blob: 9f5401527be60d4479ad02e2ae3d3272bc1077fd (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
|
#pragma once
// -----------------------------------------------------------------------
// Phylogenetics
typedef struct bio·Node
{
string name;
string comment;
double dist;
double support;
int nchild;
int ndescendent;
struct bio·Node *parent;
struct bio·Node *child[2];
struct bio·Node *sibling;
} bio·Node;
error phylo·addchild(bio·Node *parent, bio·Node* child);
bool phylo·isleaf(bio·Node *node);
typedef struct bio·Tree
{
bio·Node *root;
} bio·Tree;
/* newick i/o */
bio·Tree bio·readnewick(Stream *file, mem·Allocator heap);
error bio·writenewick(bio·Tree tree, Stream *out);
// -----------------------------------------------------------------------
// Sequences
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);
|