| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : NT_edconf.cxx // |
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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 | #include "NT_cb.h" |
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| 12 | #include "NT_local.h" |
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| 13 | |
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| 14 | #include <awt_sel_boxes.hxx> |
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| 15 | #include <aw_awars.hxx> |
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| 16 | #include <aw_root.hxx> |
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| 17 | #include <aw_msg.hxx> |
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| 18 | #include <ad_config.h> |
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| 19 | #include <arbdbt.h> |
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| 20 | #include <arb_strbuf.h> |
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| 21 | #include <arb_global_defs.h> |
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| 22 | |
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| 23 | static void init_config_awars(AW_root *root) { |
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| 24 | root->awar_string(AWAR_CONFIGURATION, "default_configuration", GLOBAL.gb_main); |
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| 25 | } |
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| 26 | |
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| 27 | // ----------------------------- |
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| 28 | // class Store_species |
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| 29 | |
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| 30 | class Store_species : virtual Noncopyable { |
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| 31 | // stores an amount of species: |
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| 32 | GBT_TREE *node; |
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| 33 | Store_species *next; |
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| 34 | public: |
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| 35 | Store_species(GBT_TREE *aNode) { |
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| 36 | node = aNode; |
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| 37 | next = 0; |
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| 38 | } |
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| 39 | ~Store_species(); |
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| 40 | |
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| 41 | Store_species* add(Store_species *list) { |
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| 42 | nt_assert(next==0); |
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| 43 | next = list; |
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| 44 | return this; |
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| 45 | } |
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| 46 | |
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| 47 | Store_species* remove() { |
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| 48 | Store_species *follower = next; |
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| 49 | next = 0; |
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| 50 | return follower; |
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| 51 | } |
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| 52 | |
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| 53 | GBT_TREE *getNode() const { return node; } |
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| 54 | |
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| 55 | void call(void (*aPizza)(GBT_TREE*)) const; |
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| 56 | }; |
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| 57 | |
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| 58 | Store_species::~Store_species() { |
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| 59 | delete next; |
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| 60 | } |
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| 61 | |
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| 62 | void Store_species::call(void (*aPizza)(GBT_TREE*)) const { |
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| 63 | aPizza(node); |
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| 64 | if (next) next->call(aPizza); |
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| 65 | } |
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| 66 | |
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| 67 | static void unmark_species(GBT_TREE *node) { |
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| 68 | nt_assert(node); |
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| 69 | nt_assert(node->gb_node); |
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| 70 | nt_assert(GB_read_flag(node->gb_node)!=0); |
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| 71 | GB_write_flag(node->gb_node, 0); |
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| 72 | } |
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| 73 | |
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| 74 | static void mark_species(GBT_TREE *node, Store_species **extra_marked_species) { |
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| 75 | nt_assert(node); |
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| 76 | nt_assert(node->gb_node); |
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| 77 | nt_assert(GB_read_flag(node->gb_node)==0); |
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| 78 | GB_write_flag(node->gb_node, 1); |
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| 79 | |
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| 80 | *extra_marked_species = (new Store_species(node))->add(*extra_marked_species); |
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| 81 | } |
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| 82 | |
