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Searched defs:dpenv (Results 1 – 25 of 46) sorted by relevance

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/dports/biology/wise/wise2.4.1/src/models/
H A Dsw_wrap.c27 …SmithWaterman(char * one,char * two,CompMat * comp,int gap,int ext,DPEnvelope * dpenv,DPRunImpl * … in Align_strings_ProteinSmithWaterman()
85 …erman(Sequence * one,Sequence * two,CompMat * comp,int gap,int ext,DPEnvelope * dpenv,DPRunImpl * … in Align_Sequences_ProteinSmithWaterman()
169 …CompMat * comp,int bentry,int bexit,int b1exit,int b_self,int b_on,DPEnvelope * dpenv,DPRunImpl * … in Align_Sequences_ProteinBlockAligner()
247 …C(Sequence * one,Sequence * two,CompMat * comp,int a, int b, int c,DPEnvelope * dpenv,DPRunImpl * … in Align_Sequences_ProteinABC()
322 …s_ABC(Protein * one,Protein * two,CompMat * comp,int a,int b,int c,DPEnvelope * dpenv,DPRunImpl * … in Align_Proteins_ABC()
355 …aterman(Protein * one,Protein * two,CompMat * comp,int gap,int ext,DPEnvelope * dpenv,DPRunImpl * … in Align_Proteins_SmithWaterman()
H A Dtest_gwhsp.c9 DPEnvelope * dpenv; in main() local
H A Dthreestateloop.c118 boolean calculate_shatter_ThreeStateLoop(ThreeStateLoop * mat,DPEnvelope * dpenv) in calculate_shatter_ThreeStateLoop()
792 …ory_ThreeStateLoop(ThreeStateScore* query,ComplexSequence* target ,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_ThreeStateLoop()
1167 PackAln * PackAln_calculate_Small_ThreeStateLoop(ThreeStateLoop * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_ThreeStateLoop()
1898 …p * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_ThreeStateLoop()
2063 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_ThreeStateLoop()
2141 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_ThreeStateLoop()
2170 …hreeStateLoop(ThreeStateLoop * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_ThreeStateLoop()
2401 …oop(ThreeStateLoop * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_ThreeStateLoop()
2541 …oop(ThreeStateLoop * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_ThreeStateLoop()
2720 boolean dc_optimised_start_end_calc_ThreeStateLoop(ThreeStateLoop *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_ThreeStateLoop()
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H A Dthreestatedp.c117 boolean calculate_shatter_ThreeStateProtein(ThreeStateProtein * mat,DPEnvelope * dpenv) in calculate_shatter_ThreeStateProtein()
706 …_ThreeStateProtein(ThreeStateScore* query,ComplexSequence* target ,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_ThreeStateProtein()
1065 PackAln * PackAln_calculate_Small_ThreeStateProtein(ThreeStateProtein * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_ThreeStateProtein()
1740 …n * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_ThreeStateProtein()
1905 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_ThreeStateProtein()
1983 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_ThreeStateProtein()
2012 …ateProtein(ThreeStateProtein * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_ThreeStateProtein()
2243 …(ThreeStateProtein * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_ThreeStateProtein()
2383 …(ThreeStateProtein * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_ThreeStateProtein()
2562 boolean dc_optimised_start_end_calc_ThreeStateProtein(ThreeStateProtein *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_ThreeStateProtein()
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H A Dfivestate.c119 boolean calculate_shatter_FiveStateProtein(FiveStateProtein * mat,DPEnvelope * dpenv) in calculate_shatter_FiveStateProtein()
886 …ry_FiveStateProtein(FiveStateScore* query,ComplexSequence* target ,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_FiveStateProtein()
1311 PackAln * PackAln_calculate_Small_FiveStateProtein(FiveStateProtein * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_FiveStateProtein()
2132 …n * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_FiveStateProtein()
2365 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_FiveStateProtein()
2443 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_FiveStateProtein()
2472 …tateProtein(FiveStateProtein * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_FiveStateProtein()
2907 …n(FiveStateProtein * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_FiveStateProtein()
3139 …n(FiveStateProtein * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_FiveStateProtein()
3386 boolean dc_optimised_start_end_calc_FiveStateProtein(FiveStateProtein *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_FiveStateProtein()
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H A Dslimdba.c117 boolean calculate_shatter_SlimDnaMatchBlock(SlimDnaMatchBlock * mat,DPEnvelope * dpenv) in calculate_shatter_SlimDnaMatchBlock()
585 … target ,DnaMatrix* comp65,Score g,Score u,Score v,Score s,Score b,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_SlimDnaMatchBlock()
944 PackAln * PackAln_calculate_Small_SlimDnaMatchBlock(SlimDnaMatchBlock * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_SlimDnaMatchBlock()
1581 …k * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_SlimDnaMatchBlock()
1739 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_SlimDnaMatchBlock()
1817 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_SlimDnaMatchBlock()
