[6381] | 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : TreeWrite.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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[2] | 10 | |
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[6381] | 11 | #include <TreeWrite.h> |
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[13625] | 12 | #include <TreeNode.h> |
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[7314] | 13 | #include <arb_strbuf.h> |
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[17110] | 14 | #include <arb_file.h> |
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[6028] | 15 | #include <xml.hxx> |
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[590] | 16 | |
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[3234] | 17 | using namespace std; |
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| 18 | |
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[6028] | 19 | #define tree_assert(cond) arb_assert(cond) |
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| 20 | |
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[10482] | 21 | inline void replace_by_underscore(char *str, const char *toReplace) { |
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| 22 | char *unwanted = strpbrk(str, toReplace); |
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| 23 | while (unwanted) { |
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| 24 | unwanted[0] = '_'; |
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| 25 | unwanted = strpbrk(unwanted+1, toReplace); |
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| 26 | } |
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| 27 | } |
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| 28 | |
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| 29 | inline bool isQuoteChar(char c) { return c == '"' || c == '\''; } |
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| 30 | inline bool whole_label_quoted(const char *label, size_t length) { return isQuoteChar(label[0]) && label[0] == label[length-1]; } |
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| 31 | |
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[18704] | 32 | |
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| 33 | const char *Node_ID_Labeler::generate(GBDATA *, GBDATA *, TreeNode *species, const char *) const { |
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| 34 | return species->name; |
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| 35 | } |
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| 36 | |
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[6066] | 37 | static void export_tree_label(const char *label, FILE *out, TREE_node_quoting qmode) { |
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[6024] | 38 | // writes a label into the Newick file |
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| 39 | // label is quoted if necessary |
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| 40 | // label may be an internal_node_label, a leaf_label or a root_label |
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[6028] | 41 | tree_assert(label); |
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[552] | 42 | |
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[6066] | 43 | const char *disallowed_chars = " \t\'\"()[]:;,"; // '(' is first problem_char |
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| 44 | const char *problem_chars = disallowed_chars+4; |
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| 45 | tree_assert(problem_chars[0] == '('); |
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| 46 | |
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[16763] | 47 | bool need_quotes = strpbrk(label, disallowed_chars); |
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[10482] | 48 | char used_quote = 0; |
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| 49 | bool force_quotes = (qmode & TREE_FORCE_QUOTES); |
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[6066] | 50 | |
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[10482] | 51 | if (force_quotes || need_quotes) { |
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[6066] | 52 | if (qmode&TREE_SINGLE_QUOTES) used_quote = '\''; |
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| 53 | else if (qmode&TREE_DOUBLE_QUOTES) used_quote = '\"'; |
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| 54 | } |
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| 55 | |
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[10482] | 56 | char *fixed_label; |
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| 57 | { |
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| 58 | size_t label_length = strlen(label); |
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[15176] | 59 | fixed_label = ARB_strduplen(label, label_length); |
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[10482] | 60 | |
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| 61 | if (whole_label_quoted(fixed_label, label_length)) { |
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| 62 | // if whole label is quoted -> remove quotes |
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[11164] | 63 | memmove(fixed_label, fixed_label+1, label_length-2); |
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| 64 | fixed_label[label_length-2] = 0; |
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[10482] | 65 | } |
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| 66 | } |
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| 67 | |
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[6066] | 68 | if (used_quote) { |
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[10482] | 69 | // replace all problematic characters if requested |
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[6066] | 70 | bool force_replace = (qmode & TREE_FORCE_REPLACE); |
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[10482] | 71 | if (force_replace) replace_by_underscore(fixed_label, problem_chars); |
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[6066] | 72 | |
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[10482] | 73 | // replace used quote by an '_' if it appears inside label |
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| 74 | char used_quote_as_string[] = { used_quote, 0 }; |
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| 75 | replace_by_underscore(fixed_label, used_quote_as_string); |
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| 76 | |
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| 77 | if (!force_quotes) { |
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[16763] | 78 | need_quotes = strpbrk(fixed_label, disallowed_chars); |
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[10482] | 79 | if (!need_quotes) used_quote = 0; // @@@ fails if both quote-types are used in one name |
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[552] | 80 | } |
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[2] | 81 | } |
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[552] | 82 | else { |
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[6066] | 83 | // unquoted label - always replace all problematic characters by '_' |
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[10482] | 84 | replace_by_underscore(fixed_label, disallowed_chars); |
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[552] | 85 | } |
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[10482] | 86 | |
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| 87 | if (used_quote) fputc(used_quote, out); |
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| 88 | fputs(fixed_label, out); |
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| 89 | if (used_quote) fputc(used_quote, out); |
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| 90 | |
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| 91 | free(fixed_label); |
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[2] | 92 | } |
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| 93 | |
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[552] | 94 | |
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| 95 | |
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[18704] | 96 | // documentation of the Newick Format is in ../../SOURCE_TOOLS/docs/newick_doc.html |
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[552] | 97 | |
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[5530] | 98 | inline void indentTo(int indent, FILE *out) { |
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| 99 | for (int i = 0; i < indent; i++) { |
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[6366] | 100 | putc(' ', out); |
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| 101 | putc(' ', out); |
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[5530] | 102 | } |
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| 103 | } |
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| 104 | |
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[13625] | 105 | static const char *export_tree_node_print(GBDATA *gb_main, FILE *out, TreeNode *tree, const char *tree_name, |
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[6024] | 106 | bool pretty, int indent, |
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[18704] | 107 | const TreeLabeler& labeler, bool save_branchlengths, |
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[6066] | 108 | bool save_bootstraps, bool save_groupnames, TREE_node_quoting qmode) |
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[2] | 109 | { |
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[16763] | 110 | const char *error = NULp; |
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[5530] | 111 | |
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| 112 | if (pretty) indentTo(indent, out); |
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[6385] | 113 | |
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[17110] | 114 | if (tree->is_leaf()) { |
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[18704] | 115 | const char *label = labeler.generate(gb_main, tree->gb_node, tree, tree_name); |
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[11488] | 116 | export_tree_label(label, out, qmode); |
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[2] | 117 | } |
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[552] | 118 | else { |
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[5530] | 119 | if (pretty) fputs("(\n", out); |
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| 120 | else putc('(', out); |
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[552] | 121 | |
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[18704] | 122 | error = export_tree_node_print(gb_main, out, tree->get_leftson(), tree_name, pretty, indent+1, labeler, save_branchlengths, save_bootstraps, save_groupnames, qmode); |
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[17110] | 123 | if (error) return error; |
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| 124 | |
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[552] | 125 | if (save_branchlengths) fprintf(out, ":%.5f", tree->leftlen); |
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| 126 | fputs(",\n", out); |
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| 127 | |
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[18704] | 128 | error = export_tree_node_print(gb_main, out, tree->get_rightson(), tree_name, pretty, indent+1, labeler, save_branchlengths, save_bootstraps, save_groupnames, qmode); |
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[552] | 129 | if (error) return error; |
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| 130 | |
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| 131 | if (save_branchlengths) fprintf(out, ":%.5f", tree->rightlen); |
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| 132 | fputc('\n', out); |
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| 133 | |
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[5530] | 134 | if (pretty) indentTo(indent, out); |
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[552] | 135 | fputc(')', out); |
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| 136 | |
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[16763] | 137 | char *bootstrap = NULp; |
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[11488] | 138 | if (save_bootstraps) { |
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| 139 | double value; |
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| 140 | switch (tree->parse_bootstrap(value)) { |
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| 141 | case REMARK_BOOTSTRAP: bootstrap = GBS_global_string_copy("%i", int(value+0.5)); break; |
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| 142 | case REMARK_OTHER: bootstrap = strdup(tree->get_remark()); break; |
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| 143 | case REMARK_NONE: break; |
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[552] | 144 | } |
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| 145 | } |
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| 146 | |
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[17110] | 147 | const char *group = (save_groupnames && tree->has_group_info()) ? tree->name : NULp; |
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[16763] | 148 | const char *label = NULp; |
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[11488] | 149 | if (group) { |
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[17110] | 150 | if (tree->keelTarget()) { |
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| 151 | error = GBS_global_string("contains a keeled group named '%s'\n" |
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| 152 | "(to export a tree, you have to correct all keeled groups)", group); |
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| 153 | } |
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| 154 | else { |
