feat: interfaces of newick io more general. can now take arbitrary readers/writers

5 files changed, 75 insertions, 32 deletions

diff --git a/Makefile b/Makefile
index 13e8c14..3b58bea 100644
--- a/Makefile
+++ b/Makefile
@@ -11,7 +11,7 @@ LIB_DIR := lib
 OBJ_DIR := build
 
 # Flags, Libraries and Includes
-CFLAGS := -g -fno-strict-aliasing -fwrapv -fms-extensions
+CFLAGS := -g -fno-strict-aliasing -fwrapv -fms-extensions -Wno-microsoft-anon-tag
 AFLAGS := -f elf64 
 INCS   := -I$(INC_DIR)
 ELIBS  := 
diff --git a/include/libbio.h b/include/libbio.h
index 9f54015..3cdab4e 100644
--- a/include/libbio.h
+++ b/include/libbio.h
@@ -25,16 +25,17 @@ typedef struct bio·Tree
 } bio·Tree;
 
 /* newick i/o */
-bio·Tree bio·readnewick(Stream *file, mem·Allocator heap);
-error    bio·writenewick(bio·Tree tree, Stream *out);
+bio·Tree bio·readnewick(io·Peeker stream, mem·Allocator heap);
+error    bio·writenewick(bio·Tree tree, io·Putter out);
 
 // -----------------------------------------------------------------------
 // Sequences
 
+#if 0
 typedef struct bio·FastaReader bio·FastaReader;
 
 /* fasta/q i/o */
 bio·Seq *bio·newfastareader(Stream *file, mem·Allocator heap);
 bio·Seq *bio·readfasta(bio·FastaParser *p);
 error    bio·writefasta(bio·Seq *seq, Stream *out);
-
+#endif
diff --git a/include/libn.h b/include/libn.h
index 67d131d..d2479e4 100644
--- a/include/libn.h
+++ b/include/libn.h
@@ -112,13 +112,13 @@ int     io·seek(Stream *s, long off, enum SeekPos origin);
 typedef struct io·Reader
 {
     int (*read)(int n, void *buf);
-};
+} io·Reader;
 
 typedef struct io·Peeker
 {
     byte  (*get)(void);
     error (*unget)(byte);
-};
+} io·Peeker;
 
 typedef struct io·FullReader
 {
diff --git a/sys/libbio/io/newick.c b/sys/libbio/io/newick.c
index 0004fac..82ea0d7 100644
--- a/sys/libbio/io/newick.c
+++ b/sys/libbio/io/newick.c
@@ -65,20 +65,20 @@ tokstr(struct Token tok)
 // TODO: Bounds checking on buffer
 static
 struct Token
-lex(Stream *s)
+lex(io·Peeker s)
 {
     byte *c;
     struct Token tok;
     static byte b[1024];
     c  = b;
-    *c = io·getbyte(s);
+    *c = s.get();
 
     if (isspace(*c)) {
         while (isspace(*c)) {
-            *(++c) = io·getbyte(s);
+            *(++c) = s.get();
         }
 
-        io·ungetbyte(s, *c);
+        s.unget(*c);
         Assert(c - b < 1024);
 
         *c        = 0;
@@ -101,11 +101,11 @@ lex(Stream *s)
     case '0': case '1': case '2': case '3': case '4':
     case '5': case '6': case '7': case '8': case '9':
         while (isdigit(*c)) {
-    NUM:    *(++c) = io·getbyte(s);
+    NUM:    *(++c) = s.get();
         }
         if (*c == '.') goto NUM;
 
-        io·ungetbyte(s, *c);
+        s.unget(*c);
         Assert(c - b < 1024);
 
         *c        = 0;
@@ -115,10 +115,10 @@ lex(Stream *s)
 
     default:
         while (isalnum(*c)) {
-            *(++c) = io·getbyte(s);
+            *(++c) = s.get();
         }
 
-        io·ungetbyte(s, *c);
+        s.unget(*c);
         Assert(c - b < 1024);
 
         *c        = '\0';
@@ -130,7 +130,7 @@ lex(Stream *s)
 
 static
 struct Token
-lex_nospace(Stream *s)
+lex_nospace(io·Peeker s)
 {
     struct Token tok;
     tok = lex(s);
@@ -147,7 +147,7 @@ struct Parser
     bio·Node    *root;
     struct Token tok;
 
