#pragma once

// -----------------------------------------------------------------------
// Phylogenetics

typedef struct bio·Node
{
    string name;
    string comment;
    double dist;
    double support;
    int    nnode;
    int    nchild;
    struct bio·Node *parent;
    struct bio·Node *sibling;
    struct bio·Node *child;
} 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·FastaReader bio·FastaReader;
typedef struct bio·FastqReader bio·FastqReader;

typedef struct bio·Seq
{
    int  len;
    byte *name;
    byte *s;
    byte *q;
} bio·Seq;

bio·FastaReader *bio·openfasta(io·Reader stream, void *s, mem·Allocator heap, void *h);
error            bio·readfasta(bio·FastaReader *rdr, bio·Seq *seq);
error            bio·closefasta(bio·FastaReader *rdr);

bio·FastqReader *bio·openfastq(io·Reader stream, void *s, mem·Allocator heap, void *h);
error            bio·readfastq(bio·FastqReader *rdr, bio·Seq *seq);
error            bio·closefastq(bio·FastqReader *rdr);

/* alignment */
enum
{
    aln·K = 20,     // kmer size (k <= 32)
    aln·L = 3,      // number of kmers / hash
    aln·N = 10,   // number of hashes
};

error aln·sketch(byte *seq, int l, uint64 *phi[aln·N], int *locs[aln·N]);
error aln·sort(uintptr len, int l, uint64 *vals);