1846 …MatchBlock(SlimDnaMatchBlock * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_SlimDnaMatchBlock()
2055 …(SlimDnaMatchBlock * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_SlimDnaMatchBlock()
2186 …(SlimDnaMatchBlock * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_SlimDnaMatchBlock()
2358 boolean dc_optimised_start_end_calc_SlimDnaMatchBlock(SlimDnaMatchBlock *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_SlimDnaMatchBlock()
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H A Destfrag3.c117 boolean calculate_shatter_EstFrag3(EstFrag3 * mat,DPEnvelope * dpenv) in calculate_shatter_EstFrag3()
962 …ence* target ,cDNAParserScore * cp,Score start_frag,Score end_frag,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_EstFrag3()
1439 PackAln * PackAln_calculate_Small_EstFrag3(EstFrag3 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_EstFrag3()
2415 …3 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_EstFrag3()
2698 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_EstFrag3()
2776 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_EstFrag3()
2805 …c_at_merge_EstFrag3(EstFrag3 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_EstFrag3()
3514 …_EstFrag3(EstFrag3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_EstFrag3()
3820 void run_up_dc_EstFrag3(EstFrag3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv… in run_up_dc_EstFrag3()
4117 boolean dc_optimised_start_end_calc_EstFrag3(EstFrag3 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_EstFrag3()
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H A Destloop3.c118 boolean calculate_shatter_EstLoop3(EstLoop3 * mat,DPEnvelope * dpenv) in calculate_shatter_EstLoop3()
1309 …GeneWiseScore* query,ComplexSequence* target ,cDNAParserScore * cp,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_EstLoop3()
1806 PackAln * PackAln_calculate_Small_EstLoop3(EstLoop3 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_EstLoop3()
2840 …3 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_EstLoop3()
3123 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_EstLoop3()
3201 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_EstLoop3()
3230 …c_at_merge_EstLoop3(EstLoop3 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_EstLoop3()
3939 …_EstLoop3(EstLoop3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_EstLoop3()
4245 void run_up_dc_EstLoop3(EstLoop3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv… in run_up_dc_EstLoop3()
4542 boolean dc_optimised_start_end_calc_EstLoop3(EstLoop3 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_EstLoop3()
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H A Destslimloop.c118 boolean calculate_shatter_EstSlimLoop3(EstSlimLoop3 * mat,DPEnvelope * dpenv) in calculate_shatter_EstSlimLoop3()
1111 …GeneWiseScore* query,ComplexSequence* target ,cDNAParserScore * cp,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_EstSlimLoop3()
1532 PackAln * PackAln_calculate_Small_EstSlimLoop3(EstSlimLoop3 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_EstSlimLoop3()
2338 …3 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_EstSlimLoop3()
2521 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_EstSlimLoop3()
2599 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_EstSlimLoop3()
2628 …ge_EstSlimLoop3(EstSlimLoop3 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_EstSlimLoop3()
2937 …Loop3(EstSlimLoop3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_EstSlimLoop3()
3103 …Loop3(EstSlimLoop3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_EstSlimLoop3()
3300 boolean dc_optimised_start_end_calc_EstSlimLoop3(EstSlimLoop3 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_EstSlimLoop3()
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H A Destwise3.c117 boolean calculate_shatter_EstWise3(EstWise3 * mat,DPEnvelope * dpenv) in calculate_shatter_EstWise3()
1141 …GeneWiseScore* query,ComplexSequence* target ,cDNAParserScore * cp,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_EstWise3()
1600 PackAln * PackAln_calculate_Small_EstWise3(EstWise3 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_EstWise3()
2563 …3 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_EstWise3()
2846 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_EstWise3()
2924 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_EstWise3()
2953 …c_at_merge_EstWise3(EstWise3 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_EstWise3()
3662 …_EstWise3(EstWise3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_EstWise3()
3968 void run_up_dc_EstWise3(EstWise3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv… in run_up_dc_EstWise3()
4265 boolean dc_optimised_start_end_calc_EstWise3(EstWise3 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_EstWise3()
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H A Dgeneloop6.c122 boolean calculate_shatter_GeneLoop6(GeneLoop6 * mat,DPEnvelope * dpenv) in calculate_shatter_GeneLoop6()
1265 …eneWiseScore* query,ComplexSequence* target ,GeneParser4Score * gp,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_GeneLoop6()
1739 PackAln * PackAln_calculate_Small_GeneLoop6(GeneLoop6 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_GeneLoop6()
2728 …6 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_GeneLoop6()
3025 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_GeneLoop6()
3103 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_GeneLoop6()