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| 83 | |
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| 84 | |
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| 85 | static GBT_TREE *rightmost_leaf(GBT_TREE *node) { |
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| 86 | nt_assert(node); |
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| 87 | while (!node->is_leaf) { |
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| 88 | node = node->rightson; |
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| 89 | nt_assert(node); |
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| 90 | } |
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| 91 | return node; |
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| 92 | } |
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| 93 | |
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| 94 | static GBT_TREE *left_neighbour_leaf(GBT_TREE *node) { |
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| 95 | if (node) { |
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| 96 | GBT_TREE *father = node->father; |
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| 97 | while (father) { |
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| 98 | if (father->rightson==node) { |
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| 99 | node = rightmost_leaf(father->leftson); |
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| 100 | nt_assert(node->is_leaf); |
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| 101 | if (!node->gb_node) { // Zombie |
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| 102 | node = left_neighbour_leaf(node); |
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| 103 | } |
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| 104 | return node; |
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| 105 | } |
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| 106 | node = father; |
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| 107 | father = node->father; |
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| 108 | } |
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| 109 | } |
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| 110 | return 0; |
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| 111 | } |
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| 112 | |
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| 113 | static int nt_build_conf_string_rek(GB_HASH *used, GBT_TREE *tree, GBS_strstruct *memfile, |
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| 114 | Store_species **extra_marked_species, int use_species_aside, |
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| 115 | int *auto_mark, int marked_at_left, int *marked_at_right) |
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| 116 | { |
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| 117 | /*! Builds a configuration string from a tree. |
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| 118 | * |
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| 119 | * @param used all species inserted by this function are stored here |
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| 120 | * @param tree used for group information |
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| 121 | * @param memfile generated configuration string is stored here |
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| 122 | * @param extra_marked_species all extra marked species are inserted here |
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| 123 | * @param use_species_aside number of species to mark left and right of marked species |
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| 124 | * @param auto_mark number species to extra-mark (if not already marked) |
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| 125 | * @param marked_at_left number of species which were marked (looking to left) |
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| 126 | * @param marked_at_right number of species which are marked (when returning from recursion) |
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| 127 | * |
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| 128 | * @return the number of marked species |
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| 129 | * |
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| 130 | * -------------------------------------------------- |
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| 131 | * Format of configuration string : [Part]+ \0 |
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| 132 | * |
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| 133 | * Part : '\A' ( Group | Species | Sai ) |
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| 134 | * |
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| 135 | * Group : ( OpenedGroup | ClosedGroup ) |
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| 136 | * OpenedGroup : 'G' GroupDef |
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| 137 | * ClosedGroup : 'F' GroupDef |
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| 138 | * GroupDef : 'groupname' [PART]* EndGroup |
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| 139 | * EndGroup : '\AE' |
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| 140 | * |
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| 141 | * SPECIES : 'L' 'speciesname' |
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| 142 | * SAI : 'S' 'sainame' |
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| 143 | * |
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| 144 | * \0 : ASCII 0 (eos) |
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| 145 | * \A : ASCII 1 |
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| 146 | */ |
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| 147 | |
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| 148 | if (!tree) return 0; |
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| 149 | if (tree->is_leaf) { |
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| 150 | if (!tree->gb_node) { |
