binaries/src/mafft/core/f2cl.c

   1 #include "mltaln.h"
   2
   3 #define DEBUG 0
   4
   5
   6 static char *comment;
   7 static char *orderfile;
   8 static int format;
   9
  10 static void fillspace( char *seq, int lenmax )
  11 {
  12         int len = strlen( seq );
  13         seq += len;
  14         lenmax -= len;
  15         while( lenmax-- ) *seq++ = ' ';
  16         *seq = 0;
  17 }
  18
  19 void setmark_clustal( int nlen, int nseq, char **seq, char *mark )
  20 {
  21         int i, j, k;
  22
  23         char *strong[] = {
  24                                         "STA",
  25                                         "NEQK",
  26                                         "NHQK",
  27                                         "NDEQ",
  28                                         "QHRK",
  29                                         "MILV",
  30                                         "MILF",
  31                                         "HY",
  32                                         "FYW",
  33                                   };
  34         int nstrong = 9;
  35         char *weaker[] = {
  36                                         "CSA",
  37                                         "ATV",
  38                                         "SAG",
  39                                         "STNK",
  40                                         "STPA",
  41                                         "SGND",
  42                                         "SNDEQK",
  43                                         "NDEQHK",
  44                                         "NEQHRK",
  45                                         "FVLIM",
  46                                         "HFY",
  47                                   };
  48         int nweaker = 11;
  49
  50         for( i=0; i<nlen; i++ )
  51         {
  52                 mark[i] = ' ';
  53                 for( j=0; j<nseq; j++ )
  54                         if( '-' == seq[j][i] ) break;
  55                 if( j != nseq )
  56                 {
  57                         continue;
  58                 }
  59                 for( j=0; j<nseq; j++ )
  60                         if( seq[0][i] != seq[j][i] ) break;
  61                 if( j == nseq )
  62                 {
  63                         mark[i] = '*';
  64                         continue;
  65                 }
  66                 for( k=0; k<nstrong; k++ )
  67                 {
  68                         for( j=0; j<nseq; j++ )
  69                         {
  70                                 if( !strchr( strong[k], seq[j][i] ) ) break;
  71                         }
  72                         if( j == nseq ) break;
  73                 }
  74                 if( k < nstrong )
  75                 {
  76                         mark[i] = ':';
  77                         continue;
  78                 }
  79                 for( k=0; k<nweaker; k++ )
  80                 {
  81                         for( j=0; j<nseq; j++ )
  82                         {
  83                                 if( !strchr( weaker[k], seq[j][i] ) ) break;
  84                         }
  85                         if( j == nseq ) break;
  86                 }
  87                 if( k < nweaker )
  88                 {
  89                         mark[i] = '.';
  90                         continue;
  91                 }
  92         }
  93         mark[nlen] = 0;
  94 }
  95
  96 void setmark( int nlen, int nseq, char **seq, char *mark )
  97 {
  98         int i, j;
  99
 100         for( i=0; i<nlen; i++ )
 101         {
 102                 mark[i] = ' ';
 103                 for( j=0; j<nseq; j++ )
 104                         if( '-' == seq[j][i] ) break;
 105                 if( j != nseq )
 106                 {
 107                         continue;
 108                 }
 109                 for( j=0; j<nseq; j++ )
 110                         if( seq[0][i] != seq[j][i] ) break;
 111                 if( j == nseq )
 112                 {
 113                         mark[i] = '*';
 114                         continue;
 115                 }
 116                 for( j=0; j<nseq; j++ )
 117                         if( amino_grp[(int)seq[0][i]] != amino_grp[(int)seq[j][i]] ) break;
 118                 if( j == nseq )
 119                 {
 120                         mark[i] = '.';
 121                         continue;
 122                 }
 123         }
 124         mark[nlen] = 0;
 125 }
 126
 127 void arguments( int argc, char *argv[] )
 128 {
 129     int c;
 130         scoremtx = 1;
 131         nblosum = 62;
 132         dorp = NOTSPECIFIED;