3132 …at_merge_GeneLoop6(GeneLoop6 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_GeneLoop6()
3789 …eneLoop6(GeneLoop6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_GeneLoop6()
4109 …eneLoop6(GeneLoop6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_GeneLoop6()
4420 boolean dc_optimised_start_end_calc_GeneLoop6(GeneLoop6 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_GeneLoop6()
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H A Dgenewise4.c119 boolean calculate_shatter_GeneWise4(GeneWise4 * mat,DPEnvelope * dpenv) in calculate_shatter_GeneWise4()
1065 …eneWiseScore* query,ComplexSequence* target ,GeneParser4Score * gp,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_GeneWise4()
1489 PackAln * PackAln_calculate_Small_GeneWise4(GeneWise4 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_GeneWise4()
2372 …4 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_GeneWise4()
2631 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_GeneWise4()
2709 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_GeneWise4()
2738 …at_merge_GeneWise4(GeneWise4 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_GeneWise4()
3311 …eneWise4(GeneWise4 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_GeneWise4()
3581 …eneWise4(GeneWise4 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_GeneWise4()
3854 boolean dc_optimised_start_end_calc_GeneWise4(GeneWise4 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_GeneWise4()
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H A Dgenomewise9.c130 boolean calculate_shatter_GenomeWise9(GenomeWise9 * mat,DPEnvelope * dpenv) in calculate_shatter_GenomeWise9()
1328 …int non_start_codon,int non_stop_codon,RandomCodonScore * rndcodon,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_GenomeWise9()
1892 PackAln * PackAln_calculate_Small_GenomeWise9(GenomeWise9 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_GenomeWise9()
2961 …9 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_GenomeWise9()
3277 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_GenomeWise9()
3355 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_GenomeWise9()
3384 …erge_GenomeWise9(GenomeWise9 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_GenomeWise9()
3987 …eWise9(GenomeWise9 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_GenomeWise9()
4328 …eWise9(GenomeWise9 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_GenomeWise9()
4658 boolean dc_optimised_start_end_calc_GenomeWise9(GenomeWise9 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_GenomeWise9()
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H A Dgwlite.c120 boolean calculate_shatter_GeneLiteModel(GeneLiteModel * mat,DPEnvelope * dpenv) in calculate_shatter_GeneLiteModel()
1114 …(GwLiteScore* query,ComplexSequence* target ,GeneParser4Score * gp,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_GeneLiteModel()
1560 PackAln * PackAln_calculate_Small_GeneLiteModel(GeneLiteModel * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_GeneLiteModel()
2457 …l * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_GeneLiteModel()
2732 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_GeneLiteModel()
2810 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_GeneLiteModel()
2839 …_GeneLiteModel(GeneLiteModel * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_GeneLiteModel()
3414 …odel(GeneLiteModel * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_GeneLiteModel()
3704 …odel(GeneLiteModel * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_GeneLiteModel()
3993 boolean dc_optimised_start_end_calc_GeneLiteModel(GeneLiteModel *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_GeneLiteModel()
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H A Dgenestretch6.c123 boolean calculate_shatter_GeneStretch6(GeneStretch6 * mat,DPEnvelope * dpenv) in calculate_shatter_GeneStretch6()
1336 …arget ,GeneParser4Score * gp,GeneralGeneModelScore * general_model,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_GeneStretch6()
1836 PackAln * PackAln_calculate_Small_GeneStretch6(GeneStretch6 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_GeneStretch6()
2863 …6 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_GeneStretch6()
3160 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_GeneStretch6()
3238 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_GeneStretch6()
3267 …ge_GeneStretch6(GeneStretch6 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_GeneStretch6()
3924 …etch6(GeneStretch6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_GeneStretch6()
4244 …etch6(GeneStretch6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_GeneStretch6()
4555 boolean dc_optimised_start_end_calc_GeneStretch6(GeneStretch6 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_GeneStretch6()
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H A Dpseudowise7.c121 boolean calculate_shatter_PseudoWise7(PseudoWise7 * mat,DPEnvelope * dpenv) in calculate_shatter_PseudoWise7()
1204 …query,ComplexSequence* target ,GeneParser4Score * gp,Score dna_ext,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_PseudoWise7()
1679 PackAln * PackAln_calculate_Small_PseudoWise7(PseudoWise7 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_PseudoWise7()
2642 …7 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_PseudoWise7()
2953 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_PseudoWise7()
