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[jalview.git] / forester / ruby / evoruby / lib / evo / io / parser / uniprot_parser.rb

diff --git a/forester/ruby/evoruby/lib/evo/io/parser/uniprot_parser.rb b/forester/ruby/evoruby/lib/evo/io/parser/uniprot_parser.rb
index a47a6b2..607804c 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/io/parser/uniprot_parser.rb
+++ b/forester/ruby/evoruby/lib/evo/io/parser/uniprot_parser.rb
@@ -23,38 +23,26 @@ module Evoruby
     DR = "DR"
     LAST = '//'
 
-    def initialize file
-      Util.check_file_for_readability file
-      @file = file
+    def initialize
+
     end
 
 
-    def parse( ids )
-      entries = Hash.new
+    def parse( lines )
       de = []
       dr = []
       id = nil
-      File.open( @file ).each do | line |
-        if line.index( ID ) == 0
-          #   puts line
-          ids.each do | i |
-            #puts " " + i
-            if line.include?( i ) && line.split[ 1 ] == i
-              id = i
-              break
-            end
-          end
-        end
-        if id != nil
+      lines.each do | line |
+
+        if line.include?( ID ) && line.index( ID ) == 0
+          id = line.split[ 1 ]
+        elsif id != nil
           if line.include?( LAST ) && line.index( LAST ) == 0
             e = UniprotEntry.new
+            e.id = id
             e.de = de
             e.dr = dr
-            entries[ id ] = e
-            puts id
-            id = nil
-            de = []
-            dr = []
+            return e
           else
             if line.include?( DE ) && line.index( DE ) == 0
               add( line, de )
@@ -64,7 +52,7 @@ module Evoruby
           end
         end
       end
-      entries
+      return nil
     end
 
     private
@@ -89,7 +77,61 @@ module Evoruby
     attr_accessor :pe
     attr_accessor :kw
 
+    def get_pdb_ids
+      ids = []
+      if dr != nil
+        dr.each do | dr |
+          if dr != nil
+            if dr =~ /PDB;\s+([A-Z0-9]{4});/
+              ids << $1
+            end
+          end
+        end
+      end
+      ids
+    end
+
+    def get_go_descriptions
+      gos = []
+      if dr != nil
+        dr.each do | dr |
+          if dr != nil
+            if dr =~ /GO;\s+GO:\d+(.+);\s+([^;]+)/
+              gos << $1
+            end
+          end
+        end
+      end
+      gos
+    end
+
+    def get_full_name
+     # DE   RecName: Full=Apoptosis regulator Bcl-2;
+    end
+
+
+     def get_reactome_descriptions
+      s = []
+      if dr != nil
+        dr.each do | dr |
+          if dr != nil
+            if dr =~ /Reactome;\s+REACT_\d+;\s+([^.]+)/
+              s << $1
+            end
+          end
+        end
+      end
+      s
+    end
+
+
   end
 
 
+
+
+
+
+
+
 end # module Evoruby