| /dports/biology/wise/wise2.4.1/src/models/ |
| H A D | statwise10.c | 798 int stopi; in PackAln_calculate_Small_StatWise10() local
1039 boolean read_hidden_StatWise10(StatWise10 * mat,int starti,int startj,int startstate,int stopi,int … in read_hidden_StatWise10()
1288 boolean read_special_strip_StatWise10(StatWise10 * mat,int stopi,int stopj,int stopstate,int * star… in read_special_strip_StatWise10()
1524 void calculate_hidden_StatWise10(StatWise10 * mat,int starti,int startj,int startstate,int stopi,in… in calculate_hidden_StatWise10()
1652 void init_hidden_StatWise10(StatWise10 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_StatWise10()
1706 boolean full_dc_StatWise10(StatWise10 * mat,int starti,int startj,int startstate,int stopi,int stop… in full_dc_StatWise10()
1784 …e_pass_StatWise10(StatWise10 * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_StatWise10()
1813 void push_dc_at_merge_StatWise10(StatWise10 * mat,int starti,int stopi,int startj,int * stopj,DPEnv… in push_dc_at_merge_StatWise10()
2084 void follow_on_dc_StatWise10(StatWise10 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope … in follow_on_dc_StatWise10()
2247 void run_up_dc_StatWise10(StatWise10 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * d… in run_up_dc_StatWise10()
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| H A D | threestateloop.c | 1176 int stopi; in PackAln_calculate_Small_ThreeStateLoop() local
1417 …hreeStateLoop(ThreeStateLoop * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in read_hidden_ThreeStateLoop()
1643 boolean read_special_strip_ThreeStateLoop(ThreeStateLoop * mat,int stopi,int stopj,int stopstate,in… in read_special_strip_ThreeStateLoop()
1898 …hreeStateLoop(ThreeStateLoop * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in calculate_hidden_ThreeStateLoop()
2011 void init_hidden_ThreeStateLoop(ThreeStateLoop * mat,int starti,int startj,int stopi,int stopj) in init_hidden_ThreeStateLoop()
2063 boolean full_dc_ThreeStateLoop(ThreeStateLoop * mat,int starti,int startj,int startstate,int stopi,… in full_dc_ThreeStateLoop()
2141 …hreeStateLoop(ThreeStateLoop * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_ThreeStateLoop()
2170 void push_dc_at_merge_ThreeStateLoop(ThreeStateLoop * mat,int starti,int stopi,int startj,int * sto… in push_dc_at_merge_ThreeStateLoop()
2401 void follow_on_dc_ThreeStateLoop(ThreeStateLoop * mat,int starti,int stopi,int startj,int stopj,DPE… in follow_on_dc_ThreeStateLoop()
2541 void run_up_dc_ThreeStateLoop(ThreeStateLoop * mat,int starti,int stopi,int startj,int stopj,DPEnve… in run_up_dc_ThreeStateLoop()
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| H A D | threestatedp.c | 1074 int stopi; in PackAln_calculate_Small_ThreeStateProtein() local
1296 …ateProtein(ThreeStateProtein * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in read_hidden_ThreeStateProtein()
1522 boolean read_special_strip_ThreeStateProtein(ThreeStateProtein * mat,int stopi,int stopj,int stopst… in read_special_strip_ThreeStateProtein()
1740 …ateProtein(ThreeStateProtein * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in calculate_hidden_ThreeStateProtein()
1853 void init_hidden_ThreeStateProtein(ThreeStateProtein * mat,int starti,int startj,int stopi,int stop… in init_hidden_ThreeStateProtein()
1905 …ateProtein(ThreeStateProtein * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in full_dc_ThreeStateProtein()
1983 …ateProtein(ThreeStateProtein * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_ThreeStateProtein()
2012 void push_dc_at_merge_ThreeStateProtein(ThreeStateProtein * mat,int starti,int stopi,int startj,int… in push_dc_at_merge_ThreeStateProtein()
2243 void follow_on_dc_ThreeStateProtein(ThreeStateProtein * mat,int starti,int stopi,int startj,int sto… in follow_on_dc_ThreeStateProtein()
2383 void run_up_dc_ThreeStateProtein(ThreeStateProtein * mat,int starti,int stopi,int startj,int stopj,… in run_up_dc_ThreeStateProtein()
