figuring out git

mjy · Mar 18, 2010 · 5f3110f · 5f3110f
1 parent e98fe4a
commit 5f3110f
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diff --git a/README.rdoc b/README.rdoc
@@ -1,6 +1,6 @@
 = nexus_parser
 
-Description goes here.
+See the test files for usage for now, lots of examples there.
 
 == Note on Patches/Pull Requests
 
@@ -14,4 +14,4 @@ Description goes here.
 
 == Copyright
 
-Copyright (c) 2010 mjy. See LICENSE for details.
+Copyright (c) 2010 Matt Yoder. See LICENSE for details.
diff --git a/lib/lexer.rb b/lib/lexer.rb
@@ -1,6 +1,6 @@
 
 
-class NexusFile::Lexer
+class NexusParser::Lexer
 
   def initialize(input)
     @input = input
@@ -21,7 +21,7 @@ def pop(token_class)
     token = read_next_token(token_class)
     @next_token = nil
     if token.class != token_class
-        raise(NexusFile::ParseError,"expected #{token_class.to_s} but received #{token.class.to_s} at #{@input[0..10]}...", caller)
+        raise(NexusParser::ParseError,"expected #{token_class.to_s} but received #{token.class.to_s} at #{@input[0..10]}...", caller)
     else
         return token
     end
@@ -38,13 +38,13 @@ def read_next_token(token_class)
         return @next_token
       else
         # now check all the tokens for a match
-        NexusFile::Tokens.nexus_file_token_list.each {|t|
+        NexusParser::Tokens.nexus_file_token_list.each {|t|
           return @next_token if match(t)
         }
       end
          # no match, either end of string or lex-error
          if @input != ''
-             raise( NexusFile::ParseError, "Lex Error, unknown token at #{@input[0..10]}...", caller)
+             raise( NexusParser::ParseError, "Lex Error, unknown token at #{@input[0..10]}...", caller)
          else
             return nil
       end

diff --git a/lib/nexus_parser.rb b/lib/nexus_parser.rb
@@ -7,13 +7,13 @@
 # outstanding issues:
 ## need to resolve Tokens Labels, ValuePair, IDs
 
-module NexusFile
+module NexusParser
 
   require File.expand_path(File.join(File.dirname(__FILE__), 'tokens'))
   require File.expand_path(File.join(File.dirname(__FILE__), 'parser'))
   require File.expand_path(File.join(File.dirname(__FILE__), 'lexer'))
 
-class NexusFile 
+class NexusParser 
 
   attr_accessor :taxa, :characters, :sets, :codings, :vars, :notes
 
@@ -117,28 +117,28 @@ def note
 end
 
 
-# constructs the NexusFile
+# constructs the NexusParser
 class Builder
 
   def initialize
-    @nf = NexusFile.new 
+    @nf = NexusParser.new 
   end
 
   def stub_taxon
-    @nf.taxa.push(NexusFile::Taxon.new) 
+    @nf.taxa.push(NexusParser::Taxon.new) 
     return @nf.taxa.size
   end
 
   def stub_chr
-    @nf.characters.push(NexusFile::Character.new)
+    @nf.characters.push(NexusParser::Character.new)
     return @nf.characters.size
   end
 
   def code_row(taxon_index, rowvector)
 
     @nf.characters.each_with_index do |c, i|
       @nf.codings[taxon_index.to_i] = [] if !@nf.codings[taxon_index.to_i]
-      @nf.codings[taxon_index.to_i][i] = NexusFile::Coding.new(:states => rowvector[i])
+      @nf.codings[taxon_index.to_i][i] = NexusParser::Coding.new(:states => rowvector[i])
 
       # !! we must update states for a given character if the state isn't found (not all states are referenced in description !! 
 
