package Bio::DOOP::ClusterSubset;

use strict;
use warnings;

=head1 NAME

  Bio::DOOP::ClusterSubset - One subset of a cluster

=head1 VERSION

Version 0.12

=cut

our $VERSION = '0.12';

=head1 SYNOPSIS

  @cluster_subsets = @{$cluster->get_all_subsets};


=head1 DESCRIPTION

  This object represents one subset of a cluster. A subset is a set of homologous sequences,
  hopefully monophyletic, grouped by evolutionary distance from the reference species (Arabidopsis
  or human).

=head1 AUTHORS

  Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary

=head1 METHODS

=cut

=head2 new

  $cluster_subset = Bio::DOOP::ClusterSubset->new($db,"123");

  You can create the object with the new method.
  The arguments are the following : Bio::DOOP::DBSQL object, subset_primary_id

=cut


sub new {
  my $self                 = {};
  my $dummy                = shift;
  my $db                   = shift;
  my $id                   = shift;

  my $ret    = $db->query("SELECT * FROM cluster_subset WHERE subset_primary_id = \"$id\";");

  if ($#$ret == -1){
     return(-1);
  }

  my @fields = @{$$ret[0]};

  $self->{DB}              = $db;
  $self->{PRIMARY}         = $id;
  $self->{TYPE}            = $fields[1];
  $self->{SEQNO}           = $fields[2];
  $self->{MOTIFNO}         = $fields[3];
  $self->{FEATNO}          = $fields[4];
  $self->{ORIG}            = $fields[5];
  $self->{CLUSTER}         = Bio::DOOP::Cluster->new_by_id($db,$fields[6]);

  $ret = $db->query("SELECT alignment_dialign,alignment_fasta FROM cluster_subset_data WHERE subset_primary_id = \"$id\";");

  if ($#$ret == -1){
     return(-1);
  }

  @fields = @{$$ret[0]};

  $self->{DIALIGN}          = $fields[0];
  $self->{FASTA}            = $fields[1];

  bless $self;
  return($self);
}

=head2 get_id

  print $cluster_subset->get_id;

  Prints out the subset primary id. This is the internal ID from the MySQL database.
  Return type: string

=cut

sub get_id {
  my $self                 = shift;
  return($self->{PRIMARY});
}

=head2 get_type

  print $cluster_subset->get_type;

  Prints out the subset type.
  Return type: string

=cut

sub get_type {
  my $self                 = shift;
  return($self->{TYPE});
}

=head2 get_seqno

  for(i = 0; i < $cluster_subset->get_seqno; i++){
      print $seq[$i];
  }
  Prints out all sequences linked to the subset.

  The get_seqno method returns the number of sequences in the subset.
  Return type: string

=cut

sub get_seqno {
  my $self                 = shift;
  return($self->{SEQNO});
}

=head2 get_featno

  if ($cluster_subset->get_featno > 4){
      print "We have lots of features!!!\n";
  }

  The get_featno method returns the total number of features in the subset.
  Return type: string

=cut

sub get_featno {
  my $self                 = shift;
  return($self->{FEATNO});
}

=head2 get_motifno

  $motifs = $cluster_subset->get_motifno;

  The get_motifno method returns the number of motifs in the subset.
  Return type: string

=cut

sub get_motifno {
  my $self                 = shift;
  return($self->{MOTIFNO});
}

=head2 get_orig

  if ($cluster_subset->get_orig eq "y") {
      print "This is the original cluster!\n";
  }
  elsif ($cluster_subset->get_orig eq "n"){
      print "This is some smaller subset!\n";
  }

  Return type: string ('y' or 'n')

=cut

sub get_orig {
  my $self                 = shift;
  return($self->{ORIG});
}

=head2 get_cluster

  $cluster_id = $cluster_subset->get_cluster;

  Returns the ID of the cluster, from which the subset originates.
  Return type: string

=cut

sub get_cluster {
  my $self                 = shift;
  return($self->{CLUSTER});
}

=head2 get_dialign

  print $cluster_subset->get_dialign;

  Prints out the dialign format alignment of the subset.
  Return type: string

=cut

sub get_dialign {
  my $self                 = shift;
  return($self->{DIALIGN});
}

=head2 get_fasta_align

  print $cluster_subset->get_fasta_align;

  Prints out the fasta format alignment of the subset.
  Return type: string

=cut

sub get_fasta_align {
  my $self                 = shift;
  return($self->{FASTA});
}

=head2 get_all_motifs

  @motifs = @{$cluster_subset->get_all_motifs};

  Returns the arrayref of all motifs associated with the subset.
  Return type: arrayref, the array containig Bio::DOOP::Motif objects

=cut

sub get_all_motifs {
  my $self                 = shift;

  my $id                   = $self->{PRIMARY};
  my $i;
  my @motifs;

  my $ret = $self->{DB}->query("SELECT motif_feature_primary_id FROM motif_feature WHERE subset_primary_id = $id;");

  if ($#$ret == -1){
     return(-1);
  }

  for($i = 0; $i < $#$ret + 1; $i++){
	  push @motifs,Bio::DOOP::Motif->new($self->{DB},$$ret[$i]->[0]);
  }

  return(\@motifs);
}

=head2 get_all_seqs

  @seq = @{$cluster_subset->get_all_seqs};

  Returns the arrayref of all sequences associated with the subset.
  Return type: arrayref, the array containig Bio::DOOP::Sequence objects

=cut

sub get_all_seqs {
  my $self                 = shift;

  my $id                   = $self->{PRIMARY};
  my @seqs;
  my $ret = $self->{DB}->query("SELECT sequence_primary_id FROM subset_xref WHERE subset_primary_id = $id;");

  if ($#$ret == -1){
     return(-1);
  }

  for(@$ret){
	  push @seqs,Bio::DOOP::Sequence->new($self->{DB},$_->[0]);
  }
  # Sorting the sequences by the following criteria:
  # The first sequence is always the reference species (Arabidopsis/Human).
  # All other sequences are sorted first by the taxon_class (B E M V in the plants and 
  # P R E H M N T F V C in the chordates ) and then by the alphabetical order.

  my $seq;
  my $i;
  my %groups;
  my @sortseqs;

  for($i = 0; $i < $#seqs+1; $i++){
     if( ($seqs[$i]->get_taxon_name eq "Arabidopsis thaliana") || 
         ($seqs[$i]->get_taxon_name eq "Homo sapiens") ) {
         $sortseqs[0] = $seqs[$i];
         next;
     }
     push @{$groups{$seqs[$i]->get_taxon_class}}, $seqs[$i];
  }

  for my $key ("Brassicaceae","eudicotyledons","Magnoliophyta","Viridiplantae"){
     if ($groups{$key}){
        push @sortseqs, sort {$a->get_taxon_name cmp $b->get_taxon_name} @{$groups{$key}};
     }
  }
  for my $key ("Primates", "Glires","Euarchontoglires" , "Cetartiodactyla","Carnivora","Laurasiatheria","Xenarthra","Afrotheria" , "Metatheria" , "Prototheria" , "Aves","Sauropsida" , "Amphibia" , "Teleostomi" , "Chondrichthyes","Vertebrata" , "Chordata"){     if ($groups{$key}){
        push @sortseqs, sort {$a->get_taxon_name cmp $b->get_taxon_name} @{$groups{$key}};
     }
  }
  return(\@sortseqs);
}

1;