From 6d244bfff2c1537e0d0723217aae3bcaf6bfd3f7 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Fri, 23 Nov 2012 17:13:03 +0000
Subject: [PATCH] Bringing in summaries as hashes
---
modules/Bio/EnsEMBL/MiscFeature.pm | 25 +++++++++++++++++++++++++
modules/Bio/EnsEMBL/SimpleFeature.pm | 22 ++++++++++++++++++++++
2 files changed, 47 insertions(+)
diff --git a/modules/Bio/EnsEMBL/MiscFeature.pm b/modules/Bio/EnsEMBL/MiscFeature.pm
index 854f2d53f4..5b30f19b35 100644
--- a/modules/Bio/EnsEMBL/MiscFeature.pm
+++ b/modules/Bio/EnsEMBL/MiscFeature.pm
@@ -376,7 +376,32 @@ sub display_id {
}
}
+=head2 summary_as_hash
+ Example : my $hash = $misc_feature->summary_as_hash();
+ Description: Generates a HashRef compatible with GFFSerializer. Adds
+ all attribute key value pairs plus MiscSet codes and names
+ Returntype : Hash
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub summary_as_hash {
+ my ($self) = @_;
+ my $hash = $self->SUPER::summary_as_hash();
+ my $attributes = $self->get_all_Attributes();
+ foreach my $attr (@{$attributes}) {
+ $hash->{$attr->name()} = $attr->value();
+ }
+ my $misc_sets = $self->get_all_MiscSets();
+ foreach my $set (@{$misc_sets}) {
+ push(@{$hash->{misc_set_code}},$set->code());
+ push(@{$hash->{misc_set_name}},$set->name());
+ }
+ return $hash;
+}
1;
diff --git a/modules/Bio/EnsEMBL/SimpleFeature.pm b/modules/Bio/EnsEMBL/SimpleFeature.pm
index e0c0ce8b6a..f0beadebb8 100644
--- a/modules/Bio/EnsEMBL/SimpleFeature.pm
+++ b/modules/Bio/EnsEMBL/SimpleFeature.pm
@@ -162,5 +162,27 @@ sub score {
return $self->{'score'};
}
+=head2 summary_as_hash
+
+ Example : my $hash = $simple_feature->summary_as_hash();
+ Description: Generates a HashRef compatible with GFFSerializer. Adds
+ score, external_name and logic_name to the basic Feature
+ hash
+ Returntype : Hash
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub summary_as_hash {
+ my ($self) = @_;
+ my $hash = $self->SUPER::summary_as_hash();
+ $hash->{score} = $self->score() if $self->score();
+ $hash->{'external_name'} = $self->display_label() if $self->display_label();
+ $hash->{'logic_name'} = $self->analysis->logic_name();
+ return $hash;
+}
+
1;
--
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