@@ -183,7 +183,7 @@ def update_chr(options = {} )
 
     # need to create the characters
 
-    raise(NexusFile::ParseError, "Can't update character of index #{@index}, it doesn't exist! This is a problem parsing the character state labels. Check the indices. It may be for this character \"#{@opt[:name]}\".") if !@nf.characters[@index]
+    raise(NexusParser::ParseError, "Can't update character of index #{@index}, it doesn't exist! This is a problem parsing the character state labels. Check the indices. It may be for this character \"#{@opt[:name]}\".") if !@nf.characters[@index]
 
     (@nf.characters[@index].name = @opt[:name]) if @opt[:name]
 
@@ -223,28 +223,28 @@ def add_note(options = {})
     # Why does mesquite differentiate b/w footnotes and annotations?!, apparently same data structure?
     when 'TEXT' # a footnote 
       if @opt[:file]
-       @nf.notes << NexusFile::Note.new(@opt)
+       @nf.notes << NexusParser::Note.new(@opt)
 
       elsif  @opt[:taxon] && @opt[:character] # its a cell, parse this case         
         @nf.codings[@opt[:taxon].to_i - 1][@opt[:character].to_i - 1].notes = [] if !@nf.codings[@opt[:taxon].to_i - 1][@opt[:character].to_i - 1].notes
-        @nf.codings[@opt[:taxon].to_i - 1][@opt[:character].to_i - 1].notes << NexusFile::Note.new(@opt)
+        @nf.codings[@opt[:taxon].to_i - 1][@opt[:character].to_i - 1].notes << NexusParser::Note.new(@opt)
 
       elsif @opt[:taxon] && !@opt[:character]
-        @nf.taxa[@opt[:taxon].to_i - 1].notes << NexusFile::Note.new(@opt)
+        @nf.taxa[@opt[:taxon].to_i - 1].notes << NexusParser::Note.new(@opt)
 
       elsif @opt[:character] && !@opt[:taxon]
 
-        @nf.characters[@opt[:character].to_i - 1].notes << NexusFile::Note.new(@opt)
+        @nf.characters[@opt[:character].to_i - 1].notes << NexusParser::Note.new(@opt)
       end
 
     when 'AN' # an annotation, rather than a footnote, same dif
       if @opt[:t] && @opt[:c]
         @nf.codings[@opt[:t].to_i - 1][@opt[:c].to_i - 1].notes = [] if !@nf.codings[@opt[:t].to_i - 1][@opt[:c].to_i - 1].notes
-        @nf.codings[@opt[:t].to_i - 1][@opt[:c].to_i - 1].notes << NexusFile::Note.new(@opt)
+        @nf.codings[@opt[:t].to_i - 1][@opt[:c].to_i - 1].notes << NexusParser::Note.new(@opt)
       elsif @opt[:t]
-        @nf.taxa[@opt[:t].to_i - 1].notes << NexusFile::Note.new(@opt)
+        @nf.taxa[@opt[:t].to_i - 1].notes << NexusParser::Note.new(@opt)
       elsif @opt[:c]
-        @nf.characters[@opt[:c].to_i - 1].notes << NexusFile::Note.new(@opt)
+        @nf.characters[@opt[:c].to_i - 1].notes << NexusParser::Note.new(@opt)
       end
     end
 
@@ -256,7 +256,7 @@ def nexus_file
 
 end # end file
 
-  # NexusFile::ParseError
+  # NexusParser::ParseError
   class ParseError < StandardError
   end
 
@@ -267,15 +267,14 @@ class ParseError < StandardError
 def parse_nexus_file(input)
   @input = input
   @input.gsub!(/\[[^\]]*\]/,'')  # strip out all comments BEFORE we parse the file
-
   # quickly peek at the input, does this look like a Nexus file? 
   if !(@input =~ /\#Nexus/i) || !(@input =~ /Begin/i) || !(@input =~ /Matrix/i) || !(@input =~ /end\;/i)
-    raise(NexusFile::ParseError, "File is missing at least some required headers, check formatting.", caller)
+    raise(NexusParser::ParseError, "File is missing at least some required headers, check formatting.", caller)
   end
 
-  builder = NexusFile::Builder.new
-  lexer = NexusFile::Lexer.new(@input)
-  NexusFile::Parser.new(lexer, builder).parse_file
+  builder = NexusParser::Builder.new
+  lexer = NexusParser::Lexer.new(@input)
+  NexusParser::Parser.new(lexer, builder).parse_file
 
   return builder.nexus_file  
 end