rbfam 0.1.0 → 0.1.1

data/lib/rbfam/helpers/common.rb

@@ -5,6 +5,10 @@ module Rbfam
     end
     
     module InstanceMethods
+      def bootstrap!(options = {})
+        tap { load_entries!(options) }
+      end
+      
       def entries!(options = {})
         remove_instance_variable(:@parsed_entries)
         entries(options)

data/lib/rbfam/modules/alignment.rb

@@ -13,7 +13,7 @@ module Rbfam
     def entries(options = {})
       options = { alignment: :seed, limit: false }.merge(options)
       
-      @parsed_entries ||= pull_from_server(options[:alignment]).split(/\n/).reject do |line| 
+      @parsed_entries ||= (pull_from_server(options[:alignment]) || "").split(/\n/).reject do |line| 
         line =~ /^#/
       end.select do |line| 
         line =~ LINE_REGEXP

data/lib/rbfam/modules/family.rb

@@ -5,13 +5,15 @@ module Rbfam
     attr_reader :family_name
     
     class << self
-      def purine;  new("RF00167"); end
-      def tpp;     new("RF00059"); end
-      def secis_1; new("RF00031"); end
-      def trna;    new("RF00005"); end
-      def let_7;   new("RF00027"); end
-      def snora71; new("RF00056"); end
-      def u7;      new("RF00066"); end
+      def purine;       new("RF00167"); end
+      def tpp;          new("RF00059"); end
+      def secis_1;      new("RF00031"); end
+      def trna;         new("RF00005"); end
+      def let_7;        new("RF00027"); end
+      def snora71;      new("RF00056"); end
+      def u7;           new("RF00066"); end
+      def rose;         new("RF00435"); end
+      def hammerhead_3; new("RF00008"); end
     end
     
     def initialize(family_name)
@@ -29,7 +31,7 @@ module Rbfam
     end
     
     def load_entries!(options = {})
-      options = { extended: false }.merge(options)
+      options = { extended: false, seed: true }.merge(options)
       
       Rbfam.script("sequences_in_mysql")
       

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbfam
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-09-10 00:00:00.000000000 Z
+date: 2012-11-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -114,4 +114,3 @@ signing_key:
 specification_version: 3
 summary: Bindings to Rfam.
 test_files: []
-has_rdoc: