Rearrangement of require and autoload so as to correctly load PhyloXM…

…L classes
csw · Oct 23, 2009 · 3137ea9 · 3137ea9
1 parent b018370
commit 3137ea9
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Showing 5 changed files with 25 additions and 15 deletions.
diff --git a/lib/bio/db/phyloxml/phyloxml_elements.rb b/lib/bio/db/phyloxml/phyloxml_elements.rb
@@ -17,6 +17,20 @@
 #
 # * https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby
 
+require 'bio/tree'
+require 'bio/sequence'
+require 'bio/reference'
+
+# Autoload definition
+module Bio
+  module PhyloXML
+    autoload :Parser, 'bio/db/phyloxml/phyloxml_parser'
+    autoload :Writer, 'bio/db/phyloxml/phyloxml_writer'
+  end
+end
+
+require 'libxml'
+
 module Bio
 
    # This is general Taxonomy class.
@@ -1157,4 +1171,4 @@ def to_xml
 
 end #module PhyloXML
 
-end #end module Bio
+end #end module Bio
diff --git a/lib/bio/db/phyloxml/phyloxml_parser.rb b/lib/bio/db/phyloxml/phyloxml_parser.rb
@@ -25,15 +25,16 @@
 # * https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby
 
 
-module Bio
-
-module PhyloXML
+require 'uri'
+require 'libxml'
 
 require 'bio/tree'
-
 require 'bio/db/phyloxml/phyloxml_elements'
 
-require 'libxml'
+
+module Bio
+
+module PhyloXML
 
 
 

diff --git a/lib/bio/db/phyloxml/phyloxml_writer.rb b/lib/bio/db/phyloxml/phyloxml_writer.rb
@@ -24,6 +24,9 @@
 #
 # * https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby
 
+require 'libxml'
+require 'bio/db/phyloxml/phyloxml_elements'
+
 module Bio
 
   module PhyloXML
@@ -222,4 +225,4 @@ def node_to_xml(tree, node, parent)
     end
 
   end
-end
+end
diff --git a/test/unit/bio/db/test_phyloxml.rb b/test/unit/bio/db/test_phyloxml.rb
@@ -13,18 +13,13 @@
 libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
 $:.unshift(libpath) unless $:.include?(libpath)
 
-require 'bio/sequence'
-require 'bio/tree'
-
 begin
   require 'libxml'
 rescue LoadError
 end
 
 if defined?(LibXML) then
-  require 'bio/db/phyloxml/phyloxml_elements'
   require 'bio/db/phyloxml/phyloxml_parser'
-  require 'bio/db/phyloxml/phyloxml_writer'
 end
 
 module Bio

diff --git a/test/unit/bio/db/test_phyloxml_writer.rb b/test/unit/bio/db/test_phyloxml_writer.rb
@@ -15,7 +15,6 @@
 libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
 $:.unshift(libpath) unless $:.include?(libpath)
 
-require 'bio/tree'
 require 'bio/command'
 
 begin
@@ -24,8 +23,6 @@
 end
 
 if defined?(LibXML) then
-  require 'bio/db/phyloxml/phyloxml_elements'
-  require 'bio/db/phyloxml/phyloxml_parser'
   require 'bio/db/phyloxml/phyloxml_writer'
 end