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