3031 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_PseudoWise7()
3060 …erge_PseudoWise7(PseudoWise7 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_PseudoWise7()
3739 …oWise7(PseudoWise7 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_PseudoWise7()
4077 …oWise7(PseudoWise7 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_PseudoWise7()
4402 boolean dc_optimised_start_end_calc_PseudoWise7(PseudoWise7 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_PseudoWise7()
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H A Dgenephase6.c208 boolean calculate_shatter_GenePhase6(GenePhase6 * mat,DPEnvelope * dpenv) in calculate_shatter_GenePhase6()
1489 …arget ,GeneParser4Score * gp,GeneralGeneModelScore * general_model,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_GenePhase6()
2049 PackAln * PackAln_calculate_Small_GenePhase6(GenePhase6 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_GenePhase6()
3212 …6 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_GenePhase6()
3509 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_GenePhase6()
3587 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_GenePhase6()
3616 …_merge_GenePhase6(GenePhase6 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_GenePhase6()
4273 …ePhase6(GenePhase6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_GenePhase6()
4593 …ePhase6(GenePhase6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_GenePhase6()
4904 boolean dc_optimised_start_end_calc_GenePhase6(GenePhase6 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_GenePhase6()
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H A Dgenewise6.c121 boolean calculate_shatter_GeneWise6(GeneWise6 * mat,DPEnvelope * dpenv) in calculate_shatter_GeneWise6()
1177 …eneWiseScore* query,ComplexSequence* target ,GeneParser4Score * gp,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_GeneWise6()
1639 PackAln * PackAln_calculate_Small_GeneWise6(GeneWise6 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_GeneWise6()
2584 …6 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_GeneWise6()
2881 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_GeneWise6()
2959 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_GeneWise6()
2988 …at_merge_GeneWise6(GeneWise6 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_GeneWise6()
3645 …eneWise6(GeneWise6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_GeneWise6()
3965 …eneWise6(GeneWise6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_GeneWise6()
4276 boolean dc_optimised_start_end_calc_GeneWise6(GeneWise6 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_GeneWise6()
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H A Dlargeblockdp.c119 boolean calculate_shatter_LargeBlockAligner(LargeBlockAligner * mat,DPEnvelope * dpenv) in calculate_shatter_LargeBlockAligner()
665 …ck_open,Score un_dual,Score un_single,Score gap_open,Score gap_ext,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_LargeBlockAligner()
1059 PackAln * PackAln_calculate_Small_LargeBlockAligner(LargeBlockAligner * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_LargeBlockAligner()
1763 …r * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_LargeBlockAligner()
1951 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_LargeBlockAligner()
2029 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_LargeBlockAligner()
2058 …ockAligner(LargeBlockAligner * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_LargeBlockAligner()
2350 …(LargeBlockAligner * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_LargeBlockAligner()
2521 …(LargeBlockAligner * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_LargeBlockAligner()
2723 boolean dc_optimised_start_end_calc_LargeBlockAligner(LargeBlockAligner *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_LargeBlockAligner()
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H A Dlocalclonewisedp.c117 boolean calculate_shatter_LocalCloneWise(LocalCloneWise * mat,DPEnvelope * dpenv) in calculate_shatter_LocalCloneWise()
781 … query_skip_start,Score query_skip,int spread,int target_special_s,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_LocalCloneWise()
1176 PackAln * PackAln_calculate_Small_LocalCloneWise(LocalCloneWise * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_LocalCloneWise()
1875 …e * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_LocalCloneWise()
2051 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_LocalCloneWise()
2129 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_LocalCloneWise()
2158 …ocalCloneWise(LocalCloneWise * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_LocalCloneWise()
2430 …ise(LocalCloneWise * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_LocalCloneWise()
2585 …ise(LocalCloneWise * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_LocalCloneWise()
2775 boolean dc_optimised_start_end_calc_LocalCloneWise(LocalCloneWise *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_LocalCloneWise()
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H A Dlocaldba.c120 boolean calculate_shatter_LocalDnaMatchBlock(LocalDnaMatchBlock * mat,DPEnvelope * dpenv) in calculate_shatter_LocalDnaMatchBlock()
838 …lexSequence* query,ComplexSequence* target ,LocalCisHitScore* lchs,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_LocalDnaMatchBlock()