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| H A D | fivestate.c | 1320 int stopi; in PackAln_calculate_Small_FiveStateProtein() local
1542 …tateProtein(FiveStateProtein * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in read_hidden_FiveStateProtein()
1885 boolean read_special_strip_FiveStateProtein(FiveStateProtein * mat,int stopi,int stopj,int stopstat… in read_special_strip_FiveStateProtein()
2132 …tateProtein(FiveStateProtein * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in calculate_hidden_FiveStateProtein()
2309 void init_hidden_FiveStateProtein(FiveStateProtein * mat,int starti,int startj,int stopi,int stopj) in init_hidden_FiveStateProtein()
2365 …tateProtein(FiveStateProtein * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in full_dc_FiveStateProtein()
2443 …tateProtein(FiveStateProtein * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_FiveStateProtein()
2472 void push_dc_at_merge_FiveStateProtein(FiveStateProtein * mat,int starti,int stopi,int startj,int *… in push_dc_at_merge_FiveStateProtein()
2907 void follow_on_dc_FiveStateProtein(FiveStateProtein * mat,int starti,int stopi,int startj,int stopj… in follow_on_dc_FiveStateProtein()
3139 void run_up_dc_FiveStateProtein(FiveStateProtein * mat,int starti,int stopi,int startj,int stopj,DP… in run_up_dc_FiveStateProtein()
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| H A D | slimdba.c | 953 int stopi; in PackAln_calculate_Small_SlimDnaMatchBlock() local
1175 …MatchBlock(SlimDnaMatchBlock * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in read_hidden_SlimDnaMatchBlock()
1388 boolean read_special_strip_SlimDnaMatchBlock(SlimDnaMatchBlock * mat,int stopi,int stopj,int stopst… in read_special_strip_SlimDnaMatchBlock()
1581 …MatchBlock(SlimDnaMatchBlock * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in calculate_hidden_SlimDnaMatchBlock()
1687 void init_hidden_SlimDnaMatchBlock(SlimDnaMatchBlock * mat,int starti,int startj,int stopi,int stop… in init_hidden_SlimDnaMatchBlock()
1739 …MatchBlock(SlimDnaMatchBlock * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in full_dc_SlimDnaMatchBlock()
1817 …MatchBlock(SlimDnaMatchBlock * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_SlimDnaMatchBlock()
1846 void push_dc_at_merge_SlimDnaMatchBlock(SlimDnaMatchBlock * mat,int starti,int stopi,int startj,int… in push_dc_at_merge_SlimDnaMatchBlock()
2055 void follow_on_dc_SlimDnaMatchBlock(SlimDnaMatchBlock * mat,int starti,int stopi,int startj,int sto… in follow_on_dc_SlimDnaMatchBlock()
2186 void run_up_dc_SlimDnaMatchBlock(SlimDnaMatchBlock * mat,int starti,int stopi,int startj,int stopj,… in run_up_dc_SlimDnaMatchBlock()
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| H A D | estfrag3.c | 1448 int stopi; in PackAln_calculate_Small_EstFrag3() local
1670 boolean read_hidden_EstFrag3(EstFrag3 * mat,int starti,int startj,int startstate,int stopi,int stop… in read_hidden_EstFrag3()
2161 boolean read_special_strip_EstFrag3(EstFrag3 * mat,int stopi,int stopj,int stopstate,int * startj,i… in read_special_strip_EstFrag3()
2415 void calculate_hidden_EstFrag3(EstFrag3 * mat,int starti,int startj,int startstate,int stopi,int st… in calculate_hidden_EstFrag3()
2646 void init_hidden_EstFrag3(EstFrag3 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_EstFrag3()
2698 boolean full_dc_EstFrag3(EstFrag3 * mat,int starti,int startj,int startstate,int stopi,int stopj,in… in full_dc_EstFrag3()
2776 boolean do_dc_single_pass_EstFrag3(EstFrag3 * mat,int starti,int startj,int startstate,int stopi,in… in do_dc_single_pass_EstFrag3()
2805 void push_dc_at_merge_EstFrag3(EstFrag3 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelop… in push_dc_at_merge_EstFrag3()
3514 void follow_on_dc_EstFrag3(EstFrag3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dp… 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()
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| H A D | estloop3.c | 1815 int stopi; in PackAln_calculate_Small_EstLoop3() local
2056 boolean read_hidden_EstLoop3(EstLoop3 * mat,int starti,int startj,int startstate,int stopi,int stop… in read_hidden_EstLoop3()
