SEXP rph_tree_prune(SEXP treeStr, SEXP seqsP, SEXP allButP) {
TreeNode *tr = rph_tree_new(treeStr);
List *names = lst_new_ptr(LENGTH(seqsP));
String *tempStr;
char *temp;
int i;
SEXP result;
for (i=0; i<LENGTH(seqsP); i++) {
tempStr = str_new_charstr(CHAR(STRING_ELT(seqsP, i)));
lst_push_ptr(names, tempStr);
}
tr_prune(&tr, names, INTEGER_VALUE(allButP), NULL);
temp = tr_to_string(tr, 1);
PROTECT(result = NEW_CHARACTER(1));
SET_STRING_ELT(result, 0, mkChar(temp));
UNPROTECT(1);
return result;
}
int main(int argc, char *argv[]) {
/* variables for options, with defaults */
TreeNode *tree = NULL, *merge_tree = NULL, *extrapolate_tree = NULL;
Hashtable *rename_hash = NULL;
double scale_factor = 1;
List *prune_names = NULL, *label = NULL, *labelType = NULL;
int prune_all_but = FALSE, tree_only = FALSE, dissect = FALSE,
name_ancestors = FALSE, with_branch = FALSE, print_branchlen=FALSE,
inNewick=FALSE, no_branchlen = FALSE, print_distance_to_root = FALSE;
TreeModel *mod = NULL, *merge_mod = NULL;
char *reroot_name = NULL, *subtree_name =NULL, *get_subtree_name = NULL,
*node_distance_name = NULL;
/* other variables */
String *suffix, *optstr;
char c;
int i, opt_idx;
TreeNode *n;
struct option long_opts[] = {
{"scale", 1, 0, 's'},
{"extrapolate", 1, 0, 'e'},
{"prune", 1, 0, 'p'},
{"prune-all-but", 1, 0, 'P'},
{"get-subtree", 1, 0, 'g'},
{"merge", 1, 0, 'm'},
{"rename", 1, 0, 'r'},
{"tree-only", 0, 0, 't'},
{"no-branchlen", 0, 0, 'N'},
{"dissect", 0, 0, 'd'},
{"name-ancestors", 0, 0, 'a'},
{"reroot", 1, 0, 'R'},
{"with-branch", 1, 0, 'B'},
{"subtree", 1, 0, 'S'},
{"branchlen", 0, 0, 'b'},
{"newick", 0, 0, 'n'},
{"label-subtree", 1, 0, 'L'},
{"label-branches", 1, 0, 'l'},
{"help", 0, 0, 'h'},
{0, 0, 0, 0}
};
while ((c = getopt_long(argc, argv, "s:p:P:g:m:r:R:B:S:D:l:L:adtNbnh",
long_opts, &opt_idx)) != -1) {
switch (c) {
case 's':
scale_factor = get_arg_dbl_bounds(optarg, 0, INFTY);
break;
case 'e':
if (!strcmp(optarg, "default")) {
optarg = smalloc(1000 * sizeof(char));
#if defined(__MINGW32__)
sprintf(optarg, "%s\\data\\exoniphy\\mammals\\cftr25_hybrid.nh",
PHAST_HOME);
#else
sprintf(optarg, "%s/data/exoniphy/mammals/cftr25_hybrid.nh",
PHAST_HOME);
#endif
}
extrapolate_tree = tr_new_from_file(phast_fopen(optarg, "r"));
break;
case 'p':
prune_names = get_arg_list(optarg);
break;
case 'P':
prune_names = get_arg_list(optarg);
prune_all_but = TRUE;
break;
case 'g':
get_subtree_name = optarg;
break;
case 'm':
suffix = str_new_charstr(optarg);
str_suffix(suffix, '.');
if (str_equals_charstr(suffix, "nh"))
merge_tree = tr_new_from_file(phast_fopen(optarg, "r"));
else {
merge_mod = tm_new_from_file(phast_fopen(optarg, "r"), 1);
merge_tree = merge_mod->tree;
}
break;
case 'r':
rename_hash = make_name_hash(optarg);
break;
case 't':
tree_only = TRUE;
break;
case 'N':
no_branchlen = TRUE;
tree_only = TRUE;
break;
case 'd':
dissect = TRUE;
break;
case 'b':
print_branchlen = TRUE;
break;
case 'D':
print_distance_to_root = TRUE;
node_distance_name = optarg;
break;
case 'R':
reroot_name = optarg;
break;
case 'B':
with_branch = TRUE;
break;
case 'a':
name_ancestors = TRUE;
break;
case 'S':
subtree_name = optarg;
break;
case 'n':
inNewick=TRUE;
break;
case 'L': //do the same for --label--subtree and --label-branches
case 'l':
if (label == NULL) {
label = lst_new_ptr(1);
labelType = lst_new_int(1);
}
optstr = str_new_charstr(optarg);
lst_push_ptr(label, optstr);
lst_push_int(labelType, (int)c);
break;
case 'h':
usage(argv[0]);
case '?':
die("Bad argument. Try '%s -h'.\n", argv[0]);
}
}
if (optind != argc - 1)
die("Input filename required. Try '%s -h'.\n", argv[0]);
if (merge_tree != NULL && extrapolate_tree != NULL)
