3_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in run_up_dc_EstLoop3()
6176 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_calc_EstLoop3()
6637 …mp = EstLoop3_EXPL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_EstLoop3()
[all …]
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| H A D | geneloop6.c | 367 temp = SIG_1_0[INSERT] + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_shatter_GeneLoop6()
1082 … GeneLoop6_VSMALL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in score_only_GeneLoop6()
1577 pau->score = mat->query->seg[i]->transition[GW_INSERT2DELETE] + (0); in recalculate_PackAln_GeneLoop6()
2300 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_hidden_GeneLoop6()
2870 … GeneLoop6_HIDDEN_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_hidden_GeneLoop6()
3545 …eLoop6_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in push_dc_at_merge_GeneLoop6()
3976 …eLoop6_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in follow_on_dc_GeneLoop6()
4251 …eLoop6_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in run_up_dc_GeneLoop6()
5783 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_calc_GeneLoop6()
6229 … GeneLoop6_EXPL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_GeneLoop6()
[all …]
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| H A D | genewise6.c | 366 temp = SIG_1_0[INSERT] + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_shatter_GeneWise6()
1037 … GeneWise6_VSMALL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in score_only_GeneWise6()
1488 pau->score = mat->query->seg[i]->transition[GW_INSERT2DELETE] + (0); in recalculate_PackAln_GeneWise6()
2182 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_hidden_GeneWise6()
2726 … GeneWise6_HIDDEN_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_hidden_GeneWise6()
3401 …eWise6_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in push_dc_at_merge_GeneWise6()
3832 …eWise6_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in follow_on_dc_GeneWise6()
4107 …eWise6_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in run_up_dc_GeneWise6()
5586 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_calc_GeneWise6()
5995 … GeneWise6_EXPL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_GeneWise6()
[all …]
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| H A D | genestretch6.c | 382 temp = SIG_1_0[INSERT] + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_shatter_GeneStretch6()
1134 …eStretch6_VSMALL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in score_only_GeneStretch6()
1656 pau->score = mat->query->seg[i]->transition[GW_INSERT2DELETE] + (0); in recalculate_PackAln_GeneStretch6()
2399 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_hidden_GeneStretch6()
3005 …eStretch6_HIDDEN_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_hidden_GeneStretch6()
3680 …etch6_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in push_dc_at_merge_GeneStretch6()
4111 …etch6_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in follow_on_dc_GeneStretch6()
4386 …etch6_DC_SHADOW_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in run_up_dc_GeneStretch6()
6042 temp = cscore - (mat->query->seg[i]->transition[GW_INSERT2DELETE]) - (0); in max_calc_GeneStretch6()
6529 … GeneStretch6_EXPL_MATRIX(mat,i-1,j-0,INSERT) + mat->query->seg[i]->transition[GW_INSERT2DELETE]; in calculate_GeneStretch6()
[all …]
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