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| 151 | *marked_at_right = marked_at_left; |
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| 152 | return 0; // Zombie |
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| 153 | } |
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| 154 | |
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| 155 | if (!GB_read_flag(tree->gb_node)) { // unmarked species |
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| 156 | if (*auto_mark) { |
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| 157 | (*auto_mark)--; |
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| 158 | mark_species(tree, extra_marked_species); |
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| 159 | } |
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| 160 | else { |
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| 161 | *marked_at_right = 0; |
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| 162 | return 0; |
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| 163 | } |
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| 164 | } |
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| 165 | else { // marked species |
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| 166 | if (marked_at_left<use_species_aside) { |
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| 167 | // on the left side there are not as many marked species as needed! |
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| 168 | |
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| 169 | nt_assert(marked_at_left>=0); |
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| 170 | |
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| 171 | GBT_TREE *leaf_at_left = tree; |
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| 172 | int step_over = marked_at_left+1; // step over myself |
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| 173 | int then_mark = use_species_aside-marked_at_left; |
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| 174 | |
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| 175 | while (step_over--) { // step over self and over any adjacent, marked species |
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| 176 | leaf_at_left = left_neighbour_leaf(leaf_at_left); |
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| 177 | } |
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| 178 | |
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| 179 | Store_species *marked_back = 0; |
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| 180 | while (leaf_at_left && then_mark--) { // then additionally mark some species |
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| 181 | if (GB_read_flag(leaf_at_left->gb_node) == 0) { // if they are not marked yet |
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| 182 | mark_species(leaf_at_left, extra_marked_species); |
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| 183 | marked_back = (new Store_species(leaf_at_left))->add(marked_back); |
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| 184 | } |
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| 185 | leaf_at_left = left_neighbour_leaf(leaf_at_left); |
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| 186 | } |
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| 187 | |
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| 188 | while (marked_back) { |
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| 189 | GBS_chrcat(memfile, 1); // Separated by 1 |
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| 190 | GBS_strcat(memfile, "L"); |
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| 191 | GBS_strcat(memfile, marked_back->getNode()->name); |
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| 192 | GBS_write_hash(used, marked_back->getNode()->name, 1); // Mark species |
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| 193 | |
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| 194 | Store_species *rest = marked_back->remove(); |
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| 195 | delete marked_back; |
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| 196 | marked_back = rest; |
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| 197 | } |
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| 198 | |
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| 199 | marked_at_left = use_species_aside; |
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| 200 | } |
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| 201 | // now use_species_aside species to left are marked! |
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| 202 | *auto_mark = use_species_aside; |
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| 203 | } |
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| 204 | |
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| 205 | GBS_chrcat(memfile, 1); // Separated by 1 |
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| 206 | GBS_strcat(memfile, "L"); |
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| 207 | GBS_strcat(memfile, tree->name); |
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| 208 | GBS_write_hash(used, tree->name, 1); // Mark species |
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| 209 | |
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| 210 | *marked_at_right = marked_at_left+1; |
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| 211 | return 1; |
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| 212 | } |
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| 213 | |
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| 214 | long oldpos = GBS_memoffset(memfile); |
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| 215 | if (tree->gb_node && tree->name) { // but we are a group |
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| 216 | GBDATA *gb_grouped = GB_entry(tree->gb_node, "grouped"); |
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| 217 | GBS_chrcat(memfile, 1); // Separated by 1 |
