diff variant_effect_predictor/Bio/EnsEMBL/Compara/SitewiseOmega.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Compara/SitewiseOmega.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,361 @@
+
+#
+# Ensembl module for Bio::EnsEMBL::Compara::SitewiseOmega
+#
+# Cared for by Albert Vilella <[e-mail]>
+#
+# Copyright Albert Vilella
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::Compara::SitewiseOmega - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 AUTHOR - Albert Vilella
+
+This modules is part of the Ensembl project http://www.ensembl.org
+
+Email [e-mail]
+
+Describe contact details here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::EnsEMBL::Compara::SitewiseOmega;
+
+use strict;
+
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(warning deprecate throw);
+
+=head2 new_fast
+
+  Arg [1]    : hash reference $hashref
+  Example    : none
+  Description: This is an ultra fast constructor which requires knowledge of
+               the objects internals to be used.
+  Returntype :
+  Exceptions : none
+  Caller     :
+
+=cut
+
+sub new_fast {
+  my ($class, $hashref) = @_;
+
+  return bless $hashref, $class;
+}
+
+=head2 member_position
+
+  Arg [1]    : Bio::EnsEMBL::Member $member
+  Arg [2]    : Bio::SimpleAlign $aln
+  Example    : $sitewise_omega->member_position($member,$aln);
+  Description: Obtain the member position for a given sitewise_omega value
+  Returntype : integer
+  Exceptions : return undef if member not in the alignment or aln_position not in member
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub member_position {
+  my ($self, $member, $aln) = @_;
+
+  throw("$member is not a Bio::EnsEMBL::Compara::Member object")
+    unless ($member->isa("Bio::EnsEMBL::Compara::Member"));
+
+  throw("$aln is not a Bio::SimpleAlign object")
+    unless ($aln->isa("Bio::SimpleAlign"));
+
+  my @seqs = $aln->each_seq_with_id($member->stable_id);
+  my $seq = $seqs[0];
+
+  my $seq_location;
+  eval { $seq_location = $seq->location_from_column($self->aln_position);};
+  return undef if ($@);
+  my $location_type;
+  eval { $location_type = $seq_location->location_type;};
+  return undef if ($@);
+  if ($seq_location->location_type eq 'EXACT') {
+    my $member_position = $seq_location->start;
+    return $member_position;
+  }
+
+  return undef;
+}
+
+=head2 adaptor
+
+  Arg [1]    : Bio::EnsEMBL::DBSQL::SitewiseOmegaAdaptor $adaptor
+  Example    : $sitewise_omega->adaptor($adaptor);
+  Description: Getter/Setter for the adaptor this object used for database
+               interaction
+  Returntype : Bio::EnsEMBL::DBSQL::SitewiseOmegaAdaptor object
+  Exceptions : thrown if the argument is not a
+               Bio::EnsEMBL::DBSQL::SitewiseOmegaAdaptor object
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub adaptor {
+  my ( $self, $adaptor ) = @_;
+
+  if (defined($adaptor)) {
+    throw("$adaptor is not a Bio::EnsEMBL::Compara::DBSQL::SitewiseOmegaAdaptor object")
+        unless ($adaptor->isa("Bio::EnsEMBL::Compara::DBSQL::SitewiseOmegaAdaptor"));
+    $self->{'adaptor'} = $adaptor;
+  }
+
+  return $self->{'adaptor'};
+}
+
+=head2 aln_position
+
+  Arg [1]    : (opt) integer
+  Example    : $sitewise_dnds->aln_position(1);
+  Description: Getter/Setter for the alignment position
+  Returntype : integer. Return 1 if value not defined
+  Exceptions : none
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub aln_position {
+    my ($self, $aln_position) = @_;
+
+    if(defined $aln_position) {
+	$self->{'aln_position'} = $aln_position;
+    }
+
+  $self->{'aln_position'}= undef unless(defined($self->{'aln_position'}));
+  return $self->{'aln_position'};
+}
+
+
+=head2 omega
+
+  Arg [1]    : (opt) integer
+  Example    : $sitewise_dnds->omega(1);
+  Description: Getter/Setter for the omega value
+  Returntype : integer. Return 1 if value not defined
+  Exceptions : none
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub omega {
+    my ($self, $omega) = @_;
+
+    if(defined $omega) {
+	$self->{'omega'} = $omega;
+    }
+
+  $self->{'omega'}= undef unless(defined($self->{'omega'}));
+  return $self->{'omega'};
+}
+
+
+=head2 omega_lower
+
+  Arg [1]    : (opt) float
+  Example    : $sitewise_dnds->omega_lower(1);
+  Description: Getter/Setter for the omega_lower value
+  Returntype : float. Return 1 if value not defined
+  Exceptions : none
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub omega_lower {
+    my ($self, $omega_lower) = @_;
+
+    if(defined $omega_lower) {
+	$self->{'omega_lower'} = $omega_lower;
+    }
+
+  $self->{'omega_lower'}= undef unless(defined($self->{'omega_lower'}));
+  return $self->{'omega_lower'};
+}
+
+
+=head2 omega_upper
+
+  Arg [1]    : (opt) float
+  Example    : $sitewise_dnds->omega_upper(1);
+  Description: Getter/Setter for the omega_upper value
+  Returntype : float. Return 1 if value not defined
+  Exceptions : none
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub omega_upper {
+    my ($self, $omega_upper) = @_;
+
+    if(defined $omega_upper) {
+	$self->{'omega_upper'} = $omega_upper;
+    }
+
+  $self->{'omega_upper'}= undef unless(defined($self->{'omega_upper'}));
+  return $self->{'omega_upper'};
+}
+
+
+=head2 optimal
+
+  Arg [1]    : (opt) float
+  Example    : $sitewise_dnds->optimal(1);
+  Description: Getter/Setter for the optimal value
+  Returntype : float. Return 1 if value not defined
+  Exceptions : none
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub optimal {
+    my ($self, $optimal) = @_;
+
+    if(defined $optimal) {
+	$self->{'optimal'} = $optimal;
+    }
+
+  $self->{'optimal'}= undef unless(defined($self->{'optimal'}));
+  return $self->{'optimal'};
+}
+
+
+=head2 threshold_on_branch_ds
+
+  Arg [1]    : (opt) float
+  Example    : $sitewise_dnds->threshold_on_branch_ds(1);
+  Description: Getter/Setter for the threshold_on_branch_ds value
+  Returntype : float. Return 1 if value not defined
+  Exceptions : none
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub threshold_on_branch_ds {
+    my ($self, $threshold_on_branch_ds) = @_;
+
+    if(defined $threshold_on_branch_ds) {
+	$self->{'threshold_on_branch_ds'} = $threshold_on_branch_ds;
+    }
+
+  $self->{'threshold_on_branch_ds'}= undef unless(defined($self->{'threshold_on_branch_ds'}));
+  return $self->{'threshold_on_branch_ds'};
+}
+
+=head2 type
+
+  Arg [1]    : (opt) integer
+  Example    : $sitewise_dnds->type(1);
+  Description: Getter/Setter for the type value
+  Returntype : integer. Return 1 if value not defined
+  Exceptions : none
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub type {
+    my ($self, $type) = @_;
+
+    if(defined $type) {
+	$self->{'type'} = $type;
+    }
+
+  $self->{'type'}= undef unless(defined($self->{'type'}));
+  return $self->{'type'};
+}
+
+
+=head2 node_id
+
+  Arg [1]    : (opt) integer
+  Example    : $sitewise_dnds->node_id(1);
+  Description: Getter/Setter for the node_id value
+  Returnnode_id : integer. Return 1 if value not defined
+  Exceptions : none
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub node_id {
+    my ($self, $node_id) = @_;
+
+    if(defined $node_id) {
+	$self->{'node_id'} = $node_id;
+    }
+
+  $self->{'node_id'}= undef unless(defined($self->{'node_id'}));
+  return $self->{'node_id'};
+}
+
+=head2 tree_node_id
+
+  Arg [1]    : (opt) integer
+  Example    : $sitewise_dnds->tree_node_id(1);
+  Description: Getter/Setter for the tree_node_id value
+  Returntree_node_id : integer. Return 1 if value not defined
+  Exceptions : none
+  Caller     : general
+  Status     : At risk
+
+=cut
+
+sub tree_node_id {
+    my ($self, $tree_node_id) = @_;
+
+    if(defined $tree_node_id) {
+	$self->{'tree_node_id'} = $tree_node_id;
+    }
+
+  $self->{'tree_node_id'}= undef unless(defined($self->{'tree_node_id'}));
+  return $self->{'tree_node_id'};
+}
+
+
+sub dbID {
+    my ($self, $dbID) = @_;
+
+    if(defined $dbID) {
+	$self->{'_dbID'} = $dbID;
+    }
+
+  $self->{'_dbID'}= undef unless(defined($self->{'_dbID'}));
+  return $self->{'_dbID'};
+}
+
+
+
+
+1;