1 | #ifndef ARBDBT_H |
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2 | #define ARBDBT_H |
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3 | |
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4 | #ifndef ARBDB_H |
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5 | #include <arbdb.h> |
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6 | #endif |
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7 | #ifndef DOWNCAST_H |
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8 | #include <downcast.h> |
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9 | #endif |
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10 | |
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11 | #define gb_assert(cond) arb_assert(cond) |
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12 | |
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13 | #define GBT_SPECIES_INDEX_SIZE 10000L |
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14 | #define GBT_SAI_INDEX_SIZE 1000L |
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15 | |
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16 | #define GB_GROUP_NAME_MAX 256 |
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17 | |
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18 | #define DEFAULT_BRANCH_LENGTH 0.1 |
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19 | |
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20 | #define ERROR_CONTAINER_PATH "tmp/message/pending" |
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21 | |
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22 | #define REMOTE_BASE "tmp/remote/" |
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23 | #define MACRO_TRIGGER_CONTAINER REMOTE_BASE "trigger" |
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24 | #define MACRO_TRIGGER_TERMINATED MACRO_TRIGGER_CONTAINER "/terminated" |
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25 | #define MACRO_TRIGGER_RECORDING MACRO_TRIGGER_CONTAINER "/recording" |
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26 | #define MACRO_TRIGGER_ERROR MACRO_TRIGGER_CONTAINER "/error" |
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27 | #define MACRO_TRIGGER_TRACKED MACRO_TRIGGER_CONTAINER "/tracked" |
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28 | |
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29 | enum GBT_RemarkType { REMARK_NONE, REMARK_BOOTSTRAP, REMARK_OTHER }; |
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30 | |
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31 | enum GBT_TreeRemoveType { |
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32 | GBT_REMOVE_MARKED = 1, |
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33 | GBT_REMOVE_UNMARKED = 2, |
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34 | GBT_REMOVE_ZOMBIES = 4, |
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35 | |
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36 | // please keep AWT_RemoveType in sync with GBT_TreeRemoveType |
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37 | // see ../SL/AP_TREE/AP_Tree.hxx@sync_GBT_TreeRemoveType__AWT_RemoveType |
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38 | |
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39 | // combined defines: |
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40 | GBT_KEEP_MARKED = GBT_REMOVE_UNMARKED|GBT_REMOVE_ZOMBIES, |
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41 | }; |
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42 | |
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43 | enum GBT_ORDER_MODE { |
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44 | GBT_BEHIND, |
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45 | GBT_INFRONTOF, |
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46 | }; |
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47 | |
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48 | enum TreeModel { ROOTED = 0, UNROOTED = 1 }; |
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49 | |
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50 | CONSTEXPR_INLINE int nodes_2_edges(int nodes) { return nodes-1; } |
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51 | CONSTEXPR_INLINE int edges_2_nodes(int nodes) { return nodes+1; } |
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52 | |
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53 | CONSTEXPR_INLINE int leafs_2_nodes(int leafs, TreeModel model) { |
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54 | //! calculate the number of nodes (leaf- plus inner-nodes) in a tree with 'leafs' leafs |
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55 | return 2*leafs-1-int(model); |
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56 | } |
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57 | CONSTEXPR_INLINE int nodes_2_leafs(int nodes, TreeModel model) { |
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58 | //! calculate the number of leafs in a tree with 'nodes' nodes |
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59 | return (nodes+1+int(model))/2; |
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60 | } |
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61 | CONSTEXPR_INLINE int leafs_2_edges(int leafs, TreeModel model) { |
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62 | //! calculate the number of edges in a tree with 'leafs' leafs |
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63 | return nodes_2_edges(leafs_2_nodes(leafs, model)); |
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64 | } |
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65 | CONSTEXPR_INLINE int edges_2_leafs(int edges, TreeModel model) { |
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66 | //! calculate the number of leafs in a tree with 'edges' edges |
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67 | return nodes_2_leafs(edges_2_nodes(edges), model); |
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68 | } |
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69 | |
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70 | #define SRT_AUTOCORRECT_TREENAME " =:\n=:*=tree_*1:tree_tree_*=tree_*1" |
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71 | #define SRT_AUTOCORRECT_ALINAME " =:\n=:*=ali_*1:ali_ali_*=ali_*1" |
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72 | |
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73 | typedef GB_ERROR (*species_callback)(GBDATA *gb_species, int *clientdata); |
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74 | |
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75 | #include <ad_t_prot.h> |
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76 | |
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77 | #define CHANGE_KEY_PATH "presets/key_data" |
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78 | #define CHANGE_KEY_PATH_GENES "presets/gene_key_data" |
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79 | #define CHANGE_KEY_PATH_EXPERIMENTS "presets/experiment_key_data" |
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80 | |
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81 | #define CHANGEKEY "key" |
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82 | #define CHANGEKEY_NAME "key_name" |
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83 | #define CHANGEKEY_TYPE "key_type" |
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84 | #define CHANGEKEY_HIDDEN "key_hidden" |
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85 | |
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86 | |
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87 | #else |
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88 | #error arbdbt.h included twice |
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89 | #endif |
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90 | |
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91 | |
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