JWS-112 Bumping version of Mafft to version 7.310.

[jabaws.git] / binaries / src / mafft / core / multi2hat3s.c

diff --git a/binaries/src/mafft/core/multi2hat3s.c b/binaries/src/mafft/core/multi2hat3s.c
index f747218..9f31020 100644 (file)
--- a/binaries/src/mafft/core/multi2hat3s.c
+++ b/binaries/src/mafft/core/multi2hat3s.c
@@ -79,12 +79,12 @@ void arguments( int argc, char *argv[] )
                                        --argc;
                                        goto nextoption;
                                case 't':
-                                       nhomologs = atoi( *++argv );
+                                       nhomologs = myatoi( *++argv );
                                        fprintf( stderr, "nhomologs = %d\n", nhomologs );
                                        --argc;
                                        goto nextoption;
                                case 'o':
-                                       seedoffset = atoi( *++argv );
+                                       seedoffset = myatoi( *++argv );
                                        fprintf( stderr, "seedoffset = %d\n", seedoffset );
                                        --argc;
                                        goto nextoption;
@@ -133,11 +133,11 @@ int countamino( char *s, int end )
        return( val );
 }
 
-static void pairalign( char name[M][B], int nlen[M], char **seq, double *effarr, int alloclen )
+static void pairalign( char **name, int nlen[M], char **seq, double *effarr, int alloclen )
 {
        int i, j;
        FILE *hat3p;
-       float pscore = 0.0; // by D.Mathog
+       double pscore = 0.0; // by D.Mathog
        static double *effarr1 = NULL;
        static double *effarr2 = NULL;
        char *aseq;
@@ -206,7 +206,7 @@ static void pairalign( char name[M][B], int nlen[M], char **seq, double *effarr,
 
 
                        fprintf( stderr, "adding %d-%d\r", i, j );
-                       putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) );
+                       putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ), 'k' );
                        for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
                        {
                                if( tmpptr->opt == -1.0 ) continue;
@@ -298,7 +298,7 @@ static void WriteOptions( FILE *fp )
 int main( int argc, char *argv[] )
 {
        static int  nlen[M];    
-       static char name[M][B], **seq;
+       static char **name, **seq;
        static char **bseq;
        static double *eff;
        int i;
@@ -330,6 +330,7 @@ int main( int argc, char *argv[] )
                exit( 1 );
        }
 
+       name = AllocateCharMtx( njob, B+1 );
        seq = AllocateCharMtx( njob, nlenmax*9+1 );
        bseq = AllocateCharMtx( njob, nlenmax*9+1 );
        alloclen = nlenmax*9;
@@ -339,7 +340,7 @@ int main( int argc, char *argv[] )
 #if 0
        Read( name, nlen, seq );
 #else
-       readData( infp, name, nlen, seq );
+       readData_pointer( infp, name, nlen, seq );
 #endif
        fclose( infp );
 
@@ -370,7 +371,8 @@ int main( int argc, char *argv[] )
        for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
 
 
-       for( i=0; i<njob; i++ ) fprintf( stdout, ">_seed_%s\n%s\n", name[i]+1, bseq[i] );
+//     for( i=0; i<njob; i++ ) fprintf( stdout, ">_seed_%s\n%s\n", name[i]+1, bseq[i] ); // CHUUI!!
+       for( i=0; i<njob; i++ ) fprintf( stdout, ">_seed_%s\n%s\n", name[i]+1, seq[i] );
 
        pairalign( name, nlen, seq, eff, alloclen );