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// =============================================================== //
// //
// File : arb_export_tree.cxx //
// Purpose : //
// //
// Institute of Microbiology (Technical University Munich) //
// http://www.arb-home.de/ //
// //
// =============================================================== //
#include <TreeWrite.h>
#include <arbdbt.h>
#include <arb_handlers.h>
#include <arb_global_defs.h>
int main(int argc, char **argv) {
int exitcode = EXIT_SUCCESS;
ARB_redirect_handlers_to(stderr, stderr);
if (argc < 2) {
fprintf(stderr,
"\n"
"arb_export_tree - exports tree from running ARB to stdout\n"
"syntax: arb_export_tree [--bifurcated] TREE_NAME [DBNAME]\n"
" --bifurcated write a bifurcated tree (default is a trifurcated tree)\n"
" --nobranchlens do not write branchlengths\n"
" --doublequotes use doublequotes (default is singlequotes)\n"
"\n"
"Note: If TREE_NAME is '\?\?\?\?' or '' an empty tree is written.\n"
" If DBNAME is not specified, the default DB server ':' will be used.\n"
);
exitcode = EXIT_FAILURE;
}
else {
GB_ERROR error = NULL;
bool trifurcated = true;
bool branchlens = true;
bool doublequotes = false;
const char *tree_name = NULL;
const char *db_name = NULL;
for (int a = 1; a < argc && !error; a++) {
if (strcmp(argv[a], "--bifurcated") == 0) trifurcated = false;
else if (strcmp(argv[a], "--nobranchlens") == 0) branchlens = false;
else if (strcmp(argv[a], "--doublequotes") == 0) doublequotes = true;
else {
if (!tree_name) tree_name = argv[a];
else if (!db_name) db_name = argv[a];
else {
error = GBS_global_string("Superfluous argument '%s'", argv[a]);
}
}
}
if (!tree_name && !error) error = "Missing argument TREE_NAME";
if (!error) {
if (!db_name) db_name = ":";
GB_shell shell;
GBDATA *gb_main = GBT_open(db_name, "r");
if (!gb_main) error = GB_await_error();
else {
{
GB_transaction ta(gb_main);
GBT_TREE *tree = GBT_read_tree(gb_main, tree_name, GBT_TREE_NodeFactory());
if (tree) {
error = TREE_export_tree(gb_main, stdout, tree, trifurcated, branchlens, doublequotes);
delete tree;
}
else {
GB_ERROR why_cant_read = GB_await_error();
if (tree_name[0] && strcmp(tree_name, NO_TREE_SELECTED) != 0) {
// if no tree selected -> no error, just export empty tree
char *warning = GBS_global_string_copy("arb_export_tree from '%s': %s", db_name, why_cant_read);
GBT_message(gb_main, warning);
free(warning);
}
}
}
if (!error) fprintf(stdout, ";\n"); // aka empty tree
GB_close(gb_main);
}
}
if (error) {
fprintf(stderr, "\narb_export_tree: Error: %s\n", error);
exitcode = EXIT_FAILURE;
}
}
return exitcode;
}
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