 133         kimuraR = NOTSPECIFIED;
 134         pamN = NOTSPECIFIED;
 135         inputfile = NULL;
 136         comment = NULL;
 137         orderfile = NULL;
 138         format = 'c';
 139
 140     while( --argc > 0 && (*++argv)[0] == '-' )
 141         {
 142         while ( (c = *++argv[0]) )
 143                 {
 144             switch( c )
 145             {
 146                                 case 'i':
 147                                         inputfile = *++argv;
 148                                         fprintf( stderr, "inputfile = %s\n", inputfile );
 149                                         --argc;
 150                                         goto nextoption;
 151                                 case 'c':
 152                                         comment = *++argv;
 153                                         fprintf( stderr, "comment = %s\n", comment );
 154                                         --argc;
 155                                         goto nextoption;
 156                                 case 'r':
 157                                         orderfile = *++argv;
 158                                         fprintf( stderr, "orderfile = %s\n", orderfile );
 159                                         --argc;
 160                                         goto nextoption;
 161                                 case 'f':
 162                                         format = 'f';
 163                                         break;
 164                                 case 'm':
 165                                         format = 'm';
 166                                         break;
 167                 default:
 168                     fprintf( stderr, "illegal option %c\n", c );
 169                     argc = 0;
 170                     break;
 171             }
 172                 }
 173                 nextoption:
 174                         ;
 175         }
 176     if( argc != 0 )
 177     {
 178         fprintf( stderr, "options: Check source file !\n" );
 179         exit( 1 );
 180     }
 181 }
 182
 183
 184 int main( int argc, char *argv[] )
 185 {
 186         static int  *nlen;
 187         static char **name, **seq, *mark;
 188         static int *order;
 189         int i;
 190         FILE *infp;
 191         FILE *orderfp;
 192         char gett[B];
 193
 194         arguments( argc, argv );
 195
 196
 197         if( inputfile )
 198         {
 199                 infp = fopen( inputfile, "r" );
 200                 if( !infp )
 201                 {
 202                         fprintf( stderr, "Cannot open %s\n", inputfile );
 203                         exit( 1 );
 204                 }
 205         }
 206         else
 207                 infp = stdin;
 208
 209         getnumlen( infp );
 210         rewind( infp );
 211
 212         seq = AllocateCharMtx( njob, nlenmax*2+1 );
 213         mark = AllocateCharVec( nlenmax*2+1 );
 214         order = AllocateIntVec( njob );
 215         name = AllocateCharMtx( njob, B+1 );
 216     nlen = AllocateIntVec( njob );
 217
 218
 219         if( orderfile )
 220         {
 221                 orderfp = fopen( orderfile, "r" );
 222                 if( !orderfile )
 223                 {
 224                         fprintf( stderr, "Cannot open %s\n", orderfile );
 225                         exit( 1 );
 226                 }
 227                 for( i=0; i<njob; i++ )
 228                 {
 229                         fgets( gett, B-1, orderfp );
 230                         order[i] = atoi( gett );
 231                 }
 232                 fclose( orderfp );
 233         }
 234         else
 235         {
 236                 for( i=0; i<njob; i++ ) order[i] = i;
 237         }
 238
 239         readData_pointer( infp, name, nlen, seq );
 240         fclose( infp );
 241
 242         if( format == 'c' ) for( i=0; i<njob; i++ ) fillspace( seq[i], nlenmax );
 243         constants( njob, seq );
 244
 245 //      initSignalSM();
 246
 247 //      initFiles();
 248
 249
 250
 251 //      setmark( nlenmax, njob, seq, mark );
 252         setmark_clustal( nlenmax, njob, seq, mark );
 253
 254         if( format == 'f' )
 255                 writeData_reorder_pointer( stdout, njob, name, nlen, seq, order );
 256         else if( format == 'c' )
 257                 clustalout_pointer( stdout, njob, nlenmax, seq, name, mark, comment, order );
 258         else if( format == 'm' )
 259                 miyataout_reorder_pointer( stdout, njob, nlenmax, name, nlen, seq, order );
 260         else
 261                 fprintf( stderr, "Unknown format\n" );
 262
 263 //      SHOWVERSION;
 264         return( 0 );
 265 }