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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
treeptrlptr
treeptrolptr
treeptrnptr
treeptrptrs
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
 


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