diff --git a/modules/Bio/EnsEMBL/Collection/Exon.pm b/modules/Bio/EnsEMBL/Collection/Exon.pm index 155a4a1d2e615678fee0488e36651ef310d8d51f..43f28c4addaca63690cdcfab259358d07cbc659a 100644 --- a/modules/Bio/EnsEMBL/Collection/Exon.pm +++ b/modules/Bio/EnsEMBL/Collection/Exon.pm @@ -2,6 +2,53 @@ package Bio::EnsEMBL::Collection::Exon; +=head1 NAME + +Bio::EnsEMBL::Collection::Exon - Feature collection implementation for +exon features. + +=head1 DESCRIPTION + +=head2 Extended feature representation + +An exon is represented by the basic feature representation (see +documentation of Bio::EnsEMBL::Collection) and by the following extended +feature representation: + +=over 4 + +=item 1. + +Phase + +=item 2. + +End phase + +=item 3. + +Stable ID + +=item 4. + +Version + +=item 5. + +Created date + +=item 6. + +Modified date + +=item 7. + +Is-current + +=back + +=cut + use strict; use warnings; @@ -48,9 +95,7 @@ sub _tables { my @tables = $this->SUPER::_tables(); - if ( $this->_lightweight() ) { - return ( $tables[0] ); - } + if ( $this->_lightweight() ) { return ( $tables[0] ) } return @tables; } @@ -70,9 +115,7 @@ sub _columns { sub _default_where_clause { my ($this) = @_; - if ( $this->_lightweight() ) { - return ''; - } + if ( $this->_lightweight() ) { return '' } return $this->SUPER::_default_where_clause(); } diff --git a/modules/Bio/EnsEMBL/Collection/RepeatFeature.pm b/modules/Bio/EnsEMBL/Collection/RepeatFeature.pm index 362a7d13817f16f5bdb90fdb02f0a01331318d0a..18736f34046477d9f3f123582d91199b11d870ee 100644 --- a/modules/Bio/EnsEMBL/Collection/RepeatFeature.pm +++ b/modules/Bio/EnsEMBL/Collection/RepeatFeature.pm @@ -2,6 +2,45 @@ package Bio::EnsEMBL::Collection::RepeatFeature; +=head1 NAME + +Bio::EnsEMBL::Collection::Exon - Feature collection implementation for +repeat features. + +=head1 DESCRIPTION + +=head2 Extended feature representation + +A repeat feature is represented by the basic feature representation (see +documentation of Bio::EnsEMBL::Collection) and by the following extended +feature representation: + +=over 4 + +=item 1. + +Hit start + +=item 2. + +Hit end + +=item 3. + +Score + +=item 4. + +Repeat consensus internal ID + +=item 5. + +Analysis internal ID + +=back + +=cut + use strict; use warnings; @@ -53,9 +92,7 @@ sub _tables { my @tables = $this->SUPER::_tables(); - if ( $this->_lightweight() ) { - return ( $tables[0] ); - } + if ( $this->_lightweight() ) { return ( $tables[0] ) } return @tables; } @@ -75,9 +112,7 @@ sub _columns { sub _default_where_clause { my ($this) = @_; - if ( $this->_lightweight() ) { - return ''; - } + if ( $this->_lightweight() ) { return '' } return $this->SUPER::_default_where_clause(); }