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print tree in the Newick format

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commit 7cc91909a9a2ecd4eb0c472417327d37241d6529 1 parent a98af46
@lh3 lh3 authored
Showing with 80 additions and 2 deletions.
  1. +61 −2 knhx.c
  2. +19 −0 knhx.h
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63 knhx.c
@@ -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
View
19 knhx.h
@@ -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
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