2547 boolean read_special_strip_EstLoop3(EstLoop3 * mat,int stopi,int stopj,int stopstate,int * startj,i… in read_special_strip_EstLoop3()
2840 void calculate_hidden_EstLoop3(EstLoop3 * mat,int starti,int startj,int startstate,int stopi,int st… in calculate_hidden_EstLoop3()
3071 void init_hidden_EstLoop3(EstLoop3 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_EstLoop3()
3123 boolean full_dc_EstLoop3(EstLoop3 * mat,int starti,int startj,int startstate,int stopi,int stopj,in… in full_dc_EstLoop3()
3201 boolean do_dc_single_pass_EstLoop3(EstLoop3 * mat,int starti,int startj,int startstate,int stopi,in… in do_dc_single_pass_EstLoop3()
3230 void push_dc_at_merge_EstLoop3(EstLoop3 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelop… in push_dc_at_merge_EstLoop3()
3939 void follow_on_dc_EstLoop3(EstLoop3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dp… 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()
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| H A D | estslimloop.c | 1541 int stopi; in PackAln_calculate_Small_EstSlimLoop3() local
1782 boolean read_hidden_EstSlimLoop3(EstSlimLoop3 * mat,int starti,int startj,int startstate,int stopi,… in read_hidden_EstSlimLoop3()
2054 boolean read_special_strip_EstSlimLoop3(EstSlimLoop3 * mat,int stopi,int stopj,int stopstate,int * … in read_special_strip_EstSlimLoop3()
2338 …en_EstSlimLoop3(EstSlimLoop3 * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in calculate_hidden_EstSlimLoop3()
2469 void init_hidden_EstSlimLoop3(EstSlimLoop3 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_EstSlimLoop3()
2521 boolean full_dc_EstSlimLoop3(EstSlimLoop3 * mat,int starti,int startj,int startstate,int stopi,int … in full_dc_EstSlimLoop3()
2599 …ss_EstSlimLoop3(EstSlimLoop3 * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_EstSlimLoop3()
2628 void push_dc_at_merge_EstSlimLoop3(EstSlimLoop3 * mat,int starti,int stopi,int startj,int * stopj,D… in push_dc_at_merge_EstSlimLoop3()
2937 void follow_on_dc_EstSlimLoop3(EstSlimLoop3 * mat,int starti,int stopi,int startj,int stopj,DPEnvel… in follow_on_dc_EstSlimLoop3()
3103 void run_up_dc_EstSlimLoop3(EstSlimLoop3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope… in run_up_dc_EstSlimLoop3()
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| H A D | estwise3.c | 1609 int stopi; in PackAln_calculate_Small_EstWise3() local
1831 boolean read_hidden_EstWise3(EstWise3 * mat,int starti,int startj,int startstate,int stopi,int stop… in read_hidden_EstWise3()
2321 boolean read_special_strip_EstWise3(EstWise3 * mat,int stopi,int stopj,int stopstate,int * startj,i… in read_special_strip_EstWise3()
2563 void calculate_hidden_EstWise3(EstWise3 * mat,int starti,int startj,int startstate,int stopi,int st… in calculate_hidden_EstWise3()
2794 void init_hidden_EstWise3(EstWise3 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_EstWise3()
2846 boolean full_dc_EstWise3(EstWise3 * mat,int starti,int startj,int startstate,int stopi,int stopj,in… in full_dc_EstWise3()
2924 boolean do_dc_single_pass_EstWise3(EstWise3 * mat,int starti,int startj,int startstate,int stopi,in… in do_dc_single_pass_EstWise3()
2953 void push_dc_at_merge_EstWise3(EstWise3 * mat,int starti,int stopi,int startj,int * stopj,DPEnvelop… in push_dc_at_merge_EstWise3()
3662 void follow_on_dc_EstWise3(EstWise3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dp… 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()
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| H A D | geneloop6.c | 1748 int stopi; in PackAln_calculate_Small_GeneLoop6() local
1989 boolean read_hidden_GeneLoop6(GeneLoop6 * mat,int starti,int startj,int startstate,int stopi,int st… in read_hidden_GeneLoop6()
2454 boolean read_special_strip_GeneLoop6(GeneLoop6 * mat,int stopi,int stopj,int stopstate,int * startj… in read_special_strip_GeneLoop6()
2728 void calculate_hidden_GeneLoop6(GeneLoop6 * mat,int starti,int startj,int startstate,int stopi,int … in calculate_hidden_GeneLoop6()