-    Stream       *file;
+    io·Peeker     file;
     mem·Allocator heap;
 };
 
@@ -280,7 +280,7 @@ parse(struct Parser *p)
         break;
 
         case tok·semi:
-            io·ungetbyte(p->file, ';');
+            p->file.unget(';');
             if (p->lev) {
                 errorf("format error: uneven number of parentheses found at ';'");
                 goto ERROR;
@@ -307,7 +307,7 @@ ERROR:
 }
 
 bio·Tree
-bio·readnewick(Stream *file, mem·Allocator heap)
+bio·readnewick(io·Peeker stream, mem·Allocator heap)
 {
     error err;
     struct Parser p;
@@ -317,7 +317,7 @@ bio·readnewick(Stream *file, mem·Allocator heap)
         .lev  = 0,
         .root = nil,
         .tok  = (struct Token){ 0 },
-        .file = file,
+        .file = stream,
         .heap = heap,
     };
     err = parse(&p);
@@ -334,7 +334,7 @@ bio·readnewick(Stream *file, mem·Allocator heap)
 // Write
 
 error
-dump(bio·Node *node, Stream *out)
+dump(bio·Node *node, io·Putter out)
 {
     byte b[24];
 
@@ -343,36 +343,35 @@ dump(bio·Node *node, Stream *out)
     }
     bio·Node *child;
     if (node->nchild) {
-        io·putbyte(out, '(');
+        out.put('(');
 
         dump(node->child[0], out);
         for (child = node->child[1]; child != nil; child = child->sibling) {
-            io·putbyte(out, ',');
+            out.put(',');
             dump(child, out);
         }
 
-        io·putbyte(out, ')');
+        out.put(')');
     }
     if (node->name) {
-        io·putstring(out, node->name);
+        out.putstr(node->name);
     }
 
     if (node->parent) {
-        io·putbyte(out, ':');
+        out.put(':');
         snprintf(b, arrlen(b), "%f", node->dist);
-        io·putstring(out, b);
+        out.putstr(b);
     }
 
     return 0;
 }
 
 error
-bio·writenewick(bio·Tree tree, Stream *out)
+bio·writenewick(bio·Tree tree, io·Putter out)
 {
     dump(tree.root, out);
-    io·putbyte(out, ';');
-    io·putbyte(out, '\n');
-    io·flush(out);
+    out.put(';');
+    out.put('\n');
 
     return 0;
 }
diff --git a/sys/libbio/test.c b/sys/libbio/test.c
index 18bb993..3941290 100644
--- a/sys/libbio/test.c
+++ b/sys/libbio/test.c
@@ -34,6 +34,45 @@ bio·free(void *ptr)
 static mem·Allocator arena = {.alloc = &bio·alloc, .realloc = &bio·realloc, .free = &bio·free };
 
 // -----------------------------------------------------------------------
+// Read/writer
+
+static Stream* INPUT;
+
+static 
+byte
+get()
+{
+    return io·getbyte(INPUT);
+}
+
+static 
+error
+unget(byte c)
+{
+    return io·ungetbyte(INPUT, c);
+}
+
+static io·Peeker peeker = {.get = &get, .unget = &unget};
+
+static Stream* OUTPUT;
+
+static 
+error
+put(byte b)
+{
+    return io·putbyte(OUTPUT, b);
+}
+
+static 
+int
+putstr(string s)
+{
+    return io·putstring(OUTPUT, s);
+}
+
+static io·Putter putter = {.put = &put, .putstr = &putstr};
+
+// -----------------------------------------------------------------------
 // Point of entry for testing
 
 void
@@ -54,11 +93,15 @@ main()
     fd[0] = io·open("/home/nolln/root/data/test/example.nwk", "r");
     fd[1] = io·open("/home/nolln/root/data/test/example.proc.nwk", "w");
 
+    INPUT  = fd[0];
+    OUTPUT = fd[1];
+
     printf("starting\n");
-    t   = bio·readnewick(fd[0], arena);
-    err = bio·writenewick(t, fd[1]);
+    t   = bio·readnewick(peeker, arena);
+    err = bio·writenewick(t, putter);
     printf("ending\n");
 
+    io·flush(fd[1]);
     io·close(fd[0]); io·close(fd[1]);
     return 0;
 }