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| 155 | if (bootstrap) label = GBS_global_string("%s:%s", bootstrap, group); |
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| 156 | else label = group; |
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| 157 | } |
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[552] | 158 | } |
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[11488] | 159 | else if (bootstrap) label = bootstrap; |
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[552] | 160 | |
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[11488] | 161 | if (label) export_tree_label(label, out, qmode); |
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[552] | 162 | |
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| 163 | free(bootstrap); |
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| 164 | } |
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| 165 | |
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[2] | 166 | return error; |
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| 167 | } |
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[3070] | 168 | |
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[610] | 169 | inline string buildNodeIdentifier(const string& parent_id, int& son_counter) { |
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| 170 | ++son_counter; |
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| 171 | if (parent_id.empty()) return GBS_global_string("n_%i", son_counter); |
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| 172 | return GBS_global_string("%s.%i", parent_id.c_str(), son_counter); |
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| 173 | } |
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[3070] | 174 | |
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[13625] | 175 | static const char *export_tree_node_print_xml(GBDATA *gb_main, TreeNode *tree, double my_length, const char *tree_name, |
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[18704] | 176 | const TreeLabeler& labeler, bool skip_folded, const string& parent_id, int& parent_son_counter) { |
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[16763] | 177 | const char *error = NULp; |
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[2] | 178 | |
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[17110] | 179 | if (tree->is_leaf()) { |
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[610] | 180 | XML_Tag item_tag("ITEM"); |
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[590] | 181 | |
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[18704] | 182 | item_tag.add_attribute("name", buildNodeIdentifier(parent_id, parent_son_counter)); |
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| 183 | item_tag.add_attribute("itemname", labeler.generate(gb_main, tree->gb_node, tree, tree_name)); |
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| 184 | item_tag.add_attribute("length", GBS_global_string("%.5f", my_length)); |
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[590] | 185 | } |
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| 186 | else { |
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[16763] | 187 | char *bootstrap = NULp; |
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[11488] | 188 | { |
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| 189 | double value; |
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| 190 | switch (tree->parse_bootstrap(value)) { |
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| 191 | case REMARK_BOOTSTRAP: bootstrap = GBS_global_string_copy("%i", int(value+0.5)); break; |
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| 192 | case REMARK_OTHER: break; // @@@ other branch-remarks are currently not saved into xml format |
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| 193 | case REMARK_NONE: break; |
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[590] | 194 | } |
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| 195 | } |
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[11488] | 196 | |
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| 197 | bool folded = false; |
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[16763] | 198 | char *groupname = NULp; |
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[590] | 199 | if (tree->name) { |
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[18704] | 200 | const char *buf = labeler.generate(gb_main, tree->gb_node, tree, tree_name); |
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[6028] | 201 | tree_assert(buf); |
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[5725] | 202 | groupname = strdup(buf); |
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[634] | 203 | |
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[5309] | 204 | GBDATA *gb_grouped = GB_entry(tree->gb_node, "grouped"); |
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[1554] | 205 | if (gb_grouped) { |
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| 206 | folded = GB_read_byte(gb_grouped); |
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| 207 | } |
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[590] | 208 | } |
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| 209 | |
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[6366] | 210 | if (my_length || bootstrap || groupname) { |
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[1554] | 211 | bool hide_this_group = skip_folded && folded; // hide folded groups only if skip_folded is true |
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[634] | 212 | |
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| 213 | XML_Tag branch_tag(hide_this_group ? "FOLDED_GROUP" : "BRANCH"); |
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[610] | 214 | string my_id = buildNodeIdentifier(parent_id, parent_son_counter); |
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[590] | 215 | |
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[610] | 216 | branch_tag.add_attribute("name", my_id); |
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| 217 | |
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| 218 | if (my_length) { |
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| 219 | branch_tag.add_attribute("length", GBS_global_string("%.5f", my_length)); |
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| 220 | } |
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[590] | 221 | if (bootstrap) { |
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[610] | 222 | branch_tag.add_attribute("bootstrap", bootstrap); |
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[6331] | 223 | freenull(bootstrap); |
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[590] | 224 | } |
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| 225 | if (groupname) { |
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[610] | 226 | branch_tag.add_attribute("groupname", groupname); |