2967 void init_hidden_GeneLoop6(GeneLoop6 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_GeneLoop6()
3025 boolean full_dc_GeneLoop6(GeneLoop6 * mat,int starti,int startj,int startstate,int stopi,int stopj,… in full_dc_GeneLoop6()
3103 boolean do_dc_single_pass_GeneLoop6(GeneLoop6 * mat,int starti,int startj,int startstate,int stopi,… in do_dc_single_pass_GeneLoop6()
3132 void push_dc_at_merge_GeneLoop6(GeneLoop6 * mat,int starti,int stopi,int startj,int * stopj,DPEnvel… in push_dc_at_merge_GeneLoop6()
3789 void follow_on_dc_GeneLoop6(GeneLoop6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * … in follow_on_dc_GeneLoop6()
4109 void run_up_dc_GeneLoop6(GeneLoop6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpe… in run_up_dc_GeneLoop6()
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| H A D | genewise4.c | 1498 int stopi; in PackAln_calculate_Small_GeneWise4() local
1720 boolean read_hidden_GeneWise4(GeneWise4 * mat,int starti,int startj,int startstate,int stopi,int st… in read_hidden_GeneWise4()
2136 boolean read_special_strip_GeneWise4(GeneWise4 * mat,int stopi,int stopj,int stopstate,int * startj… in read_special_strip_GeneWise4()
2372 void calculate_hidden_GeneWise4(GeneWise4 * mat,int starti,int startj,int startstate,int stopi,int … in calculate_hidden_GeneWise4()
2577 void init_hidden_GeneWise4(GeneWise4 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_GeneWise4()
2631 boolean full_dc_GeneWise4(GeneWise4 * mat,int starti,int startj,int startstate,int stopi,int stopj,… in full_dc_GeneWise4()
2709 boolean do_dc_single_pass_GeneWise4(GeneWise4 * mat,int starti,int startj,int startstate,int stopi,… in do_dc_single_pass_GeneWise4()
2738 void push_dc_at_merge_GeneWise4(GeneWise4 * mat,int starti,int stopi,int startj,int * stopj,DPEnvel… in push_dc_at_merge_GeneWise4()
3311 void follow_on_dc_GeneWise4(GeneWise4 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * … in follow_on_dc_GeneWise4()
3581 void run_up_dc_GeneWise4(GeneWise4 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpe… in run_up_dc_GeneWise4()
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| H A D | genomewise9.c | 1901 int stopi; in PackAln_calculate_Small_GenomeWise9() local
2142 boolean read_hidden_GenomeWise9(GenomeWise9 * mat,int starti,int startj,int startstate,int stopi,in… in read_hidden_GenomeWise9()
2592 boolean read_special_strip_GenomeWise9(GenomeWise9 * mat,int stopi,int stopj,int stopstate,int * st… in read_special_strip_GenomeWise9()
2961 void calculate_hidden_GenomeWise9(GenomeWise9 * mat,int starti,int startj,int startstate,int stopi,… in calculate_hidden_GenomeWise9()
3211 void init_hidden_GenomeWise9(GenomeWise9 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_GenomeWise9()
3277 boolean full_dc_GenomeWise9(GenomeWise9 * mat,int starti,int startj,int startstate,int stopi,int st… in full_dc_GenomeWise9()
3355 …pass_GenomeWise9(GenomeWise9 * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_GenomeWise9()
3384 void push_dc_at_merge_GenomeWise9(GenomeWise9 * mat,int starti,int stopi,int startj,int * stopj,DPE… in push_dc_at_merge_GenomeWise9()
3987 void follow_on_dc_GenomeWise9(GenomeWise9 * mat,int starti,int stopi,int startj,int stopj,DPEnvelop… in follow_on_dc_GenomeWise9()
4328 void run_up_dc_GenomeWise9(GenomeWise9 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope *… in run_up_dc_GenomeWise9()
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| H A D | gwlite.c | 1569 int stopi; in PackAln_calculate_Small_GeneLiteModel() local
1791 …_GeneLiteModel(GeneLiteModel * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in read_hidden_GeneLiteModel()
2213 boolean read_special_strip_GeneLiteModel(GeneLiteModel * mat,int stopi,int stopj,int stopstate,int … in read_special_strip_GeneLiteModel()
2457 …_GeneLiteModel(GeneLiteModel * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in calculate_hidden_GeneLiteModel()
2674 void init_hidden_GeneLiteModel(GeneLiteModel * mat,int starti,int startj,int stopi,int stopj) in init_hidden_GeneLiteModel()