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| 218 | if (gb_grouped && GB_read_byte(gb_grouped)) { |
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| 219 | GBS_strcat(memfile, "F"); |
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| 220 | } |
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| 221 | else { |
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| 222 | GBS_strcat(memfile, "G"); |
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| 223 | } |
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| 224 | |
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| 225 | GBS_strcat(memfile, tree->name); |
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| 226 | } |
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| 227 | |
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| 228 | int right_of_leftson; |
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| 229 | long nspecies = nt_build_conf_string_rek(used, tree->leftson, memfile, extra_marked_species, use_species_aside, auto_mark, marked_at_left, &right_of_leftson); |
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| 230 | nspecies += nt_build_conf_string_rek(used, tree->rightson, memfile, extra_marked_species, use_species_aside, auto_mark, right_of_leftson, marked_at_right); |
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| 231 | |
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| 232 | if (tree->gb_node && tree->name) { // but we are a group |
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| 233 | GBS_chrcat(memfile, 1); // Separated by 1 |
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| 234 | GBS_chrcat(memfile, 'E'); // Group end indicated by 'E' |
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| 235 | } |
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| 236 | |
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| 237 | if (!nspecies) { |
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| 238 | long newpos = GBS_memoffset(memfile); |
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| 239 | GBS_str_cut_tail(memfile, newpos-oldpos); // delete group info |
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| 240 | } |
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| 241 | return nspecies; |
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| 242 | } |
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| 243 | |
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| 244 | struct SAI_string_builder { |
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| 245 | GBS_strstruct *sai_middle; |
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| 246 | const char *last_group_name; |
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| 247 | }; |
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| 248 | |
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| 249 | static long nt_build_sai_string_by_hash(const char *key, long val, void *cd_sai_builder) { |
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| 250 | SAI_string_builder *sai_builder = (SAI_string_builder*)cd_sai_builder; |
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| 251 | |
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| 252 | const char *sep = strchr(key, 1); |
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| 253 | if (!sep) return val; // what's wrong |
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| 254 | |
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| 255 | GBS_strstruct *sai_middle = sai_builder->sai_middle; |
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| 256 | const char *last_group_name = sai_builder->last_group_name; |
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| 257 | |
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| 258 | if (!last_group_name || strncmp(key, last_group_name, sep-key)) { // new group |
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| 259 | if (last_group_name) { |
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| 260 | GBS_chrcat(sai_middle, 1); // Separated by 1 |
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| 261 | GBS_chrcat(sai_middle, 'E'); // End of old group |
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| 262 | } |
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| 263 | GBS_chrcat(sai_middle, 1); // Separated by 1 |
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| 264 | GBS_strcat(sai_middle, "FSAI:"); |
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| 265 | GBS_strncat(sai_middle, key, sep-key); |
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| 266 | sai_builder->last_group_name = key; |
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| 267 | } |
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| 268 | GBS_chrcat(sai_middle, 1); // Separated by 1 |
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| 269 | GBS_strcat(sai_middle, "S"); |
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| 270 | GBS_strcat(sai_middle, sep+1); |
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| 271 | return val; |
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| 272 | } |
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| 273 | |
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| 274 | |
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| 275 | static void nt_build_sai_string(GBS_strstruct *topfile, GBS_strstruct *middlefile) { |
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| 276 | //! collect all Sais, place some SAI in top area, rest in middle |
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| 277 | |
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| 278 | GBDATA *gb_sai_data = GBT_get_SAI_data(GLOBAL.gb_main); |
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| 279 | if (gb_sai_data) { |
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| 280 | GB_HASH *hash = GBS_create_hash(GB_number_of_subentries(gb_sai_data), GB_IGNORE_CASE); |
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| 281 | |
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| 282 | for (GBDATA *gb_sai = GBT_first_SAI_rel_SAI_data(gb_sai_data); gb_sai; gb_sai = GBT_next_SAI(gb_sai)) { |
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| 283 | GBDATA *gb_name = GB_search(gb_sai, "name", GB_FIND); |
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| 284 | if (gb_name) { |
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| 285 | char *name = GB_read_string(gb_name); |
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| 286 | |
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| 287 | if (strcmp(name, "HELIX") == 0 || strcmp(name, "HELIX_NR") == 0 || strcmp(name, "ECOLI") == 0) { |
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| 288 | GBS_chrcat(topfile, 1); // Separated by 1 |
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| 289 | GBS_strcat(topfile, "S"); |
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| 290 | GBS_strcat(topfile, name); |
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| 291 | } |
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| 292 | else { |
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| 293 | GBDATA *gb_gn = GB_search(gb_sai, "sai_group", GB_FIND); |
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| 294 | char *gn; |
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| 295 | |
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| 296 | if (gb_gn) gn = GB_read_string(gb_gn); |
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| 297 | else gn = strdup("SAI's"); |
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| 298 | |
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| 299 | char *cn = new char[strlen(gn) + strlen(name) + 2]; |
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| 300 | sprintf(cn, "%s%c%s", gn, 1, name); |
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| 301 | GBS_write_hash(hash, cn, 1); |
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| 302 | delete [] cn; |
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| 303 | free(gn); |
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| 304 | } |
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| 305 | free(name); |
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| 306 | } |
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| 307 | } |
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| 308 | |
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| 309 | // open surrounding SAI-group: |
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| 310 | GBS_chrcat(middlefile, 1); |
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| 311 | GBS_strcat(middlefile, "GSAI-Maingroup"); |
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| 312 | |
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| 313 | SAI_string_builder sai_builder = { middlefile, 0 }; |
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| 314 | GBS_hash_do_sorted_loop(hash, nt_build_sai_string_by_hash, GBS_HCF_sortedByKey, &sai_builder); |
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| 315 | if (sai_builder.last_group_name) { |
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| 316 | GBS_chrcat(middlefile, 1); // Separated by 1 |
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| 317 | GBS_chrcat(middlefile, 'E'); // End of old group |
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| 318 | } |
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| 319 | |
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| 320 | // close surrounding SAI-group: |
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| 321 | GBS_chrcat(middlefile, 1); |
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| 322 | GBS_chrcat(middlefile, 'E'); |
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| 323 | |
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| 324 | GBS_free_hash(hash); |
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| 325 | } |
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| 326 | } |
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| 327 | |
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| 328 | static void nt_build_conf_marked(GB_HASH *used, GBS_strstruct *file) { |
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| 329 | GBS_chrcat(file, 1); // Separated by 1 |
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| 330 | GBS_strcat(file, "FMore Sequences"); |
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| 331 | GBDATA *gb_species; |
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| 332 | for (gb_species = GBT_first_marked_species(GLOBAL.gb_main); |
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| 333 | gb_species; |
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| 334 | gb_species = GBT_next_marked_species(gb_species)) { |
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| 335 | char *name = GBT_read_string(gb_species, "name"); |
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| 336 | if (GBS_read_hash(used, name)) { |
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| 337 | free(name); |
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| 338 | continue; |
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| 339 | } |
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| 340 | GBS_chrcat(file, 1); |
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| 341 | GBS_strcat(file, "L"); |
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| 342 | GBS_strcat(file, name); |
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| 343 | free(name); |
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| 344 | } |
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| 345 | |
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| 346 | GBS_chrcat(file, 1); // Separated by 1 |
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| 347 | GBS_chrcat(file, 'E'); // Group end indicated by 'E' |
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| 348 | } |
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| 349 | |
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| 350 | enum extractType { |
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| 351 | CONF_EXTRACT, |
