fix: bug squashing with newick parser

7 files changed, 115 insertions, 166 deletions

diff --git a/compile_commands.json b/compile_commands.json
index 99168be..aa79c9d 100644
--- a/compile_commands.json
+++ b/compile_commands.json
@@ -7,146 +7,12 @@
             "-fno-strict-aliasing",
             "-fwrapv",
             "-fms-extensions",
-            "-ffreestanding",
-            "-fno-builtin",
-            "-nostdlib",
             "-Iinclude",
             "-o",
-            "build/libc/string.o",
-            "sys/libc/string.c"
+            "build/libbio/io/newick.o",
+            "sys/libbio/io/newick.c"
         ],
         "directory": "/home/nolln/root",
-        "file": "sys/libc/string.c"
-    },
-    {
-        "arguments": [
-            "clang",
-            "-c",
-            "-g",
-            "-fno-strict-aliasing",
-            "-fwrapv",
-            "-fms-extensions",
-            "-Iinclude",
-            "-o",
-            "build/libn/test.o",
-            "sys/libn/test.c"
-        ],
-        "directory": "/home/nolln/root",
-        "file": "sys/libn/test.c"
-    },
-    {
-        "arguments": [
-            "clang",
-            "-c",
-            "-g",
-            "-fno-strict-aliasing",
-            "-fwrapv",
-            "-fms-extensions",
-            "-ffreestanding",
-            "-fno-builtin",
-            "-nostdlib",
-            "-Iinclude",
-            "-o",
-            "build/libc/stdio.o",
-            "sys/libc/stdio.c"
-        ],
-        "directory": "/home/nolln/root",
-        "file": "sys/libc/stdio.c"
-    },
-    {
-        "arguments": [
-            "clang",
-            "-c",
-            "-g",
-            "-fno-strict-aliasing",
-            "-fwrapv",
-            "-fms-extensions",
-            "-Iinclude",
-            "-o",
-            "build/libn/error.o",
-            "sys/libn/error.c"
-        ],
-        "directory": "/home/nolln/root",
-        "file": "sys/libn/error.c"
-    },
-    {
-        "arguments": [
-            "clang",
-            "-c",
-            "-g",
-            "-fno-strict-aliasing",
-            "-fwrapv",
-            "-fms-extensions",
-            "-Iinclude",
-            "-o",
-            "build/libn/bufio.o",
-            "sys/libn/bufio.c"
-        ],
-        "directory": "/home/nolln/root",
-        "file": "sys/libn/bufio.c"
-    },
-    {
-        "arguments": [
-            "clang",
-            "-c",
-            "-g",
-            "-fno-strict-aliasing",
-            "-fwrapv",
-            "-fms-extensions",
-            "-Iinclude",
-            "-o",
-            "build/libn/memory.o",
-            "sys/libn/memory.c"
-        ],
-        "directory": "/home/nolln/root",
-        "file": "sys/libn/memory.c"
-    },
-    {
-        "arguments": [
-            "clang",
-            "-c",
-            "-g",
-            "-fno-strict-aliasing",
-            "-fwrapv",
-            "-fms-extensions",
-            "-Iinclude",
-            "-o",
-            "build/libn/io.o",
-            "sys/libn/io.c"
-        ],
-        "directory": "/home/nolln/root",
-        "file": "sys/libn/io.c"
-    },
-    {
-        "arguments": [
-            "clang",
-            "-c",
-            "-g",
-            "-fno-strict-aliasing",
-            "-fwrapv",
-            "-fms-extensions",
-            "-Iinclude",
-            "-o",
-            "build/libn/coro.o",
-            "sys/libn/coro.c"
-        ],
-        "directory": "/home/nolln/root",
-        "file": "sys/libn/coro.c"
-    },
-    {
-        "arguments": [
-            "clang",
-            "-c",
-            "-g",
-            "-fno-strict-aliasing",
-            "-fwrapv",
-            "-fms-extensions",
-            "-Iinclude",
-            "-o",
-            "build/libn/string.o",
-            "sys/libn/string.c"
-        ],
-        "directory": "/home/nolln/root",
-        "file": "sys/libn/string.c"
+        "file": "sys/libbio/io/newick.c"
     }
 ]
\ No newline at end of file
diff --git a/include/libbio.h b/include/libbio.h
index d8430b3..58540d4 100644
--- a/include/libbio.h
+++ b/include/libbio.h
@@ -16,7 +16,8 @@ typedef struct bio·Node
     struct bio·Node *sibling;
 } bio·Node;
 