2732 boolean full_dc_GeneLiteModel(GeneLiteModel * mat,int starti,int startj,int startstate,int stopi,in… in full_dc_GeneLiteModel()
2810 …_GeneLiteModel(GeneLiteModel * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_GeneLiteModel()
2839 void push_dc_at_merge_GeneLiteModel(GeneLiteModel * mat,int starti,int stopi,int startj,int * stopj… in push_dc_at_merge_GeneLiteModel()
3414 void follow_on_dc_GeneLiteModel(GeneLiteModel * mat,int starti,int stopi,int startj,int stopj,DPEnv… in follow_on_dc_GeneLiteModel()
3704 void run_up_dc_GeneLiteModel(GeneLiteModel * mat,int starti,int stopi,int startj,int stopj,DPEnvelo… in run_up_dc_GeneLiteModel()
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| H A D | genestretch6.c | 1845 int stopi; in PackAln_calculate_Small_GeneStretch6() local
2086 boolean read_hidden_GeneStretch6(GeneStretch6 * mat,int starti,int startj,int startstate,int stopi,… in read_hidden_GeneStretch6()
2553 boolean read_special_strip_GeneStretch6(GeneStretch6 * mat,int stopi,int stopj,int stopstate,int * … in read_special_strip_GeneStretch6()
2863 …en_GeneStretch6(GeneStretch6 * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in calculate_hidden_GeneStretch6()
3102 void init_hidden_GeneStretch6(GeneStretch6 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_GeneStretch6()
3160 boolean full_dc_GeneStretch6(GeneStretch6 * mat,int starti,int startj,int startstate,int stopi,int … in full_dc_GeneStretch6()
3238 …ss_GeneStretch6(GeneStretch6 * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_GeneStretch6()
3267 void push_dc_at_merge_GeneStretch6(GeneStretch6 * mat,int starti,int stopi,int startj,int * stopj,D… in push_dc_at_merge_GeneStretch6()
3924 void follow_on_dc_GeneStretch6(GeneStretch6 * mat,int starti,int stopi,int startj,int stopj,DPEnvel… in follow_on_dc_GeneStretch6()
4244 void run_up_dc_GeneStretch6(GeneStretch6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope… in run_up_dc_GeneStretch6()
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| H A D | pseudowise7.c | 1688 int stopi; in PackAln_calculate_Small_PseudoWise7() local
1910 boolean read_hidden_PseudoWise7(PseudoWise7 * mat,int starti,int startj,int startstate,int stopi,in… in read_hidden_PseudoWise7()
2390 boolean read_special_strip_PseudoWise7(PseudoWise7 * mat,int stopi,int stopj,int stopstate,int * st… in read_special_strip_PseudoWise7()
2642 void calculate_hidden_PseudoWise7(PseudoWise7 * mat,int starti,int startj,int startstate,int stopi,… in calculate_hidden_PseudoWise7()
2893 void init_hidden_PseudoWise7(PseudoWise7 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_PseudoWise7()
2953 boolean full_dc_PseudoWise7(PseudoWise7 * mat,int starti,int startj,int startstate,int stopi,int st… in full_dc_PseudoWise7()
3031 …pass_PseudoWise7(PseudoWise7 * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_PseudoWise7()
3060 void push_dc_at_merge_PseudoWise7(PseudoWise7 * mat,int starti,int stopi,int startj,int * stopj,DPE… in push_dc_at_merge_PseudoWise7()
3739 void follow_on_dc_PseudoWise7(PseudoWise7 * mat,int starti,int stopi,int startj,int stopj,DPEnvelop… in follow_on_dc_PseudoWise7()
4077 void run_up_dc_PseudoWise7(PseudoWise7 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope *… in run_up_dc_PseudoWise7()
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| H A D | genephase6.c | 2058 int stopi; in PackAln_calculate_Small_GenePhase6() local
2299 boolean read_hidden_GenePhase6(GenePhase6 * mat,int starti,int startj,int startstate,int stopi,int … in read_hidden_GenePhase6()
2765 boolean read_special_strip_GenePhase6(GenePhase6 * mat,int stopi,int stopj,int stopstate,int * star… in read_special_strip_GenePhase6()
3212 void calculate_hidden_GenePhase6(GenePhase6 * mat,int starti,int startj,int startstate,int stopi,in… in calculate_hidden_GenePhase6()
3451 void init_hidden_GenePhase6(GenePhase6 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_GenePhase6()
3509 boolean full_dc_GenePhase6(GenePhase6 * mat,int starti,int startj,int startstate,int stopi,int stop… in full_dc_GenePhase6()
