| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : ap_main.hxx // |
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| 4 | // Purpose : // |
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| 5 | // // |
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| 6 | // Institute of Microbiology (Technical University Munich) // |
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| 7 | // http://www.arb-home.de/ // |
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| 8 | // // |
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| 9 | // =============================================================== // |
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| 10 | |
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| 11 | #ifndef AP_MAIN_HXX |
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| 12 | #define AP_MAIN_HXX |
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| 13 | |
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| 14 | #ifndef AP_MAIN_TYPE_HXX |
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| 15 | #include "ap_main_type.hxx" |
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| 16 | #endif |
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| 17 | #ifndef AP_TREE_NLEN_HXX |
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| 18 | #include "ap_tree_nlen.hxx" |
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| 19 | #endif |
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| 20 | |
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| 21 | |
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| 22 | #define AWAR_ALIGNMENT "tmp/pars/alignment" |
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| 23 | #define AWAR_FILTER_NAME "tmp/pars/filter/name" |
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| 24 | #define AWAR_PARSIMONY "tmp/pars/parsimony" |
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| 25 | #define AWAR_BEST_PARSIMONY "tmp/pars/best_parsimony" |
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| 26 | #define AWAR_STACKPOINTER "tmp/pars/stackpointer" |
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| 27 | |
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| 28 | #define AWAR_PARS_TYPE "pars/pars_type" |
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| 29 | |
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| 30 | enum PARS_pars_type { |
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| 31 | PARS_WAGNER, |
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| 32 | PARS_TRANSVERSION |
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| 33 | }; |
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| 34 | |
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| 35 | struct PARS_commands { |
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| 36 | bool add_marked; |
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| 37 | bool add_selected; |
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| 38 | bool calc_branch_lengths; |
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| 39 | bool calc_bootstrap; |
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| 40 | bool quit; |
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| 41 | |
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| 42 | PARS_commands() |
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| 43 | : add_marked(false) |
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| 44 | , add_selected(false) |
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| 45 | , calc_branch_lengths(false) |
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| 46 | , calc_bootstrap(false) |
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| 47 | , quit(false) |
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| 48 | { |
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| 49 | } |
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| 50 | }; |
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| 51 | |
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| 52 | extern AP_main *ap_main; // @@@ elim |
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| 53 | |
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| 54 | inline AP_tree_nlen *rootNode() { |
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| 55 | return ap_main->get_root_node(); |
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| 56 | } |
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| 57 | |
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| 58 | inline AP_tree_edge *rootEdge() { |
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| 59 | return rootNode()->get_leftson()->edgeTo(rootNode()->get_rightson()); |
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| 60 | } |
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| 61 | |
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| 62 | // ------------------------------------------ |
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| 63 | // stack-aware resource management |
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| 64 | |
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| 65 | #define REUSE_EDGES |
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| 66 | |
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| 67 | inline AP_tree_nlen *StackFrameData::makeNode(AP_pars_root *proot) { |
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| 68 | return created.put(new AP_tree_nlen(proot)); |
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| 69 | } |
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| 70 | inline AP_tree_edge *StackFrameData::makeEdge(AP_tree_nlen *n1, AP_tree_nlen *n2) { |
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| 71 | #if defined(REUSE_EDGES) |
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| 72 | if (destroyed.has_edges()) { |
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| 73 | AP_tree_edge *reuse = destroyed.getEdge(); |
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| 74 | reuse->relink(n1, n2); |
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| 75 | return reuse; |
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| 76 | } |
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| 77 | #endif |
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| 78 | return created.put(new AP_tree_edge(n1, n2)); |
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| 79 | } |
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| 80 | |
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| 81 | inline void StackFrameData::destroyNode(AP_tree_nlen *node) { destroyed.put(node); } |
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| 82 | inline void StackFrameData::destroyEdge(AP_tree_edge *edge) { destroyed.put(edge); } |
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| 83 | |
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| 84 | inline AP_tree_nlen *AP_main::makeNode(AP_pars_root *proot) { |
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| 85 | return currFrame ? frameData->makeNode(proot) : new AP_tree_nlen(proot); |
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| 86 | } |
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| 87 | inline AP_tree_edge *AP_main::makeEdge(AP_tree_nlen *n1, AP_tree_nlen *n2) { |
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| 88 | return currFrame ? frameData->makeEdge(n1, n2) : new AP_tree_edge(n1, n2); |
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| 89 | } |
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| 90 | inline void AP_main::destroyNode(AP_tree_nlen *node) { |
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| 91 | if (currFrame) { |
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| 92 | ap_assert(!node->rightson && !node->leftson); // node needs to be unlinked from neighbours |
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| 93 | frameData->destroyNode(node); |
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| 94 | } |
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| 95 | else { |
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| 96 | ap_assert(!node->may_be_recollected()); |
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| 97 | delete node; // here child nodes are destroyed |
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| 98 | } |
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| 99 | } |
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| 100 | inline void AP_main::destroyEdge(AP_tree_edge *edge) { |
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| 101 | ap_assert(!edge->is_linked()); |
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| 102 | if (currFrame) { |
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| 103 | frameData->destroyEdge(edge); |
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| 104 | } |
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| 105 | else { |
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| 106 | delete edge; |
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| 107 | } |
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| 108 | } |
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| 109 | |
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| 110 | inline TreeNode *AP_pars_root::makeNode() const { |
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| 111 | return ap_main->makeNode(const_cast<AP_pars_root*>(this)); |
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| 112 | } |
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| 113 | inline void AP_pars_root::destroyNode(TreeNode *node) const { |
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| 114 | ap_main->destroyNode(DOWNCAST(AP_tree_nlen*, node)); |
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| 115 | } |
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| 116 | |
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| 117 | inline AP_tree_edge *makeEdge(AP_tree_nlen *n1, AP_tree_nlen *n2) { |
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| 118 | return ap_main->makeEdge(n1, n2); |
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| 119 | } |
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| 120 | inline void destroyEdge(AP_tree_edge *edge) { |
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| 121 | ap_main->destroyEdge(edge); |
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| 122 | } |
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| 123 | |
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| 124 | |
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| 125 | #else |
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| 126 | #error ap_main.hxx included twice |
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| 127 | #endif // AP_MAIN_HXX |
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