JWS-112 Bumping version of Mafft to version 7.310.

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

diff --git a/binaries/src/mafft/core/setdirection.c b/binaries/src/mafft/core/setdirection.c
new file mode 100644 (file)
index 0000000..6d46c5a
--- /dev/null
+++ b/binaries/src/mafft/core/setdirection.c
@@ -0,0 +1,212 @@
+#include "mltaln.h"
+
+#define DEBUG 0
+
+char *directionfile;
+static int show_R_ = 1;
+
+static int subalignment;
+static int subalignmentoffset;
+
+void arguments( int argc, char *argv[] )
+{
+    int c;
+
+       inputfile = NULL;
+       directionfile = NULL;
+       subalignment = 0;
+       subalignmentoffset = 0;
+       show_R_ = 1;
+
+    while( --argc > 0 && (*++argv)[0] == '-' )
+       {
+        while ( (c = *++argv[0]) )
+               {
+            switch( c )
+            {
+                               case 'd':
+                                       directionfile = *++argv;
+                                       fprintf( stderr, "directionfile = %s\n", directionfile );
+                                       --argc;
+                                       goto nextoption;
+                               case 'i':
+                                       inputfile = *++argv;
+                                       fprintf( stderr, "inputfile = %s\n", inputfile );
+                                       --argc;
+                                       goto nextoption;
+                               case 'H':
+                                       subalignment = 1;
+                                       subalignmentoffset = myatoi( *++argv );
+                                       --argc;
+                                       goto nextoption;
+                               case 'r':
+                                       show_R_ = 0;
+                                       break;
+                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 *difp;
+       int nlenmin;
+       char **name;
+       char **seq;
+       char *tmpseq;
+       char line[100];
+       int *nlen;
+       int i, j;
+       int nsubalignments, maxmem;
+       int **subtable = NULL;
+       int *preservegaps = NULL;
+       char firstdir;
+       char *directions;
+
+       arguments( argc, argv );
+
+       reporterr( "subalignment = %d\n", subalignment );
+       reporterr( "subalignmentoffset = %d\n", subalignmentoffset );
+
+
+       if( inputfile )
+       {
+               infp = fopen( inputfile, "r" );
+               if( !infp )
+               {
+                       fprintf( stderr, "Cannot open %s\n", inputfile );
+                       exit( 1 );
+               }
+       }
+       else
+               infp = stdin;
+
+       if( directionfile )
+       {
+               difp = fopen( directionfile, "r" );
+               if( !difp )
+               {
+                       fprintf( stderr, "Cannot open %s\n", directionfile );
+                       exit( 1 );
+               }
+       }
+       else
+       {
+               fprintf( stderr, "Give directionfile!\n" );
+       }
+
+
+       dorp = NOTSPECIFIED;
+       getnumlen_casepreserve( infp, &nlenmin );
+
+       fprintf( stderr, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
+
+       seq = AllocateCharMtx( njob, nlenmax+1 );
+       tmpseq = AllocateCharVec( MAX( B, nlenmax )+1 );
+       name = AllocateCharMtx( njob, B+1 );
+       nlen = AllocateIntVec( njob );
+       directions = calloc( njob, sizeof( int ) );
+
+       readData_pointer_casepreserve( infp, name, nlen, seq );
+
+
+
+
+
+       for( i=0; i<njob; i++ )
+       {
+               fgets( line, 99, difp );
+               if( line[0] != '_' )
+               {
+                       fprintf( stderr, "Format error!\n" );
+                       exit( 1 );
+               }
+               if( line[1] == 'R' )
+               {
+                       directions[i] = 'R';
+                       sreverse( tmpseq, seq[i] );
+                       strcpy( seq[i], tmpseq );
+
+                       strncpy( tmpseq, name[i]+1, B-3 );
+                       tmpseq[B-3] = 0;
+                       if( show_R_ )
+                       {
+                               strcpy( name[i]+1, "_R_" );
+                               strcpy( name[i]+4, tmpseq );
+                       }
+                       else
+                       {
+                               strcpy( name[i]+1, tmpseq );
+                       }
+               }
+               else if( line[1] == 'F' )
+               {
+                       directions[i] = 'F';
+               }
+               else
+               {
+                       fprintf( stderr, "Format error!\n" );
+                       exit( 1 );
+               }
+       }
+
+       if( subalignment )
+       {
+               readsubalignmentstable( njob, NULL, NULL, &nsubalignments, &maxmem );
+               reporterr(       "nsubalignments = %d\n", nsubalignments );
+               reporterr(       "maxmem = %d\n", maxmem );
+               subtable = AllocateIntMtx( nsubalignments, maxmem+1 );
+               preservegaps = AllocateIntVec( njob );
+               readsubalignmentstable( njob, subtable, preservegaps, NULL, NULL );
+
+               for( j=0; j<nsubalignments; j++ ) 
+               {
+                       reporterr( "Checking directions of sequences in subalignment%d\n", j );
+                       firstdir = directions[subtable[j][0]];
+                       reporterr( "firstdir = %c\n", firstdir );
+                       for( i=0; subtable[j][i]>-1; i++ )
+                       {
+                               if( directions[subtable[j][i]] != firstdir )
+                               {
+                                       reporterr( "\n\n#############################################################################\n" );
+                                       reporterr( "\nDirection of nucleotide sequences seems to be inconsistent.\n" );
+                                       reporterr( "Please check the following two sequences:\n" );
+                                       reporterr( "    Sequece no.%d (%s)\n", subtable[j][0]+1, name[subtable[j][0]] );
+                                       reporterr( "    Sequece no.%d (%s)\n", subtable[j][i]+1, name[subtable[j][i]] );
+                                       reporterr( "\nThese sequences are in sub alignment no.%d in your setting of --merge,\nbut their directions seem to be different.\n\n", j+1 );
+                                       reporterr( "#############################################################################\n\n\n\n" );
+                                       exit( 1 );
+                               }
+                       }
+                       reporterr( "OK!\n" );
+               }
+       }
+
+
+       for( i=0; i<njob; i++ )
+       {
+               fprintf( stdout, ">%s\n", name[i]+1 );
+               fprintf( stdout, "%s\n", seq[i] );
+       }
+
+       free( nlen );
+       FreeCharMtx( seq );
+       FreeCharMtx( name );
+       free( tmpseq );
+
+       return( 0 );
+}