3587 …e_pass_GenePhase6(GenePhase6 * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_GenePhase6()
3616 void push_dc_at_merge_GenePhase6(GenePhase6 * mat,int starti,int stopi,int startj,int * stopj,DPEnv… in push_dc_at_merge_GenePhase6()
4273 void follow_on_dc_GenePhase6(GenePhase6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope … in follow_on_dc_GenePhase6()
4593 void run_up_dc_GenePhase6(GenePhase6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * d… in run_up_dc_GenePhase6()
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| H A D | genewise6.c | 1648 int stopi; in PackAln_calculate_Small_GeneWise6() local
1870 boolean read_hidden_GeneWise6(GeneWise6 * mat,int starti,int startj,int startstate,int stopi,int st… in read_hidden_GeneWise6()
2336 boolean read_special_strip_GeneWise6(GeneWise6 * mat,int stopi,int stopj,int stopstate,int * startj… in read_special_strip_GeneWise6()
2584 void calculate_hidden_GeneWise6(GeneWise6 * mat,int starti,int startj,int startstate,int stopi,int … in calculate_hidden_GeneWise6()
2823 void init_hidden_GeneWise6(GeneWise6 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_GeneWise6()
2881 boolean full_dc_GeneWise6(GeneWise6 * mat,int starti,int startj,int startstate,int stopi,int stopj,… in full_dc_GeneWise6()
2959 boolean do_dc_single_pass_GeneWise6(GeneWise6 * mat,int starti,int startj,int startstate,int stopi,… in do_dc_single_pass_GeneWise6()
2988 void push_dc_at_merge_GeneWise6(GeneWise6 * mat,int starti,int stopi,int startj,int * stopj,DPEnvel… in push_dc_at_merge_GeneWise6()
3645 void follow_on_dc_GeneWise6(GeneWise6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * … in follow_on_dc_GeneWise6()
3965 void run_up_dc_GeneWise6(GeneWise6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpe… in run_up_dc_GeneWise6()
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| H A D | largeblockdp.c | 1068 int stopi; in PackAln_calculate_Small_LargeBlockAligner() local
1290 …ockAligner(LargeBlockAligner * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in read_hidden_LargeBlockAligner()
1551 boolean read_special_strip_LargeBlockAligner(LargeBlockAligner * mat,int stopi,int stopj,int stopst… in read_special_strip_LargeBlockAligner()
1763 …ockAligner(LargeBlockAligner * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in calculate_hidden_LargeBlockAligner()
1897 void init_hidden_LargeBlockAligner(LargeBlockAligner * mat,int starti,int startj,int stopi,int stop… in init_hidden_LargeBlockAligner()
1951 …ockAligner(LargeBlockAligner * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in full_dc_LargeBlockAligner()
2029 …ockAligner(LargeBlockAligner * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_LargeBlockAligner()
2058 void push_dc_at_merge_LargeBlockAligner(LargeBlockAligner * mat,int starti,int stopi,int startj,int… in push_dc_at_merge_LargeBlockAligner()
2350 void follow_on_dc_LargeBlockAligner(LargeBlockAligner * mat,int starti,int stopi,int startj,int sto… in follow_on_dc_LargeBlockAligner()
2521 void run_up_dc_LargeBlockAligner(LargeBlockAligner * mat,int starti,int stopi,int startj,int stopj,… in run_up_dc_LargeBlockAligner()
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| H A D | localclonewisedp.c | 1185 int stopi; in PackAln_calculate_Small_LocalCloneWise() local
1407 …ocalCloneWise(LocalCloneWise * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in read_hidden_LocalCloneWise()
1655 boolean read_special_strip_LocalCloneWise(LocalCloneWise * mat,int stopi,int stopj,int stopstate,in… in read_special_strip_LocalCloneWise()
1875 …ocalCloneWise(LocalCloneWise * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in calculate_hidden_LocalCloneWise()
1999 void init_hidden_LocalCloneWise(LocalCloneWise * mat,int starti,int startj,int stopi,int stopj) in init_hidden_LocalCloneWise()
2051 boolean full_dc_LocalCloneWise(LocalCloneWise * mat,int starti,int startj,int startstate,int stopi,… in full_dc_LocalCloneWise()