-error phylo·addchild(bio·Node* parent, bio·Node* child);
+error phylo·addchild(bio·Node *parent, bio·Node* child);
+bool  phylo·isleaf(bio·Node *node);
 
 typedef struct bio·Tree
 {
@@ -24,6 +25,7 @@ typedef struct bio·Tree
 } bio·Tree;
 
 bio·Tree bio·readnewick(Stream *file, mem·Allocator heap);
+error    bio·writenewick(bio·Tree tree, Stream *out);
 
 // -----------------------------------------------------------------------
 // Sequences
diff --git a/include/libn.h b/include/libn.h
index 203a477..c8d510f 100644
--- a/include/libn.h
+++ b/include/libn.h
@@ -104,6 +104,7 @@ int     io·readln(Stream *s, int n, byte* buf);
 error   io·putbyte(Stream *s, byte c);
 int     io·putstring(Stream *s, string str);
 vlong   io·write(Stream *s, int sz, int n, void *buf);
+int     io·flush(Stream *s);
 int     io·seek(Stream *s, long off, enum SeekPos origin);
 
 // -----------------------------------------------------------------------------
diff --git a/sys/libbio/io/newick.c b/sys/libbio/io/newick.c
index b81e1bd..5bd2d9a 100644
--- a/sys/libbio/io/newick.c
+++ b/sys/libbio/io/newick.c
@@ -33,6 +33,7 @@ struct Token {
     } lit;
 };
 
+static
 byte*
 tokstr(struct Token tok)
 {
@@ -62,6 +63,7 @@ tokstr(struct Token tok)
 // Read
 
 // TODO: Bounds checking on buffer
+static
 struct Token
 lex(Stream *s)
 {
@@ -125,13 +127,14 @@ lex(Stream *s)
     }
 }
 
+static
 struct Token
 lex_nospace(Stream *s)
 {
     struct Token tok;
     tok = lex(s);
     if (tok.kind == tok·space) {
-        lex_nospace(s);
+        tok = lex_nospace(s);
     }
 
     return tok;
@@ -147,6 +150,7 @@ struct Parser
     mem·Allocator heap;
 };
 
+static
 error
 parse(struct Parser *p)
 {
@@ -155,17 +159,20 @@ parse(struct Parser *p)
     bio·Node *root;
     struct Token tok;
 
+    node = p->root;
     for (;;) {
         tok = lex_nospace(p->file);
 
         switch (tok.kind) {
         case tok·lparen:
-            if (p->lev > 0) {
-                errorf("incorrect format: opening another node before termination of last tree\n");
+            if (!p->root && p->lev > 0) {
+                errorf("parse format: attempted to make root at non-zero level");
                 goto ERROR;
             }
+
             node = p->heap.alloc(sizeof(*node));
             memset(node, 0, sizeof(*node));
+
             if (p->root) {
                 phylo·addchild(p->root, node);
                 root = p->root;
@@ -174,12 +181,14 @@ parse(struct Parser *p)
             }
 
