#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 mem;
    void         *heap;
} 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 io, void* rdr, 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);