source: branches/help/GDE/PHYML/main.c

/*

PHYML :  a program that  computes maximum likelihood  phylogenies from
DNA or AA homologous sequences 

Copyright (C) Stephane Guindon. Oct 2003 onward

All parts of  the source except where indicated  are distributed under
the GNU public licence.  See http://www.opensource.org for details.

*/

#include "utilities.h"
#include "lk.h"
#include "optimiz.h"
#include "bionj.h"
#include "models.h"
#include "free.h"
#include "options.h"
#include "simu.h"


#ifdef PHYML

/* int T_MAX_FILE; */

int main(int argc, char **argv)
{
  seq **data;
  allseq *alldata;
  option *input;
  char *s_tree, *s_any;
  FILE *fp_phyml_tree,*fp_phyml_stats,*fp_phyml_lk,*fp_best_tree,*fp_best_tree_stats;
  arbre *tree;
  int n_otu, n_data_sets;
  matrix *mat;
  model *mod;
  time_t t_beg,t_end;
  div_t hour,min;
  int num_tree,tree_line_number;
  double best_loglk;
  

  srand(time(NULL));

  tree = NULL;
  mod  = NULL;

/*   Init_Constant(); */

  s_any = (char *)mCalloc(T_MAX_FILE,sizeof(char));

  fflush(NULL);

  input = (option *)Get_Input(argc,argv);

  Make_Model_Complete(input->mod);

  mod = input->mod;

  fp_phyml_stats = Openfile(input->phyml_stat_file,input->phyml_stat_file_open_mode);

  fprintf(fp_phyml_stats,"\n- PHYML %s -\n\n", VERSION);

  fp_phyml_tree = Openfile(input->phyml_tree_file,input->phyml_tree_file_open_mode);

  n_data_sets = 0;

  fp_phyml_lk = fopen(input->phyml_lk_file,"w");

  if(input->inputtree) Test_Multiple_Data_Set_Format(input);
  else input->n_trees = 1;
  
/*   if(input->n_data_sets > 1) input->n_trees = 1; */

  best_loglk = UNLIKELY;
  tree_line_number = 0;

  do
    {

      n_data_sets++;

      time(&t_beg);

      n_otu = 0;

      if(n_data_sets > input->n_data_sets) 
        {
          data = NULL;    
        }
      else
        {
            data = Get_Seq(input,0);
        }

      if(data)
        {
          if(n_data_sets > 1) printf("\n. Data set [#%d]\n",n_data_sets);

          printf("\n. Compressing sequences...\n");

          alldata = Compact_Seq(data,input);

          Free_Seq(data,alldata->n_otu);

          Init_Model(alldata,mod);
          
          Check_Ambiguities(alldata,input->mod->datatype,input->mod->stepsize);


          For(num_tree,input->n_trees)
            {
              if(!input->inputtree)
                {
                  printf("\n. Computing pairwise distances...\n");
                  
                  mat = ML_Dist(alldata,mod);

                  printf("\n. Building BIONJ tree...\n");
                              
                  mat->tree = Make_Tree(alldata);

                  Bionj(mat);
                                  
                  tree = mat->tree;

                  Free_Mat(mat);
                }
              else 
                {
                    if(input->n_trees > 1) printf("\n. Reading user tree [#%d]\n",tree_line_number+1);
                    else printf("\n. Reading user tree...\n");
                  
                    if(input->n_trees == 1) 
                        {
                            rewind(input->fp_input_tree);
                            tree_line_number = 0;
                        }

                    tree = Read_Tree_File(input->fp_input_tree);
                    
                    tree_line_number++;
                  
                    if(!tree) 
                        {
                            printf("\n. Missing tree for data set #%d\n",n_data_sets);
                            printf("  This data set is not analyzed.\n");
                            data = NULL;
                        }
                    
                    if(!tree->has_branch_lengths)
                        {
                            printf("\n. Computing branch length estimates...\n");
                            
                            Order_Tree_CSeq(tree,alldata);
                            
                            mat = ML_Dist(alldata,mod);
                            
                            mat->tree = tree;
                      
                            mat->method = 0;
                            
                            Bionj_Br_Length(mat);
                            
                            Free_Mat(mat);
                        }
                }
              
              if(!tree) continue;
              
              
              tree->mod        = mod;
              tree->input      = input;
              tree->data       = alldata;
              tree->both_sides = 1;
              tree->n_pattern  = tree->data->crunch_len/tree->mod->stepsize;
              
              Order_Tree_CSeq(tree,alldata);
              
              Make_Tree_4_Lk(tree,alldata,alldata->init_len);
              
              if(tree->mod->s_opt->opt_topo)
                Simu(tree,1000);
              else
                {
                  if(tree->mod->s_opt->opt_free_param)
                    Round_Optimize(tree,tree->data);
                  else
                    {
                      Lk(tree,tree->data);
                      printf("\n. Log(lk) :               * -> %15.6f ",tree->tot_loglk);
                    }
                }
              
              if(tree->mod->bootstrap) Bootstrap(tree);
              
              Update_BrLen_Invar(tree);
              
              s_tree = Write_Tree(tree);
              
              fprintf(fp_phyml_tree,"%s\n",s_tree);

              Free(s_tree);

              Unconstraint_Lk(tree);
              
              time(&t_end);
              
              hour = div(t_end-t_beg,3600);
              min  = div(t_end-t_beg,60  );
              
              min.quot -= hour.quot*60;
              
              if (input->n_data_sets==1)
                Print_Fp_Out(fp_phyml_stats, t_beg, t_end, tree, input, n_data_sets);
              else
                Print_Fp_Out_Lines(fp_phyml_stats, t_beg, t_end, tree, input, n_data_sets);
              
              printf("\n\n. Time used %dh%dm%ds\n", hour.quot,min.quot,(int)(t_end-t_beg)%60);
              printf("\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n\n");
              
              Print_Site_Lk(tree,fp_phyml_lk);
/*            fprintf(fp_phyml_lk,"%f\n",tree->tot_loglk);        */
              
              
              if((input->n_data_sets == 1) &&
                 (input->n_trees     >  1) &&
                 (tree->tot_loglk > best_loglk))
                {

                  best_loglk = tree->tot_loglk;
                  strcpy(s_any,input->seqfile);
                  fp_best_tree = fopen(s_any = strcat(s_any,"_phyml_best_tree.txt"),"w");
                  s_tree = Write_Tree(tree);
                  fprintf(fp_best_tree,"%s\n",s_tree);
                  Free(s_tree);
                  strcpy(s_any,input->seqfile);
                  fp_best_tree_stats = fopen(s_any = strcat(s_any,"_phyml_best_stat.txt"),"w");
                  Print_Fp_Out(fp_best_tree_stats, 
                               t_beg, 
                               t_end, 
                               tree, 
                               input, 
                               n_data_sets);
                  
                  fclose(fp_best_tree);
                  fclose(fp_best_tree_stats);
                }

              Free_Tree_Lk(tree);
              
              Free_Tree(tree);
              
              if(input->n_data_sets > 1) 
                  {
                      break;
                  }
            }
          Free_Cseq(alldata);
        }
    }while(data);

  Free_Model(mod);

  if(input->fp_seq ) fclose(input->fp_seq );
  if(input->fp_input_tree) fclose(input->fp_input_tree);

  fclose(fp_phyml_lk);

  fclose(fp_phyml_tree);

  fclose(fp_phyml_stats);

  Free_Input(input);    
  
  Free(s_any);

  return 0;
}

#endif
/*********************************************************/