Mac binaries

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

diff --git a/website/archive/binaries/mac/src/mafft/core/restoreu.c b/website/archive/binaries/mac/src/mafft/core/restoreu.c
new file mode 100644 (file)
index 0000000..40055da
--- /dev/null
+++ b/website/archive/binaries/mac/src/mafft/core/restoreu.c
@@ -0,0 +1,229 @@
+#include "mltaln.h"
+
+#define DEBUG 0
+
+char *alignmentfile;
+
+static void fillorichar( int nseq, int *oripos, char **a, char **s )
+{
+       int i;
+       char *pta, *pts;
+       for( i=0; i<nseq; i++ )
+       {
+               pta = a[i];
+               pts = s[oripos[i]];
+               while( *pta )
+               {
+                       if( *pta != '-' ) *pta = *pts++;
+                       if( *pta++ == 0 )
+                       {
+                               fprintf( stderr, "ERROR!!\n" );
+                               fprintf( stderr, "alignment is inconsistent with the original sequences\n" );
+                               exit( 1 );
+                       }
+               }
+               if( *pts != 0 )
+               {
+                       fprintf( stderr, "ERROR!!\n" );
+                       fprintf( stderr, "alignment is inconsistent with the original sequences\n" );
+                       exit( 1 );
+               }
+       }
+}
+
+void arguments( int argc, char *argv[] )
+{
+    int c;
+
+    while( --argc > 0 && (*++argv)[0] == '-' )
+       {
+        while ( (c = *++argv[0]) )
+               {
+            switch( c )
+            {
+                               case 'i':
+                                       inputfile = *++argv;
+                                       --argc;
+                                       goto nextoption;
+                               case 'a':
+                                       alignmentfile = *++argv;
+                                       --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;
+       FILE *alfp;
+       char **name;
+       char **aname;
+       char **oname;
+       char **seq;
+       char **aseq;
+       int *nlen;
+       int *oripos;
+       char *npt, *npt2;
+       int i, o, prelen;
+       int nlenmin;
+       int njobs, njoba;
+
+       arguments( argc, argv );
+
+       if( inputfile )
+       {
+               infp = fopen( inputfile, "r" );
+               if( !infp )
+               {
+                       fprintf( stderr, "Cannot open %s\n", inputfile );
+                       exit( 1 );
+               }
+       }
+       else
+               infp = stdin;
+
+       if( alignmentfile )
+       {
+               alfp = fopen( alignmentfile, "r" );
+               if( !alfp )
+               {
+                       fprintf( stderr, "Cannot open %s\n", alignmentfile );
+                       exit( 1 );
+               }
+       }
+       else
+       {
+               fprintf( stderr, "No alignment is given.\n" );
+               exit( 1 );
+       }
+       
+       dorp = NOTSPECIFIED;
+       getnumlen_casepreserve( infp, &nlenmin );
+       njobs = njob;
+//     fprintf( stderr, "in infp, %d x %d - %d %c\n", njob, nlenmin, nlenmax, dorp );
+
+       seq = AllocateCharMtx( njob, nlenmax+1 );
+       name = AllocateCharMtx( njob, B+1 );
+       nlen = AllocateIntVec( njob );
+       oripos = AllocateIntVec( njob );
+       readData_pointer_casepreserve( infp, name, nlen, seq );
+
+       dorp = NOTSPECIFIED;
+       getnumlen( alfp );
+       njoba = njob;
+//     fprintf( stderr, "in alfp, %d x %d %c\n", njob, nlenmax, dorp );
+       aseq = AllocateCharMtx( njob, nlenmax+1 );
+       aname = AllocateCharMtx( njob, B+1 );
+       oname = AllocateCharMtx( njob, B+1 );
+       readData_pointer( alfp, aname, nlen, aseq );
+
+       for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );
+
+       if( njoba != njobs )
+       {
+               fprintf( stderr, "ERROR!!\n" );
+               fprintf( stderr, "In input file,\n" );
+               fprintf( stderr, "njob = %d\n", njobs );
+               fprintf( stderr, "but in alignment file,\n" );
+               fprintf( stderr, "njob = %d\n", njoba );
+               exit( 1 );
+       }
+
+       for( i=0; i<njob; i++ )
+       {
+#if 0
+               if( strstr( aname[i], "_seed_" ) )
+               {
+                       npt2 = aname[i] + 7;
+                       strcpy( oname[i], "=_seed_" );
+               }
+               else
+               {
+                       npt2 = aname[i] + 1;
+                       strcpy( oname[i], "=" );
+               }
+
+               fprintf( stderr, "npt2 = %s\n", npt2 );
+
+               o = oripos[i] = atoi( npt2 );
+               npt = strstr( npt2, "_oripos_" );
+               if( npt == NULL )
+               {
+                       fprintf( stderr, "Format error!\n" );
+                       exit( 1 );
+               }
+               npt += 8;
+               strcat( oname[i], npt+1 );
+#endif
+               npt = strstr( aname[i], "_oripos_" );
+               if( npt == NULL )
+               {
+                       fprintf( stderr, "Format error!\n" );
+                       exit( 1 );
+               }
+               npt2 = npt - 2;
+               while( isdigit( *npt2-- ) );
+               npt2 += 2;
+               npt += 8;
+               o = oripos[i] = atoi( npt2 );
+//             fprintf( stderr, "npt2 = :%s:\n", npt2 );
+//             fprintf( stderr, "npt = :%s:\n", npt );
+//             fprintf( stderr, "aname[i] = :%s:\n", aname[i] );
+//             fprintf( stderr, "npt2-aname[i] = :%d:\n", npt2-aname[i] );
+
+               prelen = npt2-aname[i];
+               strncpy( oname[i], aname[i], prelen ); oname[i][prelen] = 0;
+               strcat( oname[i], npt+1 );
+
+               if( strncmp( npt, name[o], 10 ) )
+               {
+                       fprintf( stderr, "ERROR!!\n" );
+                       fprintf( stderr, "In input file,\n" );
+                       fprintf( stderr, "name[%d] = %s\n", o, name[o] );
+                       fprintf( stderr, "but in alignment file,\n" );
+                       fprintf( stderr, "name[%d] = %s\n", i, aname[i] );
+                       exit( 1 );
+               }
+#if 0
+               else
+               {
+                       fprintf( stderr, "OK!!\n" );
+                       fprintf( stderr, "In input file,\n" );
+                       fprintf( stderr, "name[%d] = %s\n", o, name[o] );
+                       fprintf( stderr, "and in alignment file,\n" );
+                       fprintf( stderr, "name[%d] = %s\n", i, aname[i] );
+                       fprintf( stderr, "\n" );
+               }
+#endif
+       }
+//     fprintf( stderr, "seq[0] = %s\n", seq[0] );
+//     fprintf( stderr, "aseq[0] = %s\n", aseq[0] );
+
+       fillorichar( njob, oripos, aseq, seq );
+
+
+       writeData_pointer( stdout, njob, oname, nlen, aseq );
+
+       FreeCharMtx( seq );
+       FreeCharMtx( aseq );
+       FreeCharMtx( name );
+       FreeCharMtx( aname );
+       free( nlen );
+
+       return( 0 );
+}