Checkin: various small changes

3 files changed, 21 insertions, 26 deletions

diff --git a/sys/libbio/fasta.c b/sys/libbio/fasta.c
index 0c47199..2feb0a4 100644
--- a/sys/libbio/fasta.c
+++ b/sys/libbio/fasta.c
@@ -176,7 +176,7 @@ bio·closeseq(bio·SeqReader *rdr)
 
     mem  = rdr->seq->mem;
     heap = rdr->seq->heap; 
-    
+
     mem.free(heap, rdr->seq);
     mem.free(heap, rdr);
 
@@ -191,7 +191,7 @@ readfasta(bio·SeqReader *rdr, bio·Seq *seq, byte hdr, byte stop)
     error  err;
     byte  *beg;
 
-    if (rdr->eof && rdr->b == rdr->bend-1)
+    if(rdr->eof && rdr->b == rdr->bend-1)
         return EOF;
 
     reset(rdr->seq);
diff --git a/sys/libbio/newick.c b/sys/libbio/newick.c
index 98d30f2..631596f 100644
--- a/sys/libbio/newick.c
+++ b/sys/libbio/newick.c
@@ -167,10 +167,10 @@ struct Parser
     bio·Node    *root;
     struct Token tok;
 
-    void         *fimpl;
+    void         *io;
     io·Peeker     file;
-    void         *himpl;
-    mem·Allocator heap;
+    void         *heap;
+    mem·Allocator mem;
 };
 
 static
@@ -184,7 +184,7 @@ parse(struct Parser *p)
 
     node = p->root;
     for (;;) {
-        tok = lex_nospace(p->file, p->fimpl);
+        tok = lex_nospace(p->file, p->io);
 
         switch (tok.kind) {
         case tok·lparen:
@@ -193,7 +193,7 @@ parse(struct Parser *p)
                 goto ERROR;
             }
 
-            node = p->heap.alloc(p->himpl, 1, sizeof(*node));
+            node = p->mem.alloc(p->heap, 1, sizeof(*node));
             memset(node, 0, sizeof(*node));
 
             if (p->root) {
@@ -231,7 +231,7 @@ parse(struct Parser *p)
             }
             node->comment = str·make("");
             while (tok.kind != tok·rbrak) {
-                tok = lex_nospace(p->file, p->fimpl);
+                tok = lex_nospace(p->file, p->io);
                 if (tok.kind == tok·eof || tok.kind == tok·nil) {
                     errorf("incorrect format: unmatched comment bracket '['");
                     goto ERROR;
@@ -246,7 +246,7 @@ parse(struct Parser *p)
         break;
 
         case tok·colon:
-            tok = lex_nospace(p->file, p->fimpl);
+            tok = lex_nospace(p->file, p->io);
             if (tok.kind != tok·number) {
                 errorf("incorrect format: expected number after colon");
                 goto ERROR;
@@ -280,7 +280,7 @@ parse(struct Parser *p)
                     goto ERROR;
                 }
 
-                node = p->heap.alloc(p->himpl, 1, sizeof(*node));
+                node = p->mem.alloc(p->heap, 1, sizeof(*node));
                 memset(node, 0, sizeof(*node));
 
                 node->name = str·make(tok.lit.s);
@@ -303,7 +303,7 @@ parse(struct Parser *p)
         break;
 
         case tok·semi:
-            p->file.unget(p->fimpl, ';');
+            p->file.unget(p->io, ';');
             if (p->lev) {
                 errorf("format error: uneven number of parentheses found at ';'");
                 goto ERROR;
@@ -329,35 +329,30 @@ ERROR:
     return 1;
 }
 
-error
+int
 bio·readnewick(io·Peeker stream, void *s, bio·Tree *tree)
 {
     error err;
     struct Parser p;
-    enum 
-    {
-        error·nil,
-        error·notree,
-        error·parse,
-    };
 
     if (!tree) {
-        return error·notree;
+        errorf("tree pointer nil");
+        return 0;
     }
 
     p = (struct Parser){ 
         .lev   = 0,
         .root  = nil,
         .tok   = (struct Token){ 0 },
-        .fimpl = s,
+        .io    = s,
         .file  = stream,
-        .himpl = tree->h,
+        .mem   = tree->mem,
         .heap  = tree->heap,
     };
     err = parse(&p);
     if (err) {
         errorf("parsing failed\n");
-        return error·parse;
+        return 0;
     }
 
     tree->root  = p.root;
@@ -367,7 +362,7 @@ bio·readnewick(io·Peeker stream, void *s, bio·Tree *tree)
     phylo·countleafs(tree->root, &tree->nleaf);
     phylo·countnodes(tree->root, &tree->root->nnode);
 
-    return error·nil;
+    return 1;
 }
 
 // -----------------------------------------------------------------------
diff --git a/sys/libbio/phylo.c b/sys/libbio/phylo.c
index 920102b..cb5c75c 100644
--- a/sys/libbio/phylo.c
+++ b/sys/libbio/phylo.c
@@ -84,7 +84,7 @@ phylo·countleafs(bio·Node *node, int *n)
 {
     error     err;
     bio·Node *child;
-    
+
     if (!node->nchild) {
         *n += 1;
     }
@@ -392,7 +392,7 @@ 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) {
         new = node;
         rotateparent(node->parent, node);
@@ -402,7 +402,7 @@ phylo·reroot(bio·Tree *tree, bio·Node *node, double d)
             rotateparent(new->parent->parent, new->parent);
         }
     } else {
-        new = tree->heap.alloc(tree->h, 1, sizeof(*new));
+        new = tree->mem.alloc(tree->heap, 1, sizeof(*new));
         memset(new, 0, sizeof(*new));
 
         phylo·addchild(new, node);