calctree.c File Reference

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <stdarg.h>
#include <ctype.h>
#include "clustalw.h"

Defines
#define	MAXERRS   10
Functions
static void	create_tree (treeptr ptree, treeptr parent)
static void	create_node (treeptr pptr, treeptr parent)
static treeptr	insert_node (treeptr pptr)
static void	skip_space (FILE *fd)
static treeptr	avail (void)
static void	set_info (treeptr p, treeptr parent, sint pleaf, char *pname, float pdist)
static treeptr	reroot (treeptr ptree, sint nseqs)
static treeptr	insert_root (treeptr p, float diff)
static float	calc_root_mean (treeptr root, float *maxdist)
static float	calc_mean (treeptr nptr, float *maxdist, sint nseqs)
static void	order_nodes (void)
static sint	calc_weight (sint leaf)
static void	group_seqs (treeptr p, sint *next_groups, sint nseqs)
static void	mark_group1 (treeptr p, sint *groups, sint n)
static void	mark_group2 (treeptr p, sint *groups, sint n)
static void	save_set (sint n, sint *groups)
static void	clear_tree_nodes (treeptr p)
void	calc_seq_weights (sint first_seq, sint last_seq, sint *sweight)
void	create_sets (sint first_seq, sint last_seq)
sint	read_tree (char *treefile, sint first_seq, sint last_seq)
void	clear_tree (treeptr p)
sint	calc_similarities (sint nseqs)
Variables
Boolean	interactive
Boolean	distance_tree
Boolean	usemenu
sint	debug
double **	tmat
sint **	sets
sint	nsets
char **	names
sint *	seq_weight
Boolean	no_weights
char	ch
FILE *	fd
treeptr *	lptr
treeptr *	olptr
treeptr *	nptr
treeptr *	ptrs
sint	nnodes = 0
sint	ntotal = 0
Boolean	rooted_tree = TRUE
static treeptr	seq_tree
static treeptr	root
static sint *	groups
static sint	numseq

---

Define Documentation

#define MAXERRS   10

---

Function Documentation

static treeptr avail (  void   )  [static]

static float calc_mean (  treeptr  nptr, float *  maxdist, sint  nseqs )  [static]

static float calc_root_mean (  treeptr  root, float *  maxdist )  [static]

void calc_seq_weights (  sint  first_seq, sint  last_seq, sint *  sweight )

sint calc_similarities (  sint  nseqs  )

static sint calc_weight (  sint  leaf  )  [static]

void clear_tree (  treeptr  p  )

static void clear_tree_nodes (  treeptr  p  )  [static]

static void create_node (  treeptr  pptr, treeptr  parent )  [static]

void create_sets (  sint  first_seq, sint  last_seq )

static void create_tree (  treeptr  ptree, treeptr  parent )  [static]

static void group_seqs (  treeptr  p, sint *  next_groups, sint  nseqs )  [static]

static treeptr insert_node (  treeptr  pptr  )  [static]

static treeptr insert_root (  treeptr  p, float  diff )  [static]

static void mark_group1 (  treeptr  p, sint *  groups, sint  n )  [static]

static void mark_group2 (  treeptr  p, sint *  groups, sint  n )  [static]

static void order_nodes (  void   )  [static]

sint read_tree (  char *  treefile, sint  first_seq, sint  last_seq )

static treeptr reroot (  treeptr  ptree, sint  nseqs )  [static]

static void save_set (  sint  n, sint *  groups )  [static]

static void set_info (  treeptr  p, treeptr  parent, sint  pleaf, char *  pname, float  pdist )  [static]

static void skip_space (  FILE *  fd  )  [static]

---

Variable Documentation

char ch

sint debug

Boolean distance_tree

FILE* fd

sint* groups [static]

Boolean interactive

treeptr* lptr

char** names

sint nnodes = 0

Boolean no_weights

treeptr* nptr

sint nsets

sint ntotal = 0

sint numseq [static]

treeptr* olptr

treeptr* ptrs

treeptr root [static]

Boolean rooted_tree = TRUE

treeptr seq_tree [static]

sint* seq_weight

sint** sets

double** tmat

Boolean usemenu

---