new mafft v 6.857 with extensions

[jabaws.git] / binaries / src / mafft / core / dndpre2.c

diff --git a/binaries/src/mafft/core/dndpre2.c b/binaries/src/mafft/core/dndpre2.c
new file mode 100644 (file)
index 0000000..e68a3c3
--- /dev/null
+++ b/binaries/src/mafft/core/dndpre2.c
@@ -0,0 +1,176 @@
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 1
+
+
+void arguments( int argc, char *argv[] )
+{
+    int c;
+
+       nblosum = 62;
+       fmodel = 0;
+       calledByXced = 0;
+       scoremtx = 0;
+       dorp = NOTSPECIFIED;
+       ppenalty = NOTSPECIFIED;
+       ppenalty_ex = NOTSPECIFIED;
+       poffset = NOTSPECIFIED;
+       kimuraR = NOTSPECIFIED;
+       pamN = NOTSPECIFIED;
+       geta2 = GETA2;
+       fftWinSize = NOTSPECIFIED;
+       fftThreshold = 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 'b':
+                                       nblosum = atoi( *++argv );
+                                       scoremtx = 1;
+                                       fprintf( stderr, "blosum %d\n", nblosum );
+                                       --argc;
+                                       goto nextoption;
+                               case 'j':
+                                       pamN = atoi( *++argv );
+                                       scoremtx = 0;
+                                       fprintf( stderr, "jtt %d\n", pamN );
+                                       --argc;
+                                       goto nextoption;
+                               case 'm':
+                                       fmodel = 1;
+                                       break;
+                               case 'r':
+                                       fmodel = -1;
+                                       break;
+                               case 'D':
+                                       dorp = 'd';
+                                       break;
+                               case 'P':
+                                       dorp = 'p';
+                                       break;
+                default:
+                    fprintf( stderr, "illegal option %c\n", c );
+                    argc = 0;
+                    break;
+            }
+               }
+               nextoption:
+                       ;
+       }
+    if( argc == 1 )
+    {
+        cut = atof( (*argv) );
+        argc--;
+    }
+    if( argc != 0 ) 
+    {
+        fprintf( stderr, "options: Check source file !\n" );
+        exit( 1 );
+    }
+       if( tbitr == 1 && outgap == 0 )
+       {
+               fprintf( stderr, "conflicting options : o, m or u\n" );
+               exit( 1 );
+       }
+       if( alg == 'C' && outgap == 0 )
+       {
+               fprintf( stderr, "conflicting options : C, o\n" );
+               exit( 1 );
+       }
+}
+
+int main( int argc, char *argv[] )
+{
+       static int  nlen[M];    
+       static char name[M][B], **seq;
+       int i, j, alloclen, c;
+       double **mtx;
+       double *self;
+       double tmpdouble;
+       FILE *fp;
+
+       arguments( argc, argv );
+
+       getnumlen( stdin );
+       rewind( stdin );
+
+       if( njob < 2 )
+       {
+               fprintf( stderr, "At least 2 sequences should be input!\n"
+                                                "Only %d sequence found.\n", njob ); 
+               exit( 1 );
+       }
+
+       seq = AllocateCharMtx( njob, nlenmax*9+1 );
+       mtx = AllocateDoubleMtx( njob, njob );
+       self = AllocateDoubleVec( njob );
+       alloclen = nlenmax*9;
+
+       readData( stdin, name, nlen, seq );
+       constants( njob, seq );
+
+
+
+
+       c = seqcheck( seq );
+       if( c )
+       {
+               fprintf( stderr, "Illeagal character %c\n", c );
+               exit( 1 );
+       }
+
+       for( i=0; i<njob; i++ ) 
+       {
+               self[i] = (double)substitution_nid( seq[i], seq[i] );
+//             fprintf( stdout, "self[%d] = %f\n", i, self[i] );
+       }
+
+       for( i=0; i<njob-1; i++ ) 
+               for( j=i+1; j<njob; j++ ) 
+               {
+                       tmpdouble = (double)substitution_score( seq[i], seq[j] );
+//                     fprintf( stdout, "tmpdouble = %f\n", tmpdouble );
+                       mtx[i][j] = ( 1.0 - tmpdouble / MIN( self[i], self[j] ) );
+                       if( mtx[i][j] < 0.95 )
+                               mtx[i][j] = - log( 1.0 - mtx[i][j] );
+                       else
+                               mtx[i][j] = 3.0;
+               }
+       
+#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 );
+
+       return( 0 );
+}