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#pragma once
// -----------------------------------------------------------------------
// Phylogenetics
typedef struct bio·Node
{
string name, comment;
double dist, support;
int nnode, nchild;
struct bio·Node *parent, *sibling, *child;
void *data;
} bio·Node;
typedef struct bio·Tree
{
bio·Node *root;
int nleaf;
mem·Allocator heap;
void *h;
} bio·Tree;
/* clade manipulation */
error phylo·addchild(bio·Node* parent, bio·Node* child);
error phylo·rmchild(bio·Node* parent, bio·Node* child);
/* clade statistics */
error phylo·countnodes(bio·Node *node, int *n);
error phylo·countleafs(bio·Node *node, int *n);
/* topological sorting */
error phylo·ladderize(bio·Node *root);
double phylo·diameter(bio·Tree tree, int *len, bio·Node **path);
/* generic computation on tree */
void *phylo·postorder(bio·Node *clade, void *(*op)(bio·Node*, void*), void *ctx);
void *phylo·preorder(bio·Node *clade, void *(*op)(bio·Node*, void*), void *ctx);
/* simple helpers */
void phylo·getleafs(bio·Tree tree, bio·Node **leafs);
/* newick i/o */
error bio·readnewick(io·Peeker stream, void*, bio·Tree* tree);
error bio·writenewick(bio·Tree tree, io·Putter out, void*);
// -----------------------------------------------------------------------
// Sequences
/* i/o */
typedef struct bio·SeqReader bio·SeqReader;
typedef struct bio·Seq
{
vlong len;
char *name;
char *s;
char *q;
} bio·Seq;
bio·SeqReader *bio·openseq(io·Reader io, void *rdr, mem·Allocator mem, void *heap);
error bio·closeseq(bio·SeqReader *rdr);
error bio·readfasta(bio·SeqReader *rdr, bio·Seq *seq);
error bio·readfastq(bio·SeqReader *rdr, bio·Seq *seq);
error bio·writefasta(io·Writer io, void *wtr, bio·Seq seq);
error bio·writefastq(io·Writer io, void *wtr, bio·Seq seq);
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