# this works as a bash include
#
#COMM SeqLab::Align - join alignment segments (&AlnJoin after &AlnSplit)
#
function flt_clwhead {
  perl -ne 'if(m/^CLUSTAL W \(/){ scalar <> } else{ print }' "$@"
}

perl -e '
    use lib shift();  # give include precedence to code directory, perl -I would not work!
    use SeqLab::Align;
    my ($fin) = @ARGV;
    open (IN,$fin); my @d; while(<IN>){ push @d,$_ }; my $d=join(q(),@d);
    my $pAln = &AlnClustalRead(\$d);
    # split
    my ($pAln5,$pAln3) = &AlnSplit($pAln,15);
    # gap linker - without effect
    my $pAlnL = [ {id=>$pAln3->[0]{id}, sequence=>q(-) } ];
    # another seq in one segment
    push @$pAln3, { %{$pAln3->[0]} }; $pAln3->[-1]{id} .= q(+);
    # join and output
    my $pAlnJ = &AlnJoin($pAln5,$pAlnL,$pAln3,$pAln5);
    print &AlnClustalSprint($pAlnJ);
  ' -- "$dircode" "$dirtest"/${setstamp}_data.aln  \
| flt_clwhead -
