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// ============================================================= //
// //
// File : arb_read_tree.cxx //
// Purpose : //
// //
// Institute of Microbiology (Technical University Munich) //
// http://www.arb-home.de/ //
// //
// ============================================================= //
#include <TreeRead.h>
#include <arb_strbuf.h>
#include <arb_defs.h>
#include <ctime>
static void add_bootstrap(GBT_TREE *node, double hundred) {
// add_bootstrap interprets the length of the branches as bootstrap value
// (this is needed by Phylip DNAPARS/PROTPARS with bootstrapping)
//
// 'hundred' specifies which value represents 100%
if (node->is_leaf) {
node->remove_remark();
return;
}
node->leftlen /= hundred;
node->rightlen /= hundred;
double left_bs = node->leftlen * 100.0;
double right_bs = node->rightlen * 100.0;
#if defined(DEBUG) && 0
fprintf(stderr, "node->leftlen = %f left_bs = %f\n", node->leftlen, left_bs);
fprintf(stderr, "node->rightlen = %f right_bs = %f\n", node->rightlen, right_bs);
#endif // DEBUG
node->leftson ->set_bootstrap(left_bs);
node->rightson->set_bootstrap(right_bs);
node->leftlen = DEFAULT_BRANCH_LENGTH; // reset branchlengths
node->rightlen = DEFAULT_BRANCH_LENGTH;
add_bootstrap(node->leftson, hundred);
add_bootstrap(node->rightson, hundred);
}
static void show_message(GBDATA *gb_main, const char *msg) {
if (gb_main) {
GBT_message(gb_main, msg);
}
else {
fflush(stdout);
printf("arb_read_tree: %s\n", msg);
}
}
static void show_error(GBDATA *gb_main, GB_ERROR error) {
if (error) show_message(gb_main, GBS_global_string("Error running arb_read_tree (%s)", error));
}
static void error_with_usage(GBDATA *gb_main, GB_ERROR error) {
fputs("Usage: arb_read_tree [options] tree_name treefile [comment]\n"
"Available options:\n"
" -db database savename specify database and savename (default is 'running ARB')\n"
" -scale factor scale branchlengths by 'factor'\n"
" -consense numberOfTrees reinterpret branchlengths as consense values\n"
" -commentFromFile file read tree comment from 'file'\n"
, stdout);
show_error(gb_main, error);
}
struct parameters {
const char *dbname;
const char *dbsavename;
const char *tree_name;
const char *treefilename;
const char *comment;
const char *commentFile;
bool scale;
double scale_factor;
bool consense;
int calculated_trees;
parameters()
: dbname(":"),
dbsavename(NULL),
tree_name(NULL),
treefilename(NULL),
comment(NULL),
commentFile(NULL),
scale(false),
scale_factor(0.0),
consense(false),
calculated_trees(0)
{
}
#define SHIFT_ARGS(off) do { argc -= off; argv += off; } while (0)
#define SHIFT_NONSWITCHES(off) do { nonSwitches -= off; nonSwitch += off; } while (0)
GB_ERROR scan(int argc, char **argv) {
GB_ERROR error = NULL;
const char *nonSwitch_buf[20];
const char **nonSwitch = nonSwitch_buf;
int nonSwitches = 0;
SHIFT_ARGS(1); // position onto first argument
while (argc>0 && !error) {
if (strcmp("-scale", argv[0]) == 0) {
scale = true;
if (argc<2) error = "-scale expects a 2nd argument (scale factor)";
else {
scale_factor = atof(argv[1]);
SHIFT_ARGS(2);
}
}
else if (strcmp("-consense", argv[0]) == 0) {
consense = true;
if (argc<2) error = "-consense expects a 2nd argument (number of trees)";
else {
calculated_trees = atoi(argv[1]);
if (calculated_trees < 1) {
error = GBS_global_string("Illegal # of trees (%i) for -consense (minimum is 1)", calculated_trees);
}
else SHIFT_ARGS(2);
}
}
else if (strcmp("-commentFromFile", argv[0]) == 0) {
if (argc<2) error = "-commentFromFile expects a 2nd argument (file containing comment)";
else {
commentFile = argv[1];
SHIFT_ARGS(2);
}
}