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[6331] | 227 | freenull(groupname); |
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[1554] | 228 | if (folded) branch_tag.add_attribute("folded", "1"); |
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[590] | 229 | } |
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[1554] | 230 | else { |
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[6028] | 231 | tree_assert(!folded); |
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[1554] | 232 | } |
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[590] | 233 | |
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[634] | 234 | if (hide_this_group) { |
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[6395] | 235 | branch_tag.add_attribute("items_in_group", GBT_count_leafs(tree)); |
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[634] | 236 | } |
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| 237 | else { |
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[8939] | 238 | int my_son_counter = 0; |
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[18704] | 239 | if (!error) error = export_tree_node_print_xml(gb_main, tree->get_leftson(), tree->leftlen, tree_name, labeler, skip_folded, my_id, my_son_counter); |
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| 240 | if (!error) error = export_tree_node_print_xml(gb_main, tree->get_rightson(), tree->rightlen, tree_name, labeler, skip_folded, my_id, my_son_counter); |
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[634] | 241 | } |
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[590] | 242 | } |
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| 243 | else { |
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[18704] | 244 | if (!error) error = export_tree_node_print_xml(gb_main, tree->get_leftson(), tree->leftlen, tree_name, labeler, skip_folded, parent_id, parent_son_counter); |
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| 245 | if (!error) error = export_tree_node_print_xml(gb_main, tree->get_rightson(), tree->rightlen, tree_name, labeler, skip_folded, parent_id, parent_son_counter); |
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[590] | 246 | } |
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| 247 | } |
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| 248 | |
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| 249 | return error; |
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| 250 | } |
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| 251 | |
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[18704] | 252 | GB_ERROR TREE_write_XML(GBDATA *gb_main, const char *db_name, const char *tree_name, const TreeLabeler& labeler, bool skip_folded, const char *path) { |
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[16763] | 253 | GB_ERROR error = NULp; |
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[590] | 254 | FILE *output = fopen(path, "w"); |
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| 255 | |
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[6100] | 256 | if (!output) error = GB_export_errorf("file '%s' could not be opened for writing", path); |
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[590] | 257 | else { |
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[11464] | 258 | GB_transaction ta(gb_main); |
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[590] | 259 | |
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[13625] | 260 | TreeNode *tree = GBT_read_tree(gb_main, tree_name, new SimpleRoot); |
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[5842] | 261 | if (!tree) error = GB_await_error(); |
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[590] | 262 | else { |
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[18717] | 263 | error = GBT_link_tree(tree, gb_main, true); |
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[590] | 264 | |
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| 265 | if (!error) { |
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[8493] | 266 | GBDATA *tree_cont = GBT_find_tree(gb_main, tree_name); |
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[5309] | 267 | GBDATA *tree_remark = GB_entry(tree_cont, "remark"); |
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[590] | 268 | |
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| 269 | XML_Document xml_doc("ARB_TREE", "arb_tree.dtd", output); |
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| 270 | |
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[610] | 271 | xml_doc.add_attribute("database", db_name); |
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| 272 | xml_doc.add_attribute("treename", tree_name); |
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[15176] | 273 | xml_doc.add_attribute("export_date", ARB_date_string()); |
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[590] | 274 | |
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[610] | 275 | if (tree_remark) { |
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| 276 | char *remark = GB_read_string(tree_remark); |
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[590] | 277 | XML_Tag remark_tag("COMMENT"); |
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| 278 | XML_Text remark_text(remark); |
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| 279 | free(remark); |
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| 280 | } |
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| 281 | |
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[610] | 282 | int my_son_counter = 0; |
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[18704] | 283 | error = export_tree_node_print_xml(gb_main, tree, 0.0, tree_name, labeler, skip_folded, "", my_son_counter); |
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[590] | 284 | } |
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| 285 | } |
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| 286 | fclose(output); |
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| 287 | } |
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| 288 | |
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| 289 | return error; |
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| 290 | } |
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| 291 | |
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[6028] | 292 | static char *complete_newick_comment(const char *comment) { |
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| 293 | // ensure that all '[' in 'comment' are closed by corresponding ']' by inserting additional brackets |
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| 294 | |
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[6655] | 295 | int openBrackets = 0; |
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| 296 | GBS_strstruct *out = GBS_stropen(strlen(comment)*1.1); |
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[6028] | 297 | |
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| 298 | for (int o = 0; comment[o]; ++o) { |
