binaries/src/ViennaRNA/Cluster/AD_main.c

   1 #include <stdio.h>
   2 #include <stdlib.h>
   3 #include <string.h>
   4 #include "split.h"
   5 #include "cluster.h"
   6 #include "distance_matrix.h"
   7 #include "treeplot.h"
   8 #include "utils.h"
   9
  10
  11 #define PUBLIC
  12 #define PRIVATE   static
  13
  14 PRIVATE void usage(void);
  15
  16 main(int argc, char *argv[])
  17 {
  18    int     i,j;
  19    float **dm;
  20    Split  *S;
  21    Union  *U;
  22    char    type[5];
  23
  24    short   Do_Split=1, Do_Wards=0, Do_Nj=0;
  25
  26    for (i=1; i<argc; i++) {
  27       if (argv[i][0]=='-') {
  28          switch ( argv[i][1] ) {
  29           case 'X':  if (argv[i][2]=='\0') { Do_Split = 1 ; break; }
  30             Do_Split = 0;
  31             Do_Wards = 0;
  32             Do_Nj    = 0;
  33             for(j=2;j<strlen(argv[i]);j++) {
  34                switch(argv[i][j]) {
  35                 case 's' :  Do_Split = 1;
  36                   break;
  37                 case 'w' :  Do_Wards = 1;
  38                   break;
  39                 case 'n' :  Do_Nj    = 1;
  40                   break;
  41                   default :
  42                   usage();
  43                }
  44             }
  45             break;
  46             default :
  47             usage();
  48          }
  49       }
  50    }
  51
  52    while ((dm=read_distance_matrix(type))!=NULL) {
  53
  54       printf_taxa_list();
  55       printf("> %s\n",type);
  56
  57       if(Do_Split) {
  58          S = split_decomposition(dm);
  59          sort_Split(S);
  60          print_Split(S);
  61          free_Split(S);
  62       }
  63       if(Do_Wards) {
  64          U = wards_cluster(dm);
  65
  66          printf_phylogeny(U,"W");
  67          PSplot_phylogeny(U,"wards.ps","Ward's Method");
  68          free(U);
  69       }
  70       if(Do_Nj) {
  71          U = neighbour_joining(dm);
  72          printf_phylogeny(U,"Nj");
  73          PSplot_phylogeny(U,"nj.ps","Neighbor Joining");
  74          free(U);
  75       }
  76       free_distance_matrix(dm);
  77    }
  78    return 0;
  79 }
  80
  81
  82 PRIVATE void usage(void)
  83 {
  84    nrerror("usage: AnalyseDist [-X[swn]]");
  85 }