Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / mafft / core / replaceu.c

diff --git a/website/archive/binaries/mac/src/mafft/core/replaceu.c b/website/archive/binaries/mac/src/mafft/core/replaceu.c
new file mode 100644 (file)
index 0000000..40be746
--- /dev/null
+++ b/website/archive/binaries/mac/src/mafft/core/replaceu.c
@@ -0,0 +1,145 @@
+#include "mltaln.h"
+
+#define DEBUG 0
+
+static int seedoffset;
+
+static void replace_unusual( int n, char **seq, char *usual, char unknown, int (*uporlow)( int ) )
+{
+       int i;
+       char *pt;
+       for( i=0; i<n; i++ )
+       {
+               pt = seq[i];
+               while( *pt )
+               {
+                       if( !strchr( usual, *pt ) ) *pt = unknown;
+                       else *pt = uporlow( *pt );
+                       pt++;
+               }
+       }
+}
+
+
+void arguments( int argc, char *argv[] )
+{
+    int c;
+
+       seedoffset = 0;
+       inputfile = NULL;
+
+    while( --argc > 0 && (*++argv)[0] == '-' )
+       {
+        while ( (c = *++argv[0]) )
+               {
+            switch( c )
+            {
+                               case 'o':
+                                       seedoffset = atoi( *++argv );
+                                       fprintf( stderr, "seedoffset = %d\n", seedoffset );
+                                       --argc;
+                                       goto nextoption;
+                               case 'i':
+                                       inputfile = *++argv;
+                                       fprintf( stderr, "inputfile = %s\n", inputfile );
+                                       --argc;
+                                       goto nextoption;
+                default:
+                    fprintf( stderr, "illegal option %c\n", c );
+                    argc = 0;
+                    break;
+            }
+               }
+               nextoption:
+                       ;
+       }
+    if( argc != 0 ) 
+    {
+        fprintf( stderr, "options: Check source file !\n" );
+        exit( 1 );
+    }
+}
+
+
+
+int main( int argc, char *argv[] )
+{
+       FILE *infp;
+       int nlenmin;
+       char **name;
+       char **seq;
+       int *nlen;
+       int i;
+       char *usual;
+
+       arguments( argc, argv );
+
+       if( inputfile )
+       {
+               infp = fopen( inputfile, "r" );
+               if( !infp )
+               {
+                       fprintf( stderr, "Cannot open %s\n", inputfile );
+                       exit( 1 );
+               }
+       }
+       else
+               infp = stdin;
+
+
+       dorp = NOTSPECIFIED;
+       getnumlen_casepreserve( infp, &nlenmin );
+
+       fprintf( stderr, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
+
+       seq = AllocateCharMtx( njob, nlenmax+1 );
+       name = AllocateCharMtx( njob, B+1 );
+       nlen = AllocateIntVec( njob );
+
+       readData_pointer_casepreserve( infp, name, nlen, seq );
+
+//     for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );
+
+#if 0
+       FILE *origfp;
+       origfp = fopen( "_original", "w" );
+       if( !origfp )
+       {
+               fprintf( stderr, "Cannot open _original\n" );
+               exit( 1 );
+       }
+       for( i=0; i<njob; i++ )
+       {
+               nlen[i] = strlen( seq[i] );
+               fprintf( origfp, ">%s\n", name[i]+1 );
+               if( seq[i][nlen[i]-1] == '\n' ) seq[i][nlen[i]-1] = 0;
+               fprintf( origfp, "%s\n", seq[i] );
+       }
+       fclose( origfp );
+#endif
+
+       if( dorp == 'p' )
+       {
+               usual = "ARNDCQEGHILKMFPSTWYVarndcqeghilkmfpstwyv-.";
+               replace_unusual( njob, seq, usual, 'X', toupper );
+       }
+       else
+       {
+               usual = "ATGCUatgcu-";
+               replace_unusual( njob, seq, usual, 'n', tolower );
+       }
+       
+
+
+       for( i=0; i<njob; i++ )
+       {
+               fprintf( stdout, ">%d_oripos_%s\n", i+seedoffset, name[i] );
+               fprintf( stdout, "%s\n", seq[i] );
+       }
+
+       free( nlen );
+       FreeCharMtx( seq );
+       FreeCharMtx( name );
+
+       return( 0 );
+}