nexus_parser 1.1.3 → 1.1.4

data/VERSION

@@ -1 +1 @@
-1.1.3
+1.1.4

data/lib/nexus_parser.rb

@@ -162,12 +162,10 @@ class Builder
   end
   
   def update_taxon(options = {})
-    
     @opt = {
       :name => ''
     }.merge!(options)
     return false if !@opt[:index] 
-    
     (@nf.taxa[@opt[:index]].name = @opt[:name]) if @opt[:name]
   end
 

data/lib/parser.rb

@@ -127,7 +127,8 @@ class NexusParser::Parser
         break 
       else
         @lexer.pop(NexusParser::Tokens::Title) if @lexer.peek(NexusParser::Tokens::Title) # not used at present
-
+        @lexer.pop(NexusParser::Tokens::LinkLine) if @lexer.peek(NexusParser::Tokens::LinkLine) # trashing these for now
+        
         parse_dimensions if @lexer.peek(NexusParser::Tokens::Dimensions)
         parse_format if @lexer.peek(NexusParser::Tokens::Format) 
         
@@ -137,6 +138,7 @@ class NexusParser::Parser
     
         # handle "\s*OPTIONS MSTAXA = UNCERTAIN;\s\n" within a characters block (sticks in an infinite loop right now)
 
+
         @lexer.pop(NexusParser::Tokens::MesquiteIDs) if @lexer.peek(NexusParser::Tokens::MesquiteIDs) # trashing these for now
         @lexer.pop(NexusParser::Tokens::MesquiteBlockID) if @lexer.peek(NexusParser::Tokens::MesquiteBlockID) # trashing these for now
     

data/lib/tokens.rb

@@ -87,6 +87,10 @@ module NexusParser::Tokens
     @regexp = Regexp.new(/\A\s*(characters\s*;)\s*/i)
   end
 
+  class LinkLine < Token
+    @regexp = Regexp.new(/\A\s*(link.*\s*;)\s*\n*/i)
+  end
+
   # note we grab EOL and ; here 
   class ValuePair < Token
     @regexp = Regexp.new(/\A\s*([\w\d\_\&]+\s*=\s*((\'[^\']+\')|(\(.*\))|(\"[^\"]+\")|([^\s\n\t;]+)))[\s\n\t;]+/i) #  returns key => value hash for tokens like 'foo=bar' or foo = 'b a ar'
@@ -261,6 +265,7 @@ module NexusParser::Tokens
       NexusParser::Tokens::RBracket,
       NexusParser::Tokens::Label, # must be before RowVec 
       NexusParser::Tokens::RowVec,
+      NexusParser::Tokens::LinkLine,
       NexusParser::Tokens::ID # need to trash this
     ]   
   end

data/nexus_parser.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{nexus_parser}
-  s.version = "1.1.3"
+  s.version = "1.1.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["mjy"]
-  s.date = %q{2010-04-09}
+  s.date = %q{2011-04-12}
   s.description = %q{A full featured and extensible Nexus file parser in Ruby. }
   s.email = %q{diapriid@gmail.com}
   s.extra_rdoc_files = [
@@ -42,17 +42,16 @@ Gem::Specification.new do |s|
   s.homepage = %q{http://github.com/mjy/nexus_parser}
   s.rdoc_options = ["--charset=UTF-8"]
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.6}
+  s.rubygems_version = %q{1.5.3}
   s.summary = %q{A Nexus file format (phylogenetic inference) parser in Ruby.}
   s.test_files = [
     "test/test_nexus_parser.rb"
   ]
 
   if s.respond_to? :specification_version then
-    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
     s.specification_version = 3
 
-    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
     else
     end
   else

data/test/test_nexus_parser.rb

@@ -930,5 +930,14 @@ class Test_Parser < Test::Unit::TestCase
     assert true, foo
   end
 
+  def test_misc
+
+    assert nf = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../test/Aptostichus.nex')) )
+    foo = parse_nexus_file(nf) 
+    assert true, foo
+  end
+
+
+
 end
 

metadata

@@ -1,12 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: nexus_parser
 version: !ruby/object:Gem::Version 
-  prerelease: false
+  hash: 27
+  prerelease: 
   segments: 
   - 1
   - 1
-  - 3
-  version: 1.1.3
+  - 4
+  version: 1.1.4
 platform: ruby
 authors: 
 - mjy
@@ -14,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-04-09 00:00:00 -04:00
+date: 2011-04-12 00:00:00 -04:00
 default_executable: 
 dependencies: []
 
@@ -59,23 +60,27 @@ rdoc_options:
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      hash: 3
       segments: 
       - 0
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      hash: 3
       segments: 
       - 0
       version: "0"
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.6
+rubygems_version: 1.5.3
 signing_key: 
 specification_version: 3
 summary: A Nexus file format (phylogenetic inference) parser in Ruby.