binaries/src/mafft/core/regtable2seq.c

   1 #include "mltaln.h"
   2
   3 #define DEBUG 0
   4
   5 char *regfile;
   6 char *eregfile;
   7
   8 void arguments( int argc, char *argv[] )
   9 {
  10     int c;
  11
  12     outnumber = 0;
  13     inputfile = NULL;
  14     regfile = NULL;
  15     eregfile = NULL;
  16
  17     while( --argc > 0 && (*++argv)[0] == '-' )
  18         {
  19         while ( (c = *++argv[0]) )
  20                 {
  21             switch( c )
  22             {
  23                                 case 'e':
  24                                         eregfile = *++argv;
  25                                         fprintf( stderr, "eregfile = %s\n", eregfile );
  26                                         --argc;
  27                                         goto nextoption;
  28                                 case 'r':
  29                                         regfile = *++argv;
  30                                         fprintf( stderr, "regfile = %s\n", regfile );
  31                                         --argc;
  32                                         goto nextoption;
  33                                 case 'i':
  34                                         inputfile = *++argv;
  35                                         fprintf( stderr, "inputfile = %s\n", inputfile );
  36                                         --argc;
  37                                         goto nextoption;
  38                                 case 'n' :
  39                                         outnumber = 1;
  40                                         break;
  41                 default:
  42                     fprintf( stderr, "illegal option %c\n", c );
  43                     argc = 0;
  44                     break;
  45             }
  46                 }
  47                 nextoption:
  48                         ;
  49         }
  50     if( argc != 0 )
  51     {
  52         fprintf( stderr, "options: Check source file !\n" );
  53         exit( 1 );
  54     }
  55 }
  56
  57 void readereg( FILE *regfp, int **regtable, char **revtable, int *outtable, int *noutpt, int *loutpt )
  58 {
  59         char gett[1000];
  60         int j;
  61         int mem;
  62         char cmem;
  63         char reg[5][100];
  64         char out[100];
  65         int startpos, endpos;
  66
  67         *noutpt = 0;
  68         *loutpt = 0;
  69         fgets( gett, 999, regfp );
  70         sscanf( gett, "%c %s %s %s %s %s", &cmem, reg[0], reg[1], reg[2], reg[3], reg[4] );
  71         if( cmem != 'e' )
  72         {
  73                 fprintf( stderr, "Format error\n" );
  74                 exit( 1 );
  75         }
  76         for( j=0; j<5; j++ )
  77         {
  78                 sscanf( reg[j], "%d-%d-%c", regtable[0]+(j*2), regtable[0]+(j*2)+1, revtable[0]+j );
  79                 fprintf( stderr, "%d %d-%d\n", 0, regtable[0][j*2], regtable[0][j*2+1] );
  80                 startpos = regtable[0][j*2];
  81                 endpos   = regtable[0][j*2+1];
  82                 if( startpos > endpos )
  83                 {
  84                         endpos   = regtable[0][j*2];
  85                         startpos = regtable[0][j*2+1];
  86                 }
  87                 if( startpos != -1 && endpos != -1 )
  88                         *loutpt += endpos - startpos + 1;
  89         }
  90
  91         while( 1 )
  92         {
  93                 fgets( gett, 999, regfp );
  94                 if( feof( regfp ) ) break;
  95                 sscanf( gett, "%d o=%s", &mem, out );
  96                 if( mem >= njob )
  97                 {
  98                         fprintf( stderr, "Out of range\n" );
  99                         exit( 1 );
 100                 }
 101                 outtable[mem] = atoi( out );
 102                 if( outtable[mem] ) *noutpt += 1;
 103         }
 104 }
 105
 106 void readreg( FILE *regfp, int **regtable, char **revtable, int *outtable )
 107 {
 108         char gett[1000];
 109         int j;
 110         int mem;
 111         char reg[5][100];
 112         char out[100];
 113
 114         while( 1 )
 115         {
 116                 fgets( gett, 999, regfp );
 117                 if( feof( regfp ) ) break;
 118                 sscanf( gett, "%d %s %s %s %s %s o=%s", &mem, reg[0], reg[1], reg[2], reg[3], reg[4], out );
 119                 if( mem >= njob )
 120                 {
 121                         fprintf( stderr, "Out of range\n" );
 122                         exit( 1 );
 123                 }
 124                 for( j=0; j<5; j++ )
 125                 {
 126                         sscanf( reg[j], "%d-%d-%c", regtable[mem]+(j*2), regtable[mem]+(j*2)+1, revtable[mem]+j );
 127                         fprintf( stderr, "%d %d-%d\n", mem, regtable[mem][j*2], regtable[mem][j*2+1] );
 128                 }
 129                 outtable[mem] = atoi( out );
 130         }
 131 }
 132
 133 int main( int argc, char *argv[] )
 134 {
 135         FILE *infp;
 136         FILE *regfp;
 137         int nlenmin;
 138         int **regtable;
 139         char **revtable;
 140         int *outtable;
 141         int i, nout, lout;
 142         char **outseq;
 143         char **name;
 144
 145         arguments( argc, argv );
 146
 147         if( inputfile )
 148         {
 149                 infp = fopen( inputfile, "r" );
 150                 if( !infp )
 151                 {
 152                         fprintf( stderr, "Cannot open %s\n", inputfile );
 153                         exit( 1 );
 154                 }
 155         }
 156         else
 157                 infp = stdin;
 158
 159         dorp = NOTSPECIFIED;
 160         getnumlen_nogap( infp, &nlenmin );
 161
 162         if( regfile )
 163         {
 164                 regfp = fopen( regfile, "r" );
 165                 if( !regfp )
 166                 {
 167                         fprintf( stderr, "Cannot open %s\n", regfile );
 168                         exit( 1 );
 169                 }
 170                 regtable = AllocateIntMtx( njob, 5*2 );
 171                 revtable = AllocateCharMtx( njob, 5 );
 172                 outtable = AllocateIntVec( njob );
 173                 readreg( regfp, regtable, revtable, outtable );
 174                 cutData( infp, regtable, revtable, outtable );
 175         }
 176         else if( eregfile )
 177         {
 178                 regfp = fopen( eregfile, "r" );
 179                 if( !regfp )
 180                 {
 181                         fprintf( stderr, "Cannot open %s\n", eregfile );
 182                         exit( 1 );
 183                 }
 184                 regtable = AllocateIntMtx( 1, 5*2 );
 185                 revtable = AllocateCharMtx( 1, 5 );
 186                 outtable = AllocateIntVec( njob );
 187                 readereg( regfp, regtable, revtable, outtable, &nout, &lout );
 188                 fprintf( stderr, "nout = %d, lout = %d\n", nout, lout );
 189
 190                 outseq = AllocateCharMtx( nout, lout+1 );
 191                 name = AllocateCharMtx( nout, B );
 192
 193                 cutAlignment( infp, regtable, revtable, outtable, name, outseq );
 194                 fprintf( stderr, "gappick! nout = %d\n", nout );
 195                 commongappick( nout, outseq );
 196                 for( i=0; i<nout; i++ )
 197                 {
 198                         fprintf( stdout, "%s\n", name[i] );
 199                         fprintf( stdout, "%s\n", outseq[i] );
 200                 }
 201         }
 202         else
 203         {
 204                 catData( infp );
 205         }
 206
 207         fprintf( stderr, "Strategy:\n" );
 208         fprintf( stderr, " Not-Aligned\n" );
 209
 210 //      fprintf( stdout, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
 211         return( 0 );
 212 }