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| 352 | CONF_MARK, |
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| 353 | CONF_UNMARK, |
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| 354 | CONF_INVERT, |
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| 355 | CONF_COMBINE // logical AND |
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| 356 | }; |
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| 357 | |
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| 358 | static void nt_extract_configuration(AW_window *aww, extractType ext_type) { |
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| 359 | GB_transaction ta(GLOBAL.gb_main); |
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| 360 | AW_root *aw_root = aww->get_root(); |
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| 361 | char *cn = aw_root->awar(AWAR_CONFIGURATION)->read_string(); |
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| 362 | |
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| 363 | if (strcmp(cn, NO_CONFIG_SELECTED) == 0) { |
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| 364 | aw_message("Please select a configuration"); |
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| 365 | } |
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| 366 | else { |
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| 367 | GBDATA *gb_configuration = GBT_find_configuration(GLOBAL.gb_main, cn); |
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| 368 | if (!gb_configuration) { |
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| 369 | aw_message(GBS_global_string("Configuration '%s' not found in the database", cn)); |
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| 370 | } |
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| 371 | else { |
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| 372 | GBDATA *gb_middle_area = GB_search(gb_configuration, "middle_area", GB_STRING); |
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| 373 | char *md = 0; |
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| 374 | size_t unknown_species = 0; |
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| 375 | bool refresh = false; |
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| 376 | |
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| 377 | if (gb_middle_area) { |
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| 378 | GB_HASH *was_marked = NULL; // only used for CONF_COMBINE |
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| 379 | |
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| 380 | switch (ext_type) { |
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| 381 | case CONF_EXTRACT: |
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| 382 | GBT_mark_all(GLOBAL.gb_main, 0); // unmark all for extract |
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| 383 | refresh = true; |
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| 384 | break; |
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| 385 | case CONF_COMBINE: { |
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| 386 | // store all marked species in hash and unmark them |
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| 387 | was_marked = GBS_create_hash(GBT_get_species_count(GLOBAL.gb_main), GB_IGNORE_CASE); |
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| 388 | for (GBDATA *gbd = GBT_first_marked_species(GLOBAL.gb_main); gbd; gbd = GBT_next_marked_species(gbd)) { |
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| 389 | int marked = GB_read_flag(gbd); |
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| 390 | if (marked) { |
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| 391 | GBS_write_hash(was_marked, GBT_read_name(gbd), 1); |
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| 392 | GB_write_flag(gbd, 0); |
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| 393 | } |
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| 394 | } |
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| 395 | |
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| 396 | refresh = refresh || GBS_hash_count_elems(was_marked); |
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| 397 | break; |
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| 398 | } |
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| 399 | default: |
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| 400 | break; |
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| 401 | } |
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| 402 | |
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| 403 | md = GB_read_string(gb_middle_area); |
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| 404 | if (md) { |
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| 405 | char *p; |
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| 406 | char tokens[2]; |
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| 407 | tokens[0] = 1; |
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| 408 | tokens[1] = 0; |
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| 409 | for (p = strtok(md, tokens); p; p = strtok(NULL, tokens)) { |
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| 410 | if (p[0] == 'L') { |
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| 411 | const char *species_name = p+1; |
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| 412 | GBDATA *gb_species = GBT_find_species(GLOBAL.gb_main, species_name); |
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| 413 | |
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| 414 | if (gb_species) { |
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| 415 | int oldmark = GB_read_flag(gb_species); |
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| 416 | int newmark = oldmark; |
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| 417 | switch (ext_type) { |
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| 418 | case CONF_EXTRACT: |
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| 419 | case CONF_MARK: newmark = 1; break; |
