binaries/src/mafft/core/dndpre.c

   1 #include "mltaln.h"
   2
   3 #define TEST 0
   4
   5 static int treeout = 0;
   6
   7
   8 void arguments( int argc, char *argv[] )
   9 {
  10     int c;
  11
  12         alg = 'X';
  13         fmodel = 0;
  14         treeout = 0;
  15         scoremtx = 1;
  16         nblosum = 62;
  17         dorp = NOTSPECIFIED;
  18         inputfile = NULL;
  19         ppenalty = NOTSPECIFIED; //?
  20         ppenalty_ex = NOTSPECIFIED; //?
  21         poffset = NOTSPECIFIED; //?
  22         kimuraR = NOTSPECIFIED;
  23         pamN = NOTSPECIFIED;
  24
  25     while( --argc > 0 && (*++argv)[0] == '-' )
  26         {
  27         while ( (c = *++argv[0]) )
  28                 {
  29             switch( c )
  30             {
  31                                 case 't':
  32                                         treeout = '1';
  33                                         break;
  34                                 case 'D':
  35                                         dorp = 'd';
  36                                         break;
  37                                 case 'a':
  38                                         fmodel = 1;
  39                                         break;
  40                                 case 'P':
  41                                         dorp = 'p';
  42                                         break;
  43                                 case 'i':
  44                                         inputfile = *++argv;
  45                                         fprintf( stderr, "inputfile = %s\n", inputfile );
  46                                         --argc;
  47                                         goto nextoption;
  48             }
  49                 }
  50                 nextoption:
  51                         ;
  52         }
  53     if( argc != 0 )
  54         {
  55                 fprintf( stderr, "options: Check source file !\n" );
  56                 exit( 1 );
  57         }
  58 }
  59
  60 int main( int argc, char **argv )
  61 {
  62         int i, j;
  63         char **seq;
  64         static char name[M][B];
  65         static int nlen[M];
  66         float *selfscore;
  67         double **mtx;
  68         FILE *fp;
  69         FILE *infp;
  70         float ssi, ssj, bunbo;
  71
  72
  73         arguments( argc, argv );
  74
  75         if( inputfile )
  76         {
  77                 infp = fopen( inputfile, "r" );
  78                 if( !infp )
  79                 {
  80                         fprintf( stderr, "Cannot open %s\n", inputfile );
  81                         exit( 1 );
  82                 }
  83         }
  84         else
  85                 infp = stdin;
  86
  87 #if 0
  88         PreRead( stdin, &njob, &nlenmax );
  89 #else
  90         getnumlen( infp );
  91 #endif
  92         rewind( infp );
  93
  94         seq = AllocateCharMtx( njob, nlenmax+1 );
  95         mtx = AllocateDoubleMtx( njob, njob );
  96         selfscore = AllocateFloatVec( njob );
  97
  98 #if 0
  99         FRead( stdin, name, nlen, seq );
 100 #else
 101         readData( infp, name, nlen, seq );
 102 #endif
 103         fclose( infp );
 104
 105         constants( njob, seq );
 106
 107 #if 0
 108         for( i=0; i<njob-1; i++ )
 109         {
 110                 fprintf( stderr, "%4d/%4d\r", i+1, njob );
 111                 for( j=i+1; j<njob; j++ )
 112                         mtx[i][j] = (double)substitution_hosei( seq[i], seq[j] );
 113 //                      fprintf( stderr, "i=%d,j=%d, l=%d &&&  %f\n", i, j, nlen[0], mtx[i][j] );
 114         }
 115 #else // 061003
 116         for( i=0; i<njob; i++ )
 117         {
 118                 selfscore[i] = (float)naivepairscore11( seq[i], seq[i], penalty );
 119
 120         }
 121         for( i=0; i<njob-1; i++ )
 122         {
 123                 ssi = selfscore[i];
 124                 fprintf( stderr, "%4d/%4d\r", i+1, njob );
 125                 for( j=i+1; j<njob; j++ )
 126                 {
 127                         ssj = selfscore[j];
 128                         bunbo = MIN( ssi, ssj );
 129                         if( bunbo == 0.0 )
 130                                 mtx[i][j] = 1.0;
 131                         else
 132                                 mtx[i][j] = 1.0 - (double)naivepairscore11( seq[i], seq[j], penalty ) / bunbo;
 133 //                              mtx[i][j] = 1.0 - (double)naivepairscore11( seq[i], seq[j], penalty ) / MIN( selfscore[i], selfscore[j] );
 134 //                      fprintf( stderr, "i=%d,j=%d, l=%d### %f, score = %d\n", i, j, nlen[0], mtx[i][j], naivepairscore11( seq[i], seq[j], penalty )  );
 135                 }
 136         }
 137 #endif
 138
 139 #if TEST
 140         for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
 141                 fprintf( stdout, "i=%d, j=%d, mtx[][] = %f\n", i, j, mtx[i][j] );
 142 #endif
 143
 144         fp = fopen( "hat2", "w" );
 145         WriteHat2( fp, njob, name, mtx );
 146         fclose( fp );
 147 #if 0
 148         if( treeout )
 149         {
 150                 int ***topol;
 151                 double **len;
 152
 153                 topol = AllocateIntCub( njob, 2, njob );
 154                 len = AllocateDoubleMtx( njob, njob );
 155                 veryfastsupg_double_outtree( njob, mtx, topol, len );
 156         }
 157 #endif
 158         SHOWVERSION;
 159         exit( 0 );
 160 /*
 161         res = system( ALNDIR "/spgsdl < hat2"  );
 162         if( res ) exit( 1 );
 163         else exit( 0 );
 164 */
 165 }