=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut

=pod 

=head1 NAME

Bio::EnsEMBL::Compara::StableId::Map

=head1 DESCRIPTION

A smart container object that maintains clusterid-2-clustername and clusterid-2-mappingscore relationships,
can load from file or save to file.

=cut

package Bio::EnsEMBL::Compara::StableId::Map;

use strict;
use warnings;
use Bio::EnsEMBL::Utils::Argument;  # import 'rearrange()'

sub new {
    my $class = shift @_;

    my $self = bless { }, $class;

    my ($type, $filename) =
         rearrange([qw(type filename) ], @_);

    $self->type($type)       if(defined($type));

    if($filename) {
        $self->load($filename);
    }

    return $self;
}

sub load {
    my $self     = shift @_;
    my $filename = shift @_;

    open(MAPFILE, $filename) || die "Could not open mapfile '$filename': $@";
    while(my $line=<MAPFILE>) {
        chomp $line;
            # support both formats during the switching period:
        my @syll = split(/\s+/, $line);
        my $clid   = shift @syll;
        my $score  = pop @syll;
        my $clname = pop @syll;

        $self->clid2clname($clid, $clname);
        $self->clid2score($clid,  $score);
    }
    close MAPFILE;
}

sub save {
    my $self     = shift @_;
    my $filename = shift @_;

    open(MAPFILE, ">$filename") || die "Could not open mapfile '$filename' for writing: $@";
    foreach my $clid (@{ $self->get_all_clids }) {
        print MAPFILE join("\t", $clid, $self->clid2clname($clid), $self->clid2score($clid))."\n";
    }
    close MAPFILE;
}

sub type {
    my $self = shift @_;

    if(@_) {
        $self->{'_type'} = shift @_;
    }
    return $self->{'_type'};
}

sub clid2clname {   # class_id -> class_name (1-to-1)
    my $self       = shift @_;
    my $clid  = shift @_;

    my $hash = $self->{'_clid2clname'} ||= {};

    if(@_) {
        $hash->{$clid} = shift @_;
    }
    return $hash->{$clid};
}

sub clid2score {   # class_id -> mapping score
    my $self       = shift @_;
    my $clid  = shift @_;

    my $hash = $self->{'_clid2score'} ||= {};

    if(@_) {
        $hash->{$clid} = shift @_;
    }
    return $hash->{$clid};
}

sub get_all_clids {
    my $self       = shift @_;

    return [ sort {$a<=>$b} keys %{ $self->{'_clid2clname'} ||= {} } ];
}

1;