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| 299 | switch (comment[o]) { |
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| 300 | case '[': |
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| 301 | openBrackets++; |
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| 302 | break; |
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| 303 | case ']': |
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| 304 | if (openBrackets == 0) { |
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| 305 | GBS_chrcat(out, '['); // insert one |
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| 306 | } |
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| 307 | else { |
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| 308 | openBrackets--; |
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| 309 | } |
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| 310 | break; |
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| 311 | |
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| 312 | default: |
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| 313 | break; |
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| 314 | } |
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| 315 | GBS_chrcat(out, comment[o]); |
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| 316 | } |
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| 317 | |
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| 318 | while (openBrackets>0) { |
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| 319 | GBS_chrcat(out, ']'); // insert one |
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| 320 | openBrackets--; |
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| 321 | } |
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| 322 | |
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[6325] | 323 | tree_assert(openBrackets == 0); |
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[6028] | 324 | |
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| 325 | return GBS_strclose(out); |
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| 326 | } |
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| 327 | |
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[18704] | 328 | GB_ERROR TREE_write_Newick(GBDATA *gb_main, const char *tree_name, const TreeLabeler& labeler, bool save_branchlengths, bool save_bootstraps, bool save_groupnames, bool pretty, TREE_node_quoting quoteMode, const char *path) { |
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[17110] | 329 | // userland newick exporter |
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| 330 | // see also: testcode newick exporter in ../../ARBDB/adtree.cxx@NEWICK_EXPORTER |
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| 331 | |
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[16763] | 332 | GB_ERROR error = NULp; |
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[552] | 333 | FILE *output = fopen(path, "w"); |
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[2] | 334 | |
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[12138] | 335 | if (!output) error = GBS_global_string("file '%s' could not be opened for writing", path); |
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[552] | 336 | else { |
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[11464] | 337 | GB_transaction ta(gb_main); |
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[2] | 338 | |
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[13625] | 339 | TreeNode *tree = GBT_read_tree(gb_main, tree_name, new SimpleRoot); |
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[5842] | 340 | if (!tree) error = GB_await_error(); |
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[552] | 341 | else { |
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[18717] | 342 | error = GBT_link_tree(tree, gb_main, true); |
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[552] | 343 | |
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| 344 | if (!error) { |
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[16763] | 345 | char *remark = NULp; |
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[8493] | 346 | GBDATA *tree_cont = GBT_find_tree(gb_main, tree_name); |
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[5309] | 347 | GBDATA *tree_remark = GB_entry(tree_cont, "remark"); |
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[552] | 348 | |
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[6028] | 349 | if (tree_remark) { |
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| 350 | remark = GB_read_string(tree_remark); |
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| 351 | } |
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[5564] | 352 | { |
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[6028] | 353 | const char *saved_to = GBS_global_string("%s saved to %s", tree_name, path); |
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[15425] | 354 | freeset(remark, GBS_log_action_to(remark, saved_to, true)); |
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[5564] | 355 | } |
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[6028] | 356 | |
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| 357 | if (remark) { |
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| 358 | char *wellformed = complete_newick_comment(remark); |
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| 359 | |
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| 360 | tree_assert(wellformed); |
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| 361 | |
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| 362 | fputc('[', output); fputs(wellformed, output); fputs("]\n", output); |
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| 363 | free(wellformed); |
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| 364 | } |
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[552] | 365 | free(remark); |
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[5564] | 366 | if (!error) { |
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[18704] | 367 | error = export_tree_node_print(gb_main, output, tree, tree_name, pretty, 0, labeler, save_branchlengths, save_bootstraps, save_groupnames, quoteMode); |
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[5564] | 368 | } |
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[552] | 369 | } |
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| 370 | |
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[13625] | 371 | destroy(tree); |
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[552] | 372 | } |
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| 373 | |
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| 374 | fprintf(output, ";\n"); |
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| 375 | fclose(output); |
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[17110] | 376 | |
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| 377 | if (error) { |