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| 420 | case CONF_UNMARK: newmark = 0; break; |
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| 421 | case CONF_INVERT: newmark = !oldmark; break; |
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| 422 | case CONF_COMBINE: { |
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| 423 | nt_assert(!oldmark); // should have been unmarked above |
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| 424 | newmark = GBS_read_hash(was_marked, species_name); // mark if was_marked |
|---|
| 425 | break; |
|---|
| 426 | } |
|---|
| 427 | default: nt_assert(0); break; |
|---|
| 428 | } |
|---|
| 429 | if (newmark != oldmark) { |
|---|
| 430 | GB_write_flag(gb_species, newmark); |
|---|
| 431 | refresh = true; |
|---|
| 432 | } |
|---|
| 433 | } |
|---|
| 434 | else { |
|---|
| 435 | unknown_species++; |
|---|
| 436 | } |
|---|
| 437 | } |
|---|
| 438 | } |
|---|
| 439 | } |
|---|
| 440 | |
|---|
| 441 | if (was_marked) GBS_free_hash(was_marked); |
|---|
| 442 | } |
|---|
| 443 | |
|---|
| 444 | if (unknown_species>0) { |
|---|
| 445 | aw_message(GBS_global_string("configuration '%s' contains %zu unknown species", cn, unknown_species)); |
|---|
| 446 | } |
|---|
| 447 | |
|---|
| 448 | if (refresh) aw_root->awar(AWAR_TREE_REFRESH)->touch(); |
|---|
| 449 | |
|---|
| 450 | free(md); |
|---|
| 451 | } |
|---|
| 452 | } |
|---|
| 453 | free(cn); |
|---|
| 454 | } |
|---|
| 455 | |
|---|
| 456 | static void nt_delete_configuration(AW_window *aww) { |
|---|
| 457 | GB_transaction transaction_var(GLOBAL.gb_main); |
|---|
| 458 | char *cn = aww->get_root()->awar(AWAR_CONFIGURATION)->read_string(); |
|---|
| 459 | GBDATA *gb_configuration = GBT_find_configuration(GLOBAL.gb_main, cn); |
|---|
| 460 | if (gb_configuration) { |
|---|
| 461 | GB_ERROR error = GB_delete(gb_configuration); |
|---|
| 462 | if (error) aw_message(error); |
|---|
| 463 | } |
|---|
| 464 | free(cn); |
|---|
| 465 | } |
|---|
| 466 | |
|---|
| 467 | |
|---|
| 468 | static GB_ERROR nt_create_configuration(AW_window *, GBT_TREE *tree, const char *conf_name, int use_species_aside) { |
|---|
| 469 | char *to_free = NULL; |
|---|
| 470 | GB_ERROR error = NULL; |
|---|
| 471 | |
|---|
| 472 | if (!conf_name) { |
|---|
| 473 | char *existing_configs = awt_create_string_on_configurations(GLOBAL.gb_main); |
|---|
| 474 | conf_name = to_free = aw_string_selection2awar("CREATE CONFIGURATION", "Enter name of configuration:", AWAR_CONFIGURATION, existing_configs, NULL); |
|---|
| 475 | free(existing_configs); |
|---|
| 476 | } |
|---|
| 477 | |
|---|
| 478 | if (!conf_name || !conf_name[0]) error = "no config name given"; |
|---|
| 479 | else { |
|---|
| 480 | if (use_species_aside==-1) { |
|---|
| 481 | static int last_used_species_aside = 3; |
|---|
| 482 | { |
|---|
| 483 | const char *val = GBS_global_string("%i", last_used_species_aside); |
|---|
| 484 | char *use_species = aw_input("How many extra species to view aside marked:", val); |
|---|
| 485 | if (use_species) use_species_aside = atoi(use_species); |
|---|
| 486 | free(use_species); |
|---|
| 487 | } |
|---|
| 488 | |
|---|
| 489 | if (use_species_aside<1) error = "illegal number of 'species aside'"; |
|---|
| 490 | else last_used_species_aside = use_species_aside; // remember for next time |
|---|
| 491 | } |
|---|
| 492 | |
|---|
| 493 | if (!error) { |
|---|
| 494 | GB_transaction ta(GLOBAL.gb_main); // open close transaction |
|---|
| 495 | GB_HASH *used = GBS_create_hash(GBT_get_species_count(GLOBAL.gb_main), GB_MIND_CASE); |
|---|
| 496 | GBS_strstruct *topfile = GBS_stropen(1000); |
|---|
| 497 | GBS_strstruct *topmid = GBS_stropen(10000); |
|---|
| 498 | { |
|---|
| 499 | GBS_strstruct *middlefile = GBS_stropen(10000); |
|---|
| 500 | nt_build_sai_string(topfile, topmid); |
|---|
| 501 | |
|---|
| 502 | if (use_species_aside) { |
|---|
| 503 | Store_species *extra_marked_species = 0; |
|---|
| 504 | int auto_mark = 0; |
|---|
| 505 | int marked_at_right; |
|---|
| 506 | |
|---|
| 507 | nt_build_conf_string_rek(used, tree, middlefile, &extra_marked_species, use_species_aside, &auto_mark, use_species_aside, &marked_at_right); |
|---|
| 508 | if (extra_marked_species) { |
|---|
| 509 | extra_marked_species->call(unmark_species); |
|---|
| 510 | delete extra_marked_species; |
|---|
| 511 | } |
|---|
| 512 | } |
|---|
| 513 | else { |
|---|
| 514 | int dummy_1=0, dummy_2; |
|---|
| 515 | nt_build_conf_string_rek(used, tree, middlefile, 0, 0, &dummy_1, 0, &dummy_2); |
|---|
| 516 | } |
|---|
| 517 | nt_build_conf_marked(used, topmid); |
|---|
| 518 | char *mid = GBS_strclose(middlefile); |
|---|
| 519 | GBS_strcat(topmid, mid); |
|---|
| 520 | free(mid); |
|---|
| 521 | } |
|---|
| 522 | |
|---|
| 523 | { |
|---|
| 524 | char *middle = GBS_strclose(topmid); |
|---|
| 525 | char *top = GBS_strclose(topfile); |
|---|
| 526 | GBDATA *gb_config = GBT_create_configuration(GLOBAL.gb_main, conf_name); |
|---|
| 527 | |
|---|
| 528 | if (!gb_config) error = GB_await_error(); |
|---|
| 529 | else { |
|---|
| 530 | error = GBT_write_string(gb_config, "top_area", top); |
|---|
| 531 | if (!error) error = GBT_write_string(gb_config, "middle_area", middle); |
|---|
| 532 | } |
|---|
| 533 | |
|---|
| 534 | free(middle); |
|---|
| 535 | free(top); |
|---|
| 536 | } |
|---|
| 537 | GBS_free_hash(used); |
|---|
| 538 | } |
|---|
| 539 | } |
|---|
| 540 | |
|---|
| 541 | free(to_free); |
|---|
| 542 | return error; |
|---|
| 543 | } |
|---|
| 544 | |
|---|
| 545 | static void nt_store_configuration(AW_window*, AWT_canvas *ntw) { |
|---|
| 546 | GB_ERROR err = nt_create_configuration(0, nt_get_tree_root_of_canvas(ntw), 0, 0); |
|---|
| 547 | aw_message_if(err); |
|---|
| 548 | } |
|---|
| 549 | |
|---|
| 550 | static void nt_rename_configuration(AW_window *aww) { |
|---|
| 551 | AW_awar *awar_curr_cfg = aww->get_root()->awar(AWAR_CONFIGURATION); |
|---|
| 552 | char *old_name = awar_curr_cfg->read_string(); |
|---|
| 553 | GB_ERROR err = 0; |
|---|
| 554 | |
|---|
| 555 | GB_transaction ta(GLOBAL.gb_main); |
