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print tree in the Newick format

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This commit is contained in:
Heng Li 2012-12-18 20:18:20 -05:00
parent a98af4643f
commit 7cc91909a9
2 changed files with 80 additions and 2 deletions
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63
knhx.c
View File

@ -91,17 +91,76 @@ knhx1_t *kn_parse(const char *nhx, int *_n, int *_error)
return ret;
}
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif
static inline int kputsn(const char *p, int l, kstring_t *s)
{
if (s->l + l + 1 >= s->m) {
s->m = s->l + l + 2;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
}
memcpy(s->s + s->l, p, l);
s->l += l; s->s[s->l] = 0;
return l;
}
static inline int kputc(int c, kstring_t *s)
{
if (s->l + 1 >= s->m) {
s->m = s->l + 2;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
}
s->s[s->l++] = c; s->s[s->l] = 0;
return c;
}
static void format_node_recur(const knhx1_t *node, const knhx1_t *p, kstring_t *s, char *numbuf)
{
if (p->n) {
int i;
kputc('(', s);
for (i = 0; i < p->n; ++i) {
if (i) kputc(',', s);
format_node_recur(node, &node[p->child[i]], s, numbuf);
}
kputc(')', s);
if (p->name) kputsn(p->name, strlen(p->name), s);
if (p->d >= 0) {
sprintf(numbuf, ":%g", p->d);
kputsn(numbuf, strlen(numbuf), s);
}
} else kputsn(p->name, strlen(p->name), s);
}
void kn_format(const knhx1_t *node, int root, kstring_t *s) // TODO: get rid of recursion
{
char numbuf[128];
format_node_recur(node, &node[root], s, numbuf);
}
#ifdef KNHX_MAIN
int main(int argc, char *argv[])
{
char *s = "((a[abc],d1)x:0.5,((b[&&NHX:S=MOUSE],h2)[&&NHX:S=HUMAN:B=99][blabla][&&NHX:K=foo],c))";
knhx1_t *node;
int i, n, error;
int i, j, n, error;
kstring_t str;
node = kn_parse(s, &n, &error);
for (i = 0; i < n; ++i) {
knhx1_t *p = node + i;
printf("%s[%d]: %d,%d,%lg\n", p->name, i, p->parent, p->n, p->d);
printf("[%d] %s\t%d\t%d\t%g", i, p->name, p->parent, p->n, p->d);
for (j = 0; j < p->n; ++j)
printf("\t%d", p->child[j]);
putchar('\n');
}
str.l = str.m = 0; str.s = 0;
kn_format(node, n-1, &str);
puts(str.s);
free(str.s);
return 0;
}
#endif

19
knhx.h
View File

@ -13,4 +13,23 @@ typedef struct {
double d;
} knhx1_t;
#ifndef KSTRING_T
#define KSTRING_T kstring_t
typedef struct __kstring_t {
size_t l, m;
char *s;
} kstring_t;
#endif
#ifdef __cplusplus
extern "C" {
#endif
knhx1_t *kn_parse(const char *nhx, int *_n, int *_error);
void kn_format(const knhx1_t *node, int root, kstring_t *s);
#ifdef __cplusplus
}
#endif
#endif