else if (strcmp("-db", argv[0]) == 0) {
if (argc<3) error = "-db expects two arguments (database and savename)";
else {
dbname = argv[1];
dbsavename = argv[2];
SHIFT_ARGS(3);
}
}
else {
nonSwitch[nonSwitches++] = argv[0];
SHIFT_ARGS(1);
}
}
if (!error) {
if (!nonSwitches) error = "Missing argument 'tree_name'";
else {
tree_name = nonSwitch[0];
SHIFT_NONSWITCHES(1);
}
}
if (!error) {
if (!nonSwitches) error = "Missing argument 'treefile'";
else {
treefilename = nonSwitch[0];
SHIFT_NONSWITCHES(1);
}
}
if (!error && nonSwitches>0) {
comment = nonSwitch[0];
SHIFT_NONSWITCHES(1);
}
if (!error && nonSwitches>0) {
error = GBS_global_string("unexpected argument(s): %s ..", nonSwitch[0]);
}
return error;
}
};
int main(int argc, char **argv) {
parameters param;
GB_ERROR error = param.scan(argc, argv);
GBDATA *gb_main = NULL;
GBDATA *gb_msg_main = NULL;
bool connectToArb = strcmp(param.dbname, ":") == 0;
GB_shell shell;
if (!error || connectToArb) {
gb_main = GB_open(param.dbname, connectToArb ? "r" : "rw");
if (connectToArb) gb_msg_main = gb_main;
}
if (error) error_with_usage(gb_main, error);
else {
if (!gb_main) {
if (connectToArb) error = "you have to start an arbdb server first";
else error = GBS_global_string("can't open db (Reason: %s)", GB_await_error());
}
char *comment_from_file = 0;
char *comment_from_treefile = 0;
GBT_TREE *tree = 0;
if (!error) {
if (param.commentFile) {
comment_from_file = GB_read_file(param.commentFile);
if (!comment_from_file) {
comment_from_file = GBS_global_string_copy("Error reading from comment-file '%s':\n%s", param.commentFile, GB_await_error());
}
}
show_message(gb_msg_main, GBS_global_string("Reading tree from '%s' ..", param.treefilename));
{
char *warnings = 0;
bool allow_length_scaling = !param.consense && !param.scale;
tree = TREE_load(param.treefilename, GBT_TREE_NodeFactory(), &comment_from_treefile, allow_length_scaling, &warnings);
if (!tree) {
error = GB_await_error();
}
else if (warnings) {
show_message(gb_msg_main, warnings);
free(warnings);
}
}
}
if (!error) {
if (param.scale) {
show_message(gb_msg_main, GBS_global_string("Scaling branch lengths by factor %f", param.scale_factor));
TREE_scale(tree, param.scale_factor, 1.0);
}
if (param.consense) {
if (param.calculated_trees < 1) {
error = "Minimum for -consense is 1";
}
else {
show_message(gb_msg_main, GBS_global_string("Reinterpreting branch lengths as consense values (%i trees)", param.calculated_trees));
add_bootstrap(tree, param.calculated_trees);
}
}
}
if (!error) {
error = GB_begin_transaction(gb_main);
if (!error && tree->is_leaf) error = "Cannot load tree (need at least 2 leafs)";
if (!error) error = GBT_write_tree(gb_main, param.tree_name, tree);
if (!error) {
// write tree comment
const char *comments[] = {
param.comment,
comment_from_file,
comment_from_treefile,
};
GBS_strstruct *buf = GBS_stropen(5000);
bool empty = true;
for (size_t c = 0; c<ARRAY_ELEMS(comments); c++) {
if (comments[c]) {
if (!empty) GBS_chrcat(buf, '\n');
GBS_strcat(buf, comments[c]);
empty = false;
}
}
char *cmt = GBS_strclose(buf);
error = GBT_write_tree_remark(gb_main, param.tree_name, cmt);
free(cmt);
}
error = GB_end_transaction(gb_main, error);
}
if (error) show_error(gb_main, error);
else show_message(gb_msg_main, GBS_global_string("Tree %s read into the database", param.tree_name));
delete tree;
free(comment_from_file);
free(comment_from_treefile);
}
if (gb_main) {
if (!error && !connectToArb) {
error = GB_save_as(gb_main, param.dbsavename, "a");
if (error) show_error(gb_main, error);
}
GB_close(gb_main);
}
return error ? EXIT_FAILURE : EXIT_SUCCESS;
}
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