             p->lev++;
-            err = parse(p);
+            p->root = node;
+            p->tok  = tok;
+            err     = parse(p);
             if (err) {
                 goto ERROR;
             }
             if (p->tok.kind != tok·rparen) {
-                errorf("incorrect format: closing parentheses expected to proceed opening\n");
+                errorf("incorrect format: closing parentheses expected to proceed opening");
                 goto ERROR;
             }
             p->root = root;
@@ -193,14 +202,14 @@ parse(struct Parser *p)
         /* Comments */
         case tok·lbrak:
             if (!node) {
-                errorf("incorrect format: comment found in disallowed region\n");
+                errorf("incorrect format: comment found in disallowed region");
                 goto ERROR;
             }
             node->comment = str·new("");
             while (tok.kind != tok·rbrak) {
                 tok = lex_nospace(p->file);
                 if (tok.kind == tok·eof || tok.kind == tok·nil) {
-                    errorf("incorrect format: unmatched comment bracket '['\n");
+                    errorf("incorrect format: unmatched comment bracket '['");
                     goto ERROR;
                 }
                 str·append(node->comment, tokstr(tok));
@@ -208,18 +217,18 @@ parse(struct Parser *p)
         break;
 
         case tok·rbrak:
-           errorf("incorrect format: end comment token found in disallowed region\n");
+           errorf("incorrect format: end comment token found in disallowed region");
            goto ERROR;
         break;
 
         case tok·colon:
             tok = lex_nospace(p->file);
             if (tok.kind != tok·number) {
-                errorf("incorrect format: expected number after colon\n");
+                errorf("incorrect format: expected number after colon");
                 goto ERROR;
             }
             if (node == nil) {
-                errorf("parse error: attempting to set distance of nil node\n");
+                errorf("parse error: attempting to set distance of nil node");
                 goto ERROR;
             }
             node->dist = tok.lit.x;
@@ -230,23 +239,28 @@ parse(struct Parser *p)
         break;
 
         case tok·ident:
-            if (p->tok.kind != tok·rparen) {
+            if (p->tok.kind == tok·rparen) {
                 if (!node) {
-                    errorf("parse error: attempting to set name of nil node\n");
+                    errorf("parse error: attempting to set name of nil node");
                     goto ERROR;
                 }
                 node->name = str·new(tok.lit.s);
+                printf("settting name %s\n", node->name);
             } else {
-                if (p->tok.kind != tok·comma) {
-                    errorf("format error: misplaced identifier found\n");
+                if (p->tok.kind != tok·lparen && p->tok.kind != tok·comma) {
+                    errorf("format error: misplaced identifier for leaf found");
                     goto ERROR;
                 }
-                if (!node) {
-                    errorf("parse error: attempting to create child for no parent\n");
+
+                if (!p->root) {
+                    errorf("parse error: attempting to create child for no parent");
                     goto ERROR;
                 }
+
                 node = p->heap.alloc(sizeof(*node));
                 memset(node, 0, sizeof(*node));
+                node->name = str·new(tok.lit.s);
+
                 phylo·addchild(p->root, node);
             }
         break;
@@ -254,12 +268,12 @@ parse(struct Parser *p)
         case tok·number:
             if (p->tok.kind == tok·rparen) {
                 if (p->lev == 0) {
-                    errorf("format error: support value on root not supported\n");
+                    errorf("format error: support value on root not supported");
                     goto ERROR;
                 }
                 node->support = tok.lit.x;
             } else {
-                errorf("format error: found number in unexpected location\n");
+                errorf("format error: found number in unexpected location");
                 goto ERROR;
             }
         break;
@@ -267,23 +281,22 @@ parse(struct Parser *p)
         case tok·semi:
             io·ungetbyte(p->file, ';');
             if (p->lev) {
-                errorf("format error: uneven number of parentheses found at ';'\n");
+                errorf("format error: uneven number of parentheses found at ';'");
+                goto ERROR;
             }
             goto DONE;
-        break;
 
         case tok·eof:
             goto DONE;
-        break;
 
         default: 
+            errorf("parse error: unrecognized token");
             goto ERROR;
         }
 
         p->tok = tok;
     }
 
-
 DONE:
     p->tok = tok;
     return 0;
@@ -299,6 +312,13 @@ bio·readnewick(Stream *file, mem·Allocator heap)
     struct Parser p;
     bio·Tree tree;
 
