Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/mafft/core/score.c b/website/archive/binaries/mac/src/mafft/core/score.c
deleted file mode 100644 (file)
index 1906cdb..0000000
--- a/website/archive/binaries/mac/src/mafft/core/score.c
+++ /dev/null
@@ -1,96 +0,0 @@
-#include "mltaln.h"
-
-#define DEBUG 0
-
-void arguments( int argc, char *argv[] )
-{
-    int c;
-
-       ppenalty = NOTSPECIFIED;
-       ppenalty_ex = NOTSPECIFIED;
-       poffset = NOTSPECIFIED;
-       kimuraR = NOTSPECIFIED;
-       pamN = NOTSPECIFIED;
-       scoremtx = NOTSPECIFIED;
-
-    while( --argc > 0 && (*++argv)[0] == '-' )
-       {
-        while ( ( c = *++argv[0] ) )
-               {
-            switch( c )
-            {
-                               case 'f':
-                                       ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
-                                       fprintf( stderr, "ppenalty = %d\n", ppenalty );
-                                       --argc;
-                                       goto nextoption;
-                               case 'g':
-                                       ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
-                                       fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
-                                       --argc;
-                                       goto nextoption;
-                               case 'h':
-                                       poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
-                                       fprintf( stderr, "poffset = %d\n", poffset );
-                                       --argc;
-                                       goto nextoption;
-                               case 'k':
-                                       kimuraR = atoi( *++argv );
-                                       fprintf( stderr, "kimuraR = %d\n", kimuraR );
-                                       --argc;
-                                       goto nextoption;
-                               case 'D':
-                                       scoremtx = -1;
-                                       break;
-                               case 'P':
-                                       scoremtx = 0;
-                                       break;
-                default:
-                    fprintf( stderr, "illegal option %c\n", c );
-                    argc = 0;
-                    break;
-            }
-               }
-               nextoption:
-                       ;
-       }
-    if( argc == 1 )
-    {
-        cut = atof( (*argv) );
-        argc--;
-    }
-}
-
-
-int main( int ac, char **av )
-{
-       int nlen[M];
-       static char name[M][B], **seq;
-       double score;
-       extern double score_calc_for_score( int, char ** );
-
-       arguments( ac, av );
-
-       getnumlen( stdin );
-       rewind( stdin );
-
-       seq = AllocateCharMtx( njob, nlenmax );
-
-       readData( stdin, name, nlen, seq );
-
-       if( !isaligned( njob, seq ) ) ErrorExit( "Not aligned." );
-
-       constants( njob, seq );
-
-       score = score_calc_for_score( njob, seq );
-       if( scoremtx == 0 ) score += offset;
-
-       fprintf( stdout, "score = %f\n", score );
-       if     ( scoremtx ==  0 ) fprintf( stdout, "JTT %dPAM\n", pamN );
-       else if( scoremtx ==  1 ) fprintf( stdout, "Dayhoff( machigai ga aru )\n" );
-       else if( scoremtx ==  2 ) fprintf( stdout, "M-Y\n" );
-       else if( scoremtx == -1 ) fprintf( stdout, "DNA 1:%d\n", kimuraR );
-
-       fprintf( stdout, "gap penalty = %+6.2f, %+6.2f, %+6.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
-       exit( 0 );
-}