diff options
Diffstat (limited to 'src/libbio')
| -rw-r--r-- | src/libbio/fasta.c | 9 | ||||
| -rw-r--r-- | src/libbio/newick.c | 16 | ||||
| -rw-r--r-- | src/libbio/phylo.c | 14 |
3 files changed, 19 insertions, 20 deletions
diff --git a/src/libbio/fasta.c b/src/libbio/fasta.c index eb0d090..e6f0dd3 100644 --- a/src/libbio/fasta.c +++ b/src/libbio/fasta.c @@ -45,7 +45,7 @@ grow(struct SeqBuf **sb, int min) return 1; } - memcpy(new, old, sizeof(*new) + (*sb)->cap); + mem·copy(new, sizeof(*new) + (*sb)->cap, old); new->cap = newcap; new->it = new->b + (old->it - old->b); @@ -96,7 +96,7 @@ push(struct SeqBuf **sb, int n, void *buf) } seq = *sb; - memcpy(seq->it, buf, n); + mem·copy(seq->it, n, buf); seq->it += n; return 0; @@ -184,8 +184,7 @@ bio·closeseq(bio·SeqReader *rdr) } -static -int +static int readfasta(bio·SeqReader *rdr, bio·Seq *seq, byte hdr, byte stop) { int err; @@ -375,7 +374,7 @@ bio·writefasta(io·Writer io, void *wtr, bio·Seq seq) b = buf; } *b++ = '\n'; - memcpy(b, seq.s+i, d); + mem·copy(b, d, seq.s+i); b += d; } diff --git a/src/libbio/newick.c b/src/libbio/newick.c index a855cea..a555379 100644 --- a/src/libbio/newick.c +++ b/src/libbio/newick.c @@ -50,8 +50,8 @@ tokstr(struct Token tok) case tok·comma: return ","; case tok·semi: return ";"; case tok·colon: return ":"; - case tok·number: - snprintf(b, arrlen(b), "%f", tok.lit.x); + case tok·number: + fmt·nsprint(b, arrlen(b), "%f", tok.lit.x); return b; default: return nil; @@ -80,8 +80,8 @@ lex(io·Peeker s, void* fp) c = b; *c = s.get(fp); - if (isspace(*c)) { - while (isspace(*c)) { + if(utf8·isspace(*c)){ + while(utf8·isspace(*c)){ *(++c) = s.get(fp); } @@ -107,7 +107,7 @@ lex(io·Peeker s, void* fp) case '.': case '0': case '1': case '2': case '3': case '4': case '5': case '6': case '7': case '8': case '9': - while (isdigit(*c)) { + while(utf8·isdigit(*c)){ NUM: *(++c) = s.get(fp); } if (*c == '.') goto NUM; @@ -194,7 +194,7 @@ parse(struct Parser *p) } node = p->mem.alloc(p->heap, 1, sizeof(*node)); - memset(node, 0, sizeof(*node)); + mem·set(node, sizeof(*node), 0); if (p->root) { phylo·addchild(p->root, node); @@ -281,7 +281,7 @@ parse(struct Parser *p) } node = p->mem.alloc(p->heap, 1, sizeof(*node)); - memset(node, 0, sizeof(*node)); + mem·set(node, sizeof(*node), 0); node->name = string·make(tok.lit.s); @@ -396,7 +396,7 @@ dump(bio·Node *node, void *impl, io·Putter out) if (node->parent) { out.put(impl, ':'); - snprintf(b, arrlen(b), "%f", node->dist); + fmt·nsprint(b, arrlen(b), "%f", node->dist); out.puts(impl, b); } diff --git a/src/libbio/phylo.c b/src/libbio/phylo.c index 41b0f04..1b0ae59 100644 --- a/src/libbio/phylo.c +++ b/src/libbio/phylo.c @@ -328,11 +328,11 @@ phylo·diameter(bio·Tree tree, int *len, bio·Node **path) sort·nodedists(n, fbuf, nbuf); path[0] = nbuf[n-1]; - printf("first end '%s'\n", path[0]->name); + fmt·print("first end '%s'\n", path[0]->name); n = phylo·getdistsfrom(path[0], n, fbuf, nbuf); sort·nodedists(n, fbuf, nbuf); - printf("second end '%s'\n", nbuf[n-1]->name); + fmt·print("second end '%s'\n", nbuf[n-1]->name); *len = 0; @@ -393,17 +393,17 @@ phylo·reroot(bio·Tree *tree, bio·Node *node, double d) // TODO: should check that node is part of this tree? // TODO: should we check if node->parent != nil? - if (fabs(d) < PREC) { + if(fabs(d) < PREC){ new = node; rotateparent(node->parent, node); - } else if (fabs(d-node->dist) < PREC) { + }else if(fabs(d-node->dist) < PREC){ new = node->parent; if (new->parent->parent) { rotateparent(new->parent->parent, new->parent); } - } else { + }else{ new = tree->mem.alloc(tree->heap, 1, sizeof(*new)); - memset(new, 0, sizeof(*new)); + mem·set(new, sizeof(*new), 0); phylo·addchild(new, node); node->parent = new; @@ -415,7 +415,7 @@ phylo·reroot(bio·Tree *tree, bio·Node *node, double d) node->parent->parent = new; } - printf("number of children on old root: %d\n", tree->root->nchild); + fmt·print("number of children on old root: %d\n", tree->root->nchild); tree->root = new; tree->nleaf = 0; |