die("ERROR: Can't use --merge and --extrapolate together");
set_seed(-1);
suffix = str_new_charstr(argv[optind]);
str_suffix(suffix, '.');
if (inNewick || str_equals_charstr(suffix, "nh")) {
tree = tr_new_from_file(phast_fopen(argv[optind], "r"));
tree_only = TRUE; /* can't output tree model in this case */
}
else {
mod = tm_new_from_file(phast_fopen(argv[optind], "r"), 1);
tree = mod->tree;
}
if (prune_names != NULL) {
tr_prune(&tree, prune_names, prune_all_but, NULL);
if (mod != NULL) mod->tree = tree; /* root may have changed */
}
if (get_subtree_name != NULL) {
n = tr_get_node(tree, get_subtree_name);
if (n == NULL) {
tr_name_ancestors(tree);
n = tr_get_node(tree, get_subtree_name);
if (n == NULL) {
die("ERROR: no node named '%s'.\n", subtree_name);
}
}
tr_prune_supertree(&tree, n);
if (mod != NULL) mod->tree = tree;
}
if (merge_tree != NULL) {
tree = tr_hybrid(tree, merge_tree);
if (mod != NULL) mod->tree = tree;
}
else if (extrapolate_tree != NULL) {
tr_scale_by_subtree(extrapolate_tree, tree);
tree = extrapolate_tree;
if (mod != NULL) mod->tree = tree;
}
if (scale_factor != 1) {
if (subtree_name == NULL)
tr_scale(tree, scale_factor);
else {
n = tr_get_node(tree, subtree_name);
if (n == NULL) die("ERROR: no node named '%s'.\n", subtree_name);
tr_scale_subtree(tree, n, scale_factor, with_branch);
}
}
if (name_ancestors)
tr_name_ancestors(tree);
if (rename_hash != NULL) {
char *newname;
for (i = 0; i < tree->nnodes; i++) {
n = lst_get_ptr(tree->nodes, i);
if (n->name != NULL && n->name[0] != '\0' &&
(newname = hsh_get(rename_hash, n->name)) != (char*)-1) {
strcpy(n->name, newname);
}
}
}
if (reroot_name != NULL) {
n = tr_get_node(tree, reroot_name);
if (n == NULL) die("ERROR: no node named '%s'.\n", reroot_name);
tr_reroot(tree, n, with_branch);
if (mod != NULL) mod->tree = with_branch ? n->parent : n;
tree = with_branch ? n->parent : n;
}
if (label != NULL) {
for (i=0; i < lst_size(label); i++) {
String *currstr = (String*)lst_get_ptr(label, i), *arg1, *labelVal;
List *tmplst = lst_new_ptr(10);
String *nodename;
int j;
str_split(currstr, ":", tmplst);
if (lst_size(tmplst) != 2)
die("ERROR: bad argument to --label-branches or --label-subtree.\n");
arg1 = lst_get_ptr(tmplst, 0);
labelVal = lst_get_ptr(tmplst, 1);
lst_clear(tmplst);
if (lst_get_int(labelType, i) == (int)'l') {
str_split(arg1, ",", tmplst);
for (j=0; j < lst_size(tmplst); j++) {
nodename = (String*)lst_get_ptr(tmplst, j);
tr_label_node(tree, nodename->chars, labelVal->chars);
}
lst_free_strings(tmplst);
} else if (lst_get_int(labelType, i) == (int)'L') {
int include_leading_branch = FALSE;
TreeNode *node;
nodename = arg1;
node = tr_get_node(tree, nodename->chars);
if (node == NULL && nodename->chars[nodename->length-1] == '+') {
nodename->chars[--nodename->length] = '\0';
node = tr_get_node(tree, nodename->chars);
include_leading_branch = TRUE;
}
tr_label_subtree(tree, nodename->chars, include_leading_branch,
labelVal->chars);
} else die("ERROR got label_type %c\n", lst_get_int(labelType, (char)i));
str_free(arg1);
str_free(labelVal);
lst_free(tmplst);
str_free(currstr);
}
lst_free(label);
lst_free(labelType);
}
if (dissect)
tr_print_nodes(stdout, tree);
if (print_branchlen)
printf("TOTAL_TREE_LEN: %f\n", tr_total_len(tree));
if (print_distance_to_root) {
TreeNode *node = tr_get_node(tree, node_distance_name);
if (node == NULL)
die("ERROR: no node named '%s'.\n", node_distance_name);
printf("length(root-%s): %f\n", node_distance_name,
tr_distance_to_root(node));
}
if (dissect==0 && print_branchlen==0 && print_distance_to_root==0) {
if (tree_only)
tr_print(stdout, tree, no_branchlen==FALSE);
else
tm_print(stdout, mod);
}
return 0;
}