From b48327d357e0818d1a6ae2a064cfa7d1567e1242 Mon Sep 17 00:00:00 2001
From: Nicholas Noll <nbnoll@eml.cc>
Date: Sun, 5 Dec 2021 15:17:44 -0800
Subject: feat(huge): huge refactor (in progress).

Commented out libc includes to uncover all explicit dependencies.
A large fraction has now been ported over (no testing).
I did not port over the command line tools, such as the rc shell.
These will be done independently - as of now I just want the library to
stand independent.

Compilation currently fails due to the lack of math functions.
---
 src/libbio/fasta.c  |  9 ++++-----
 src/libbio/newick.c | 16 ++++++++--------
 src/libbio/phylo.c  | 14 +++++++-------
 3 files changed, 19 insertions(+), 20 deletions(-)

(limited to 'src/libbio')

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;
 
-- 
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