if( $self->{'_seq'}->{$name} ) { $self->warn("Replacing one sequence [$name]\n") unless $self->verbose < 0; }

##</code><code>##

hit1_AM161438.1_1-497/20-516             gAGAAACCCUGGAA
hit1_AM161438.1_1-497/1-1:497-993        gGAAAAUCCGUCGA
hit1_EF374296.1_1-432/1-432              uauGGAAACWUACU
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

##</code><code>##

-------------------- WARNING ---------------------
MSG: Replacing one sequence [hit1_EF374296.1_1-432/1-432]

---------------------------------------------------

##</code><code>##

use strict;
use warnings;
use MyAlign;

my $aln = new MyAlign;
open ( ALIGN, "<inputAlignmentFile" ) or die "failed to open inputAlignmentFile";
$aln -> read_alignment ( \*ALIGN );
close ALIGN;

##</code><code>##

use Bio::SimpleAlign;

sub new {
    my $caller = shift;
    my $class  = ref( $caller ) || $caller;
    my $self   = $class -> SUPER::new();
    return $self;
}

sub read_alignment {
    my $self = shift;
    my $in = shift;
    my( %align, %c2name, $count );
    while( <$in> ) {
        /^([^\#]\S+)\s+([A-Za-z\.\-]+)\s*/ && do {      
            my $name = $1;
            my $seq = $2;
            if( ! defined $align{$name}  ) {
                $count++;
                $c2name{$count} = $name;
            }
            $align{$name} .= $seq;
            next;
        };
    }
    $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;
	} 
        my $seq = new Bio::LocatableSeq( '-seq'=>$align{$name}, '-id'=>$seqname,
		'-start'=>$start, '-end'=>$end, '-strand'=>$strand, '-type'=>'aligned' );
        $self -> add_seq($seq);
        $count++;
    }
    return $count; 
}