new mafft v 6.857 with extensions

[jabaws.git] / binaries / src / mafft / core / dndpre_score.c

diff --git a/binaries/src/mafft/core/dndpre_score.c b/binaries/src/mafft/core/dndpre_score.c
new file mode 100644 (file)
index 0000000..a911d0a
--- /dev/null
+++ b/binaries/src/mafft/core/dndpre_score.c
@@ -0,0 +1,54 @@
+#include "mltaln.h"
+
+#define TEST 0
+
+int main()
+{
+       int i, j;
+       char **seq;
+       static char name[M][B];
+       static int nlen[M];
+       double **mtx;
+       FILE *fp;
+       int res;
+
+       scoremtx = NOTSPECIFIED;
+
+#if 0
+       PreRead( stdin, &njob, &nlenmax );
+#else
+       getnumlen( stdin );
+#endif
+       rewind( stdin );
+
+       seq = AllocateCharMtx( njob, nlenmax+1 );
+       mtx = AllocateDoubleMtx( njob, njob );
+
+#if 0
+       FRead( stdin, name, nlen, seq );
+#else
+       readData( stdin, name, nlen, seq );
+#endif
+
+       for( i=0; i<njob-1; i++ ) 
+       {
+               fprintf( stderr, "%4d/%4d\r", i+1, njob );
+               for( j=i+1; j<njob; j++ ) 
+                       mtx[i][j] = (double)substitution_score( seq[i], seq[j] );
+       }
+       
+#if TEST
+       for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ ) 
+               fprintf( stdout, "i=%d, j=%d, mtx[][] = %f\n", i, j, mtx[i][j] );
+#endif
+
+       fp = fopen( "hat2", "w" );
+       WriteHat2( fp, njob, name, mtx );
+       fclose( fp );
+       exit( 0 );
+/*
+       res = system( ALNDIR "/spgsdl < hat2"  );
+       if( res ) exit( 1 );
+       else exit( 0 );
+*/
+}