| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : arb_export_tree.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 <TreeWrite.h> |
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| 12 | #include <TreeNode.h> |
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| 13 | #include <arb_handlers.h> |
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| 14 | #include <arb_global_defs.h> |
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| 15 | |
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| 16 | int main(int argc, char **argv) { |
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| 17 | int exitcode = EXIT_SUCCESS; |
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| 18 | |
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| 19 | ARB_redirect_handlers_to(stderr, stderr); |
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| 20 | |
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| 21 | if (argc < 2) { |
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| 22 | fprintf(stderr, |
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| 23 | "\n" |
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| 24 | "arb_export_tree - exports tree from running ARB to stdout\n" |
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| 25 | "syntax: arb_export_tree [--bifurcated] TREE_NAME [DBNAME]\n" |
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| 26 | " --bifurcated write a bifurcated tree (default is a trifurcated tree)\n" |
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| 27 | " --nobranchlens do not write branchlengths\n" |
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| 28 | " --doublequotes use doublequotes (default is singlequotes)\n" |
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| 29 | "\n" |
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| 30 | "Note: If TREE_NAME is '\?\?\?\?' or '' an empty tree is written.\n" |
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| 31 | " If DBNAME is not specified, the default DB server ':' will be used.\n" |
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| 32 | ); |
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| 33 | exitcode = EXIT_FAILURE; |
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| 34 | } |
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| 35 | else { |
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| 36 | GB_ERROR error = NULL; |
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| 37 | bool trifurcated = true; |
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| 38 | bool branchlens = true; |
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| 39 | bool doublequotes = false; |
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| 40 | const char *tree_name = NULL; |
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| 41 | const char *db_name = NULL; |
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| 42 | |
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| 43 | for (int a = 1; a < argc && !error; a++) { |
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| 44 | if (strcmp(argv[a], "--bifurcated") == 0) trifurcated = false; |
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| 45 | else if (strcmp(argv[a], "--nobranchlens") == 0) branchlens = false; |
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| 46 | else if (strcmp(argv[a], "--doublequotes") == 0) doublequotes = true; |
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| 47 | else { |
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| 48 | if (!tree_name) tree_name = argv[a]; |
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| 49 | else if (!db_name) db_name = argv[a]; |
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| 50 | else { |
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| 51 | error = GBS_global_string("Superfluous argument '%s'", argv[a]); |
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| 52 | } |
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| 53 | } |
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| 54 | } |
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| 55 | |
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| 56 | if (!tree_name && !error) error = "Missing argument TREE_NAME"; |
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| 57 | |
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| 58 | if (!error) { |
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| 59 | if (!db_name) db_name = ":"; |
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| 60 | |
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| 61 | GB_shell shell; |
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| 62 | GBDATA *gb_main = GBT_open(db_name, "r"); |
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| 63 | |
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| 64 | if (!gb_main) error = GB_await_error(); |
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| 65 | else { |
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| 66 | { |
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| 67 | GB_transaction ta(gb_main); |
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| 68 | |
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| 69 | TreeNode *tree = GBT_read_tree(gb_main, tree_name, new SimpleRoot); |
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| 70 | if (tree) { |
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| 71 | error = TREE_export_tree(gb_main, stdout, tree, trifurcated, branchlens, doublequotes); |
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| 72 | UNCOVERED(); |
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| 73 | destroy(tree); |
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| 74 | } |
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| 75 | else { |
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| 76 | GB_ERROR why_cant_read = GB_await_error(); |
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| 77 | if (tree_name[0] && strcmp(tree_name, NO_TREE_SELECTED) != 0) { |
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| 78 | // if no tree selected -> no error, just export empty tree |
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| 79 | char *warning = GBS_global_string_copy("arb_export_tree from '%s': %s", db_name, why_cant_read); |
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| 80 | GBT_message(gb_main, warning); |
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| 81 | free(warning); |
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| 82 | } |
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| 83 | } |
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| 84 | } |
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| 85 | |
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| 86 | if (!error) fprintf(stdout, ";\n"); // aka empty tree |
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| 87 | GB_close(gb_main); |
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| 88 | } |
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| 89 | } |
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| 90 | |
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| 91 | if (error) { |
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| 92 | fprintf(stderr, "\narb_export_tree: Error: %s\n", error); |
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| 93 | exitcode = EXIT_FAILURE; |
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| 94 | } |
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| 95 | |
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| 96 | } |
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| 97 | return exitcode; |
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| 98 | } |
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| 99 | |
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