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| 378 | GB_unlink_or_warn(path, &error); |
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| 379 | } |
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[2] | 380 | } |
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| 381 | |
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| 382 | return error; |
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| 383 | } |
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[6065] | 384 | |
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| 385 | // -------------------------------------------------------------------------------- |
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| 386 | |
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| 387 | static void export_tree_node_print_remove(char *str) { |
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| 388 | int i = 0; |
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| 389 | while (char c = str[i]) { |
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| 390 | if (c == '\'' || c == '\"') str[i] = '.'; |
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| 391 | i++; |
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| 392 | } |
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| 393 | } |
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| 394 | |
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[13625] | 395 | static void export_tree_rek(TreeNode *tree, FILE *out, bool export_branchlens, bool dquot) { |
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[17110] | 396 | if (tree->is_leaf()) { |
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[6065] | 397 | export_tree_node_print_remove(tree->name); |
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| 398 | fprintf(out, |
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| 399 | dquot ? " \"%s\" " : " '%s' ", |
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| 400 | tree->name); |
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| 401 | } |
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| 402 | else { |
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| 403 | fputc('(', out); |
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[13625] | 404 | export_tree_rek(tree->get_leftson(), out, export_branchlens, dquot); if (export_branchlens) fprintf(out, ":%.5f,", tree->leftlen); |
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| 405 | export_tree_rek(tree->get_rightson(), out, export_branchlens, dquot); if (export_branchlens) fprintf(out, ":%.5f", tree->rightlen); |
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[6065] | 406 | fputc(')', out); |
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| 407 | |
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| 408 | if (tree->name) { |
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| 409 | export_tree_node_print_remove(tree->name); |
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| 410 | fprintf(out, |
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| 411 | dquot ? "\"%s\"" : "'%s'", |
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| 412 | tree->name); |
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| 413 | } |
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| 414 | } |
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| 415 | } |
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| 416 | |
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[18665] | 417 | // @@@ maybe replace TREE_export_tree by TREE_write_Newick (need some additional parameters: no comment, trifurcation) |
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[6065] | 418 | |
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[13625] | 419 | GB_ERROR TREE_export_tree(GBDATA *, FILE *out, TreeNode *tree, bool triple_root, bool export_branchlens, bool dquot) { |
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[6366] | 420 | if (triple_root) { |
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[13625] | 421 | TreeNode *one, *two, *three; |
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[17110] | 422 | if (tree->is_leaf()) { |
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[17336] | 423 | return GB_export_error("Tree is too small, minimum 3 nodes"); |
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[6065] | 424 | } |
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[17110] | 425 | if (tree->leftson->is_leaf() && tree->rightson->is_leaf()) { |
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[17336] | 426 | return GB_export_error("Tree is too small, minimum 3 nodes"); |
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[6065] | 427 | } |
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[17110] | 428 | if (tree->leftson->is_leaf()) { |
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[13625] | 429 | one = tree->get_leftson(); |
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| 430 | two = tree->get_rightson()->get_leftson(); |
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| 431 | three = tree->get_rightson()->get_rightson(); |
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[6345] | 432 | } |
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| 433 | else { |
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[13625] | 434 | one = tree->get_leftson()->get_leftson(); |
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| 435 | two = tree->get_leftson()->get_rightson(); |
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| 436 | three = tree->get_rightson(); |
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[6065] | 437 | } |
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| 438 | fputc('(', out); |
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| 439 | export_tree_rek(one, out, export_branchlens, dquot); if (export_branchlens) fprintf(out, ":%.5f", 1.0); fputc(',', out); |
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| 440 | export_tree_rek(two, out, export_branchlens, dquot); if (export_branchlens) fprintf(out, ":%.5f", 1.0); fputc(',', out); |
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| 441 | export_tree_rek(three, out, export_branchlens, dquot); if (export_branchlens) fprintf(out, ":%.5f", 1.0); |
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| 442 | fputc(')', out); |
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| 443 | } |
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| 444 | else { |
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| 445 | export_tree_rek(tree, out, export_branchlens, dquot); |
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| 446 | } |
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[16763] | 447 | return NULp; |
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[6065] | 448 | } |
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[18704] | 449 | |
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| 450 | |
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