+    p = (struct Parser){ 
+        .lev  = 0,
+        .root = nil,
+        .tok  = (struct Token){ 0 },
+        .file = file,
+        .heap = heap,
+    };
     err = parse(&p);
     if (err) {
         errorf("parsing failed\n");
@@ -311,3 +331,45 @@ bio·readnewick(Stream *file, mem·Allocator heap)
 
 // -----------------------------------------------------------------------
 // Write
+
+error
+dump(bio·Node *node, Stream *out)
+{
+    if (!node) {
+        return 1;
+    }
+    bio·Node *child;
+    if (node->nchild) {
+        io·putbyte(out, '(');
+
+        dump(node->child[0], out);
+        for (child = node->child[1]; child != nil; child = child->sibling) {
+            io·putbyte(out, ',');
+            dump(child, out);
+        }
+
+        io·putbyte(out, ')');
+    }
+    if (node->name) {
+        io·putstring(out, node->name);
+    }
+
+    if (node->parent) {
+        io·putbyte(out, ':');
+        // TODO(nnoll): Format float
+        io·putbyte(out, '0');
+    }
+
+    return 0;
+}
+
+error
+bio·writenewick(bio·Tree tree, Stream *out)
+{
+    dump(tree.root, out);
+    io·putbyte(out, ';');
+    io·putbyte(out, '\n');
+    io·flush(out);
+
+    return 0;
+}
diff --git a/sys/libbio/phylo.c b/sys/libbio/phylo.c
index 8033e35..374cd08 100644
--- a/sys/libbio/phylo.c
+++ b/sys/libbio/phylo.c
@@ -6,9 +6,15 @@ error
 phylo·addchild(bio·Node* parent, bio·Node* child)
 {
     bio·Node *it, *sibling;
-    if (parent->nchild < 2) {
+    switch (parent->nchild) {
+    case 1:
+        parent->child[0]->sibling = child;
+    case 0:
         parent->child[parent->nchild++] = child;
-    } else {
+    break;
+
+    default:
+        sibling = parent->child[1];
         for (it = parent->child[1]->sibling; it != nil; it = it->sibling) {
             sibling = it;
         }
@@ -16,5 +22,6 @@ phylo·addchild(bio·Node* parent, bio·Node* child)
         parent->nchild++;
     }
 
+    child->parent = parent;
     return 0;
 }
diff --git a/sys/libbio/test.c b/sys/libbio/test.c
index 00345c4..18bb993 100644
--- a/sys/libbio/test.c
+++ b/sys/libbio/test.c
@@ -47,14 +47,19 @@ main()
 {
     init();
 
+    error err;
     bio·Tree t;
-    Stream   *fd;
+    Stream   *fd[2];
+
+    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");
 
-    fd = io·open("/home/nolln/root/data/test/example.nwk", "r");
     printf("starting\n");
-    t  = bio·readnewick(fd, arena);
-    io·close(fd);
+    t   = bio·readnewick(fd[0], arena);
+    err = bio·writenewick(t, fd[1]);
     printf("ending\n");
+
+    io·close(fd[0]); io·close(fd[1]);
     return 0;
 }
 
diff --git a/sys/libn/io.c b/sys/libn/io.c
index 922dec3..7eec74e 100644
--- a/sys/libn/io.c
+++ b/sys/libn/io.c
@@ -67,6 +67,12 @@ io·write(Stream *s, int sz, int n, void *buf)
     return fwrite(buf, sz, n, s);
 }
 
+int
+io·flush(Stream *s)
+{
+    return fflush(s);
+}
+
 // -----------------------------------------------------------------------
 // Seek