2129 …ocalCloneWise(LocalCloneWise * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_LocalCloneWise()
2158 void push_dc_at_merge_LocalCloneWise(LocalCloneWise * mat,int starti,int stopi,int startj,int * sto… in push_dc_at_merge_LocalCloneWise()
2430 void follow_on_dc_LocalCloneWise(LocalCloneWise * mat,int starti,int stopi,int startj,int stopj,DPE… in follow_on_dc_LocalCloneWise()
2585 void run_up_dc_LocalCloneWise(LocalCloneWise * mat,int starti,int stopi,int startj,int stopj,DPEnve… in run_up_dc_LocalCloneWise()
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| H A D | localdba.c | 1291 int stopi; in PackAln_calculate_Small_LocalDnaMatchBlock() local
1513 …atchBlock(LocalDnaMatchBlock * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in read_hidden_LocalDnaMatchBlock()
1903 boolean read_special_strip_LocalDnaMatchBlock(LocalDnaMatchBlock * mat,int stopi,int stopj,int stop… in read_special_strip_LocalDnaMatchBlock()
2156 …atchBlock(LocalDnaMatchBlock * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in calculate_hidden_LocalDnaMatchBlock()
2358 void init_hidden_LocalDnaMatchBlock(LocalDnaMatchBlock * mat,int starti,int startj,int stopi,int st… in init_hidden_LocalDnaMatchBlock()
2416 …atchBlock(LocalDnaMatchBlock * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in full_dc_LocalDnaMatchBlock()
2494 …atchBlock(LocalDnaMatchBlock * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_LocalDnaMatchBlock()
2523 void push_dc_at_merge_LocalDnaMatchBlock(LocalDnaMatchBlock * mat,int starti,int stopi,int startj,i… in push_dc_at_merge_LocalDnaMatchBlock()
3038 void follow_on_dc_LocalDnaMatchBlock(LocalDnaMatchBlock * mat,int starti,int stopi,int startj,int s… in follow_on_dc_LocalDnaMatchBlock()
3307 void run_up_dc_LocalDnaMatchBlock(LocalDnaMatchBlock * mat,int starti,int stopi,int startj,int stop… in run_up_dc_LocalDnaMatchBlock()
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| H A D | geneloop21.c | 3099 int stopi; in PackAln_calculate_Small_GeneLoop21() local
3340 boolean read_hidden_GeneLoop21(GeneLoop21 * mat,int starti,int startj,int startstate,int stopi,int … in read_hidden_GeneLoop21()
4366 boolean read_special_strip_GeneLoop21(GeneLoop21 * mat,int stopi,int stopj,int stopstate,int * star… in read_special_strip_GeneLoop21()
4893 void calculate_hidden_GeneLoop21(GeneLoop21 * mat,int starti,int startj,int startstate,int stopi,in… in calculate_hidden_GeneLoop21()
5484 void init_hidden_GeneLoop21(GeneLoop21 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_GeneLoop21()
5572 boolean full_dc_GeneLoop21(GeneLoop21 * mat,int starti,int startj,int startstate,int stopi,int stop… in full_dc_GeneLoop21()
5650 …e_pass_GeneLoop21(GeneLoop21 * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_GeneLoop21()
5679 void push_dc_at_merge_GeneLoop21(GeneLoop21 * mat,int starti,int stopi,int startj,int * stopj,DPEnv… in push_dc_at_merge_GeneLoop21()
7318 void follow_on_dc_GeneLoop21(GeneLoop21 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope … in follow_on_dc_GeneLoop21()
8144 void run_up_dc_GeneLoop21(GeneLoop21 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * d… in run_up_dc_GeneLoop21()
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| H A D | genewise21.c | 3513 int stopi; in PackAln_calculate_Small_GeneWise21() local
3754 boolean read_hidden_GeneWise21(GeneWise21 * mat,int starti,int startj,int startstate,int stopi,int … in read_hidden_GeneWise21()
4782 boolean read_special_strip_GeneWise21(GeneWise21 * mat,int stopi,int stopj,int stopstate,int * star… in read_special_strip_GeneWise21()
5516 void calculate_hidden_GeneWise21(GeneWise21 * mat,int starti,int startj,int startstate,int stopi,in… in calculate_hidden_GeneWise21()
6107 void init_hidden_GeneWise21(GeneWise21 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_GeneWise21()
6195 boolean full_dc_GeneWise21(GeneWise21 * mat,int starti,int startj,int startstate,int stopi,int stop… in full_dc_GeneWise21()
6273 …e_pass_GeneWise21(GeneWise21 * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in do_dc_single_pass_GeneWise21()
