From 03a364ad93cc7ba813952e5fff9372f7ece0ef89 Mon Sep 17 00:00:00 2001 From: Brian Osborne Date: Mon, 14 Jul 2014 18:24:26 -0400 Subject: [PATCH] Add to documentation, reorganize code a bit --- Bio/SeqFeature/Generic.pm | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/Bio/SeqFeature/Generic.pm b/Bio/SeqFeature/Generic.pm index 7365b0f69..cefb9fd82 100644 --- a/Bio/SeqFeature/Generic.pm +++ b/Bio/SeqFeature/Generic.pm @@ -180,7 +180,8 @@ sub new { -phase the phase of the feature (0..2) -primary_tag primary tag -primary (synonym for -primary_tag) - -source source tag + -source_tag source tag + -source (synonym for -source_tag) -frame frame -score score value -tag a reference to a tag/value hash @@ -196,7 +197,7 @@ sub set_attributes { my ($self,@args) = @_; my ($start, $end, $strand, $primary_tag, $source_tag, $primary, $source, $frame, $score, $tag, $gff_string, $gff1_string, - $seqname, $seqid, $annot, $location,$display_name, $pid,$phase) = + $seqname, $seqid, $annot, $location, $display_name, $pid, $phase) = $self->_rearrange([qw(START END STRAND @@ -224,18 +225,20 @@ sub set_attributes { $self->_from_gff_stream($gff1_string); }; - $pid && $self->primary_id($pid); - $primary_tag && $self->primary_tag($primary_tag); - $source_tag && $self->source_tag($source_tag); - $primary && $self->primary_tag($primary); - $source && $self->source_tag($source); - defined $start && $self->start($start); - defined $end && $self->end($end); - defined $strand && $self->strand($strand); - defined $frame && $self->frame($frame); - defined $display_name && $self->display_name($display_name); - defined $score && $self->score($score); - $annot && $self->annotation($annot); + $pid && $self->primary_id($pid); + $primary_tag && $self->primary_tag($primary_tag); + $source_tag && $self->source_tag($source_tag); + $primary && $self->primary_tag($primary); + $source && $self->source_tag($source); + $annot && $self->annotation($annot); + defined $start && $self->start($start); + defined $end && $self->end($end); + defined $strand && $self->strand($strand); + defined $frame && $self->frame($frame); + defined $display_name && $self->display_name($display_name); + defined $score && $self->score($score); + defined $phase && $self->phase($phase); + if($seqname) { $self->warn("-seqname is deprecated. Please use -seq_id instead."); $seqid = $seqname unless $seqid; @@ -246,7 +249,6 @@ sub set_attributes { $self->add_tag_value($t, UNIVERSAL::isa($tag->{$t}, "ARRAY") ? @{$tag->{$t}} : $tag->{$t}); } }; - defined $phase && $self->phase($phase); } -- 2.11.4.GIT