use strict;
use warnings;

++$|; ## buffering off

my %align;
my $count = 0;
my %c2name;

use Bio::SimpleAlign;

my $self = Bio::SimpleAlign->new();


print "---> Reading data\n";
while( <DATA> ) {
	/^([^\#]\S+)\s+([A-Za-z\.\-]+)\s*/ && do {      
		my $name = $1;
		my $seq = $2;
		if( ! defined $align{$name}  ) {
			$count++;
			$c2name{$count} = $name;
		}
		$align{$name} .= $seq;
		print "Count >$count< - Adding Name >$name<\n\tSeq >$seq<\n";
	};
    }
    
    print "---> Forming alignment\n";
    
    $count = 0;
    foreach my $no ( sort { $a <=> $b } keys %c2name ) {
        my $name = $c2name{$no};
	my( $seqname, $start, $end, $strand );
        if( $name =~ /(\S+)\/(\d+)-(\d+)$/ ) {
            $seqname = $1; $start = $2; $end = $3;
        } elsif ( $name =~ /(\S+)\/(\d+)-(\d+):(\d+)-(\d+)/ ) {
	    $seqname = $1; my $ns = $2; my $s = $3; my $e = $4; my $ne = $5;
            $start = "$ns-$s"; $end = "$e-$ne"; # surprise: this is legal
	    $strand = 1;
	} 
		
                ## make sure id is unique
		#$seqname .= 'x' while ( exists $align{id}{$seqname} );
		#++$align{id}{$seqname};

		print "Name >$name<\n\tID >$seqname<\n";
        my $seq = new Bio::LocatableSeq( '-seq'=>$align{$name}, '-id'=>$seqname,
		'-start'=>$start, '-end'=>$end, '-strand'=>$strand, '-type'=>'aligned' );
        $self -> add_seq($seq);
        $count++;
    }
    print "Count : $count\n";

__DATA__
hit1_EF374296.1_1-432/1-432              uauGGAAACWUACU
hit1_AM161438.1_1-497/20-516             gAGAAACCCUGGAA
hit1_AM161438.1_1-497/1-1:497-993        gGAAAAUCCGUCGA
hit1_EF374296.1_1-432/1-1:432-863        UGAAAAUCCGUCGA
hit1_EF374296.1_509-949/509-509:949-1389 GGAAAAUCCGUCGA
hit1_EF374296.1_509-949/938-1382         AUAGUAAGAGGAAA
hit1_EF374297.1_30-470/30-30:470-910     GGAAAAUCCGUCGA