|---|
| 556 | |
|---|
| 557 | char *new_name = aw_input("Rename selection", "Enter the new name of the selection", old_name); |
|---|
| 558 | if (new_name) { |
|---|
| 559 | GBDATA *gb_existing_cfg = GBT_find_configuration(GLOBAL.gb_main, new_name); |
|---|
| 560 | if (gb_existing_cfg) err = GBS_global_string("There is already a selection named '%s'", new_name); |
|---|
| 561 | else { |
|---|
| 562 | GBDATA *gb_old_cfg = GBT_find_configuration(GLOBAL.gb_main, old_name); |
|---|
| 563 | if (gb_old_cfg) { |
|---|
| 564 | GBDATA *gb_name = GB_entry(gb_old_cfg, "name"); |
|---|
| 565 | if (gb_name) { |
|---|
| 566 | err = GB_write_string(gb_name, new_name); |
|---|
| 567 | if (!err) awar_curr_cfg->write_string(new_name); |
|---|
| 568 | } |
|---|
| 569 | else err = "Selection has no name"; |
|---|
| 570 | } |
|---|
| 571 | else err = "Can't find that selection"; |
|---|
| 572 | } |
|---|
| 573 | free(new_name); |
|---|
| 574 | } |
|---|
| 575 | |
|---|
| 576 | if (err) aw_message(err); |
|---|
| 577 | free(old_name); |
|---|
| 578 | } |
|---|
| 579 | |
|---|
| 580 | static AW_window *create_configuration_admin_window(AW_root *root, AWT_canvas *ntw) { |
|---|
| 581 | static AW_window_simple *existing_aws[MAX_NT_WINDOWS] = { MAX_NT_WINDOWS_NULLINIT }; |
|---|
| 582 | |
|---|
| 583 | int ntw_id = NT_get_canvas_id(ntw); |
|---|
| 584 | if (!existing_aws[ntw_id]) { |
|---|
| 585 | init_config_awars(root); |
|---|
| 586 | |
|---|
| 587 | AW_window_simple *aws = new AW_window_simple; |
|---|
| 588 | aws->init(root, "SPECIES_SELECTIONS", "Species Selections"); |
|---|
| 589 | aws->load_xfig("nt_selection.fig"); |
|---|
| 590 | |
|---|
| 591 | aws->at("close"); |
|---|
| 592 | aws->callback((AW_CB0)AW_POPDOWN); |
|---|
| 593 | aws->create_button("CLOSE", "CLOSE", "C"); |
|---|
| 594 | |
|---|
| 595 | aws->at("help"); |
|---|
| 596 | aws->callback(makeHelpCallback("configuration.hlp")); |
|---|
| 597 | aws->create_button("HELP", "HELP", "H"); |
|---|
| 598 | |
|---|
| 599 | aws->at("list"); |
|---|
| 600 | awt_create_selection_list_on_configurations(GLOBAL.gb_main, aws, AWAR_CONFIGURATION, false); |
|---|
| 601 | |
|---|
| 602 | aws->at("store"); |
|---|
| 603 | aws->callback(makeWindowCallback(nt_store_configuration, ntw)); |
|---|
| 604 | aws->create_button(GBS_global_string("STORE_%i", ntw_id), "STORE", "S"); |
|---|
| 605 | |
|---|
| 606 | aws->at("extract"); |
|---|
| 607 | aws->callback(makeWindowCallback(nt_extract_configuration, CONF_EXTRACT)); |
|---|
| 608 | aws->create_button("EXTRACT", "EXTRACT", "E"); |
|---|
| 609 | |
|---|
| 610 | aws->at("mark"); |
|---|
| 611 | aws->callback(makeWindowCallback(nt_extract_configuration, CONF_MARK)); |
|---|
| 612 | aws->create_button("MARK", "MARK", "M"); |
|---|
| 613 | |
|---|
| 614 | aws->at("unmark"); |
|---|
| 615 | aws->callback(makeWindowCallback(nt_extract_configuration, CONF_UNMARK)); |
|---|
| 616 | aws->create_button("UNMARK", "UNMARK", "U"); |
|---|
| 617 | |
|---|
| 618 | aws->at("invert"); |
|---|
| 619 | aws->callback(makeWindowCallback(nt_extract_configuration, CONF_INVERT)); |
|---|
| 620 | aws->create_button("INVERT", "INVERT", "I"); |
|---|
| 621 | |
|---|
| 622 | aws->at("combine"); |
|---|
| 623 | aws->callback(makeWindowCallback(nt_extract_configuration, CONF_COMBINE)); |
|---|
| 624 | aws->create_button("COMBINE", "COMBINE", "C"); |
|---|
| 625 | |
|---|
| 626 | aws->at("delete"); |
|---|
| 627 | aws->callback(nt_delete_configuration); |
|---|
| 628 | aws->create_button("DELETE", "DELETE", "D"); |
|---|
| 629 | |
|---|
| 630 | aws->at("rename"); |
|---|
| 631 | aws->callback(nt_rename_configuration); |
|---|
| 632 | aws->create_button("RENAME", "RENAME", "R"); |
|---|
| 633 | |
|---|
| 634 | existing_aws[ntw_id] = aws; |
|---|
| 635 | } |
|---|
| 636 | return existing_aws[ntw_id]; |
|---|
| 637 | } |
|---|
| 638 | |
|---|
| 639 | void NT_popup_configuration_admin(AW_window *aw_main, AW_CL cl_ntw, AW_CL) { |
|---|
| 640 | AW_window *aww = create_configuration_admin_window(aw_main->get_root(), (AWT_canvas*)cl_ntw); |
|---|
| 641 | aww->activate(); |
|---|
| 642 | } |
|---|
| 643 | |
|---|
| 644 | // ----------------------------------------- |
|---|
| 645 | // various ways to start the editor |
|---|
| 646 | |
|---|
| 647 | #define CONFNAME "default_configuration" |
|---|
| 648 | |
|---|
| 649 | static void nt_start_editor_on_configuration(AW_window *aww) { |
|---|
| 650 | aww->hide(); |
|---|
| 651 | |
|---|
| 652 | const char *cn = aww->get_root()->awar(AWAR_CONFIGURATION)->read_char_pntr(); |
|---|
| 653 | const char *com = GBS_global_string("arb_edit4 -c '%s' &", cn); |
|---|
| 654 | |
|---|
| 655 | aw_message_if(GBK_system(com)); |
|---|
| 656 | } |
|---|
| 657 | |
|---|
| 658 | AW_window *NT_create_startEditorOnOldConfiguration_window(AW_root *awr) { |
|---|
| 659 | static AW_window_simple *aws = 0; |
|---|
| 660 | if (!aws) { |
|---|
| 661 | init_config_awars(awr); |
|---|
| 662 | |
|---|
| 663 | aws = new AW_window_simple; |
|---|
| 664 | aws->init(awr, "SELECT_CONFIGURATION", "SELECT A CONFIGURATION"); |
|---|
| 665 | aws->at(10, 10); |
|---|
| 666 | aws->auto_space(0, 0); |
|---|
| 667 | awt_create_selection_list_on_configurations(GLOBAL.gb_main, aws, AWAR_CONFIGURATION, false); |
|---|
| 668 | aws->at_newline(); |
|---|
| 669 | |
|---|
| 670 | aws->callback((AW_CB0)nt_start_editor_on_configuration); |
|---|
| 671 | aws->create_button("START", "START"); |
|---|
| 672 | |
|---|
| 673 | aws->callback(AW_POPDOWN); |
|---|
| 674 | aws->create_button("CLOSE", "CLOSE", "C"); |
|---|
| 675 | |
|---|
| 676 | aws->window_fit(); |
|---|
| 677 | } |
|---|
| 678 | return aws; |
|---|
| 679 | } |
|---|
| 680 | |
|---|
| 681 | void NT_start_editor_on_tree(AW_window *, AW_CL cl_use_species_aside, AW_CL cl_ntw) { |
|---|
| 682 | GB_ERROR error = nt_create_configuration(0, nt_get_tree_root_of_canvas((AWT_canvas*)cl_ntw), CONFNAME, (int)cl_use_species_aside); |
|---|
| 683 | if (!error) error = GBK_system("arb_edit4 -c " CONFNAME " &"); |
|---|
| 684 | aw_message_if(error); |
|---|
| 685 | } |
|---|
| 686 | |
|---|
| 687 | |
|---|