6302 void push_dc_at_merge_GeneWise21(GeneWise21 * mat,int starti,int stopi,int startj,int * stopj,DPEnv… in push_dc_at_merge_GeneWise21()
7941 void follow_on_dc_GeneWise21(GeneWise21 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope … in follow_on_dc_GeneWise21()
8767 void run_up_dc_GeneWise21(GeneWise21 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * d… in run_up_dc_GeneWise21()
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| H A D | abc.c | 1174 int stopi; in PackAln_calculate_Small_abc() local
1396 boolean read_hidden_abc(abc * mat,int starti,int startj,int startstate,int stopi,int stopj,int stop… in read_hidden_abc()
1606 boolean read_special_strip_abc(abc * mat,int stopi,int stopj,int stopstate,int * startj,int * start… in read_special_strip_abc()
1796 void calculate_hidden_abc(abc * mat,int starti,int startj,int startstate,int stopi,int stopj,int st… in calculate_hidden_abc()
1896 void init_hidden_abc(abc * mat,int starti,int startj,int stopi,int stopj) in init_hidden_abc()
1946 boolean full_dc_abc(abc * mat,int starti,int startj,int startstate,int stopi,int stopj,int stopstat… in full_dc_abc()
2024 boolean do_dc_single_pass_abc(abc * mat,int starti,int startj,int startstate,int stopi,int stopj,in… 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()
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| H A D | clonewisedp.c | 1281 int stopi; in PackAln_calculate_Small_CloneWise() local
1522 boolean read_hidden_CloneWise(CloneWise * mat,int starti,int startj,int startstate,int stopi,int st… in read_hidden_CloneWise()
1770 boolean read_special_strip_CloneWise(CloneWise * mat,int stopi,int stopj,int stopstate,int * startj… in read_special_strip_CloneWise()
2027 void calculate_hidden_CloneWise(CloneWise * mat,int starti,int startj,int startstate,int stopi,int … in calculate_hidden_CloneWise()
2151 void init_hidden_CloneWise(CloneWise * mat,int starti,int startj,int stopi,int stopj) in init_hidden_CloneWise()
2203 boolean full_dc_CloneWise(CloneWise * mat,int starti,int startj,int startstate,int stopi,int stopj,… in full_dc_CloneWise()
2281 boolean do_dc_single_pass_CloneWise(CloneWise * mat,int starti,int startj,int startstate,int stopi,… in do_dc_single_pass_CloneWise()
2310 void push_dc_at_merge_CloneWise(CloneWise * mat,int starti,int stopi,int startj,int * stopj,DPEnvel… in push_dc_at_merge_CloneWise()
2582 void follow_on_dc_CloneWise(CloneWise * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * … in follow_on_dc_CloneWise()
2737 void run_up_dc_CloneWise(CloneWise * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpe… in run_up_dc_CloneWise()
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| H A D | estquick3.c | 1217 int stopi; in PackAln_calculate_Small_EstQuick3() local
1439 boolean read_hidden_EstQuick3(EstQuick3 * mat,int starti,int startj,int startstate,int stopi,int st… in read_hidden_EstQuick3()
1685 boolean read_special_strip_EstQuick3(EstQuick3 * mat,int stopi,int stopj,int stopstate,int * startj… in read_special_strip_EstQuick3()
1881 void calculate_hidden_EstQuick3(EstQuick3 * mat,int starti,int startj,int startstate,int stopi,int … in calculate_hidden_EstQuick3()
2002 void init_hidden_EstQuick3(EstQuick3 * mat,int starti,int startj,int stopi,int stopj) in init_hidden_EstQuick3()
2054 boolean full_dc_EstQuick3(EstQuick3 * mat,int starti,int startj,int startstate,int stopi,int stopj,… in full_dc_EstQuick3()
2132 boolean do_dc_single_pass_EstQuick3(EstQuick3 * mat,int starti,int startj,int startstate,int stopi,… in do_dc_single_pass_EstQuick3()
2161 void push_dc_at_merge_EstQuick3(EstQuick3 * mat,int starti,int stopi,int startj,int * stopj,DPEnvel… in push_dc_at_merge_EstQuick3()
2430 void follow_on_dc_EstQuick3(EstQuick3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * … in follow_on_dc_EstQuick3()
2582 void run_up_dc_EstQuick3(EstQuick3 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpe… in run_up_dc_EstQuick3()
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