1282 PackAln * PackAln_calculate_Small_LocalDnaMatchBlock(LocalDnaMatchBlock * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_LocalDnaMatchBlock()
2156 …k * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_LocalDnaMatchBlock()
2416 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_LocalDnaMatchBlock()
2494 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_LocalDnaMatchBlock()
2523 …atchBlock(LocalDnaMatchBlock * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_LocalDnaMatchBlock()
3038 …LocalDnaMatchBlock * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_LocalDnaMatchBlock()
3307 …LocalDnaMatchBlock * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_LocalDnaMatchBlock()
3581 boolean dc_optimised_start_end_calc_LocalDnaMatchBlock(LocalDnaMatchBlock *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_LocalDnaMatchBlock()
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H A Dgeneloop21.c140 boolean calculate_shatter_GeneLoop21(GeneLoop21 * mat,DPEnvelope * dpenv) in calculate_shatter_GeneLoop21()
2277 …e * gp21,RandomCodonScore * rndcodon,RandomModelDNAScore * rndbase,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_GeneLoop21()
3090 PackAln * PackAln_calculate_Small_GeneLoop21(GeneLoop21 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_GeneLoop21()
4893 …1 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_GeneLoop21()
5572 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_GeneLoop21()
5650 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_GeneLoop21()
5679 …_merge_GeneLoop21(GeneLoop21 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_GeneLoop21()
7318 …eLoop21(GeneLoop21 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_GeneLoop21()
8144 …eLoop21(GeneLoop21 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_GeneLoop21()
8837 boolean dc_optimised_start_end_calc_GeneLoop21(GeneLoop21 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_GeneLoop21()
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H A Dgenewise21.c147 boolean calculate_shatter_GeneWise21(GeneWise21 * mat,DPEnvelope * dpenv) in calculate_shatter_GeneWise21()
2603 …e * gp21,RandomCodonScore * rndcodon,RandomModelDNAScore * rndbase,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_GeneWise21()
3504 PackAln * PackAln_calculate_Small_GeneWise21(GeneWise21 * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_GeneWise21()
5516 …1 * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_GeneWise21()
6195 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_GeneWise21()
6273 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_GeneWise21()
6302 …_merge_GeneWise21(GeneWise21 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_GeneWise21()
7941 …eWise21(GeneWise21 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_GeneWise21()
8767 …eWise21(GeneWise21 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_GeneWise21()
9460 boolean dc_optimised_start_end_calc_GeneWise21(GeneWise21 *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_GeneWise21()
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H A Dabc.c116 boolean calculate_shatter_abc(abc * mat,DPEnvelope * dpenv) in calculate_shatter_abc()
819 …ce* query,ComplexSequence* target ,CompMat* comp,int a,int b,int c,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_abc()
1165 PackAln * PackAln_calculate_Small_abc(abc * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_abc()
1796 …c * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_abc()
1946 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_abc()
2024 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_abc()
2053 void push_dc_at_merge_abc(abc * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_abc()
2261 void follow_on_dc_abc(abc * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int pe… in follow_on_dc_abc()
2382 void run_up_dc_abc(abc * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_… in run_up_dc_abc()
2546 boolean dc_optimised_start_end_calc_abc(abc *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_abc()
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H A Dclonewisedp.c118 boolean calculate_shatter_CloneWise(CloneWise * mat,DPEnvelope * dpenv) in calculate_shatter_CloneWise()
861 … query_skip_start,Score query_skip,int spread,int target_special_s,DPEnvelope * dpenv,DPRunImpl * … in PackAln_bestmemory_CloneWise()
1272 PackAln * PackAln_calculate_Small_CloneWise(CloneWise * mat,DPEnvelope * dpenv) in PackAln_calculate_Small_CloneWise()
2027 …e * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv) in calculate_hidden_CloneWise()
2203 …rtstate,int stopi,int stopj,int stopstate,PackAln * out,int * donej,int totalj,DPEnvelope * dpenv) in full_dc_CloneWise()
2281 …starti,int startj,int startstate,int stopi,int stopj,int stopstate,DPEnvelope * dpenv,int perc_don… in do_dc_single_pass_CloneWise()
2310 …at_merge_CloneWise(CloneWise * mat,int starti,int stopi,int startj,int * stopj,DPEnvelope * dpenv) in push_dc_at_merge_CloneWise()
2582 …loneWise(CloneWise * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in follow_on_dc_CloneWise()
2737 …loneWise(CloneWise * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpenv,int perc_don… in run_up_dc_CloneWise()
2927 boolean dc_optimised_start_end_calc_CloneWise(CloneWise *mat,DPEnvelope * dpenv) in dc_optimised_start_end_calc_CloneWise()
[all …]

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