lib/seqtrimnext/classes/params.rb in seqtrimnext-2.0.33 vs lib/seqtrimnext/classes/params.rb in seqtrimnext-2.0.35

@@ -10,10 +10,11 @@
   def initialize(path)
     @params = {}
     @comments = {}
     # @param_order={}
     @mids = {}
+    @ab_adapters={}
     @linkers = {}
     @clusters = {}
 
     @plugin_comments = {}
 
@@ -52,32 +53,40 @@
       end
 
     end
   end# end def
 
-  # Load mid's file
-  def load_mids(path_file)
+  def load_db_fastas(path_file)
+    res={}
     if File.exists?(path_file)
       ff = FastaFile.new(path_file)
       ff.each {|n,f|
         # @mid_sizes[n]=f.size
-        @mids[n]=f
+        res[n]=f
       }
 
       ff.close
     end
+    return res
   end
 
   # Load mid's file
+  def load_mids(path_file)
+    @mids=load_db_fastas(path_file)
+    # puts @mids
+  end
+
+  # Load ab_adapters file
+  def load_ab_adapters(path_file)
+    @ab_adapters=load_db_fastas(path_file)
+        # puts @ab_adapters
+  end
+
+  # Load mid's file
   def load_linkers(path_file)
-    if File.exists?(path_file)
-      ff = FastaFile.new(path_file)
-      ff.each {|n,f|
-        @linkers[n]=f
-      }
-      ff.close
-    end
+    @linkers=load_db_fastas(path_file)
+        # puts @linkers
   end
 
   def load_repeated_seqs(file_path)
     @clusters={}
 
@@ -88,11 +97,11 @@
         #puts line,line[0]
         # en ruby19 line[0] da el caracter, no el chr
         #if (line[0]!=62) && (line[0]!=48)
         if (line[0]!='>'[0]) && (line[0]!='0'[0])
           #puts line
-          #puts line,line[0]
+          # puts line,line[0]
           if line =~ />([^\.]+)\.\.\.\s/
             #puts 'ok'
             @clusters[$1]=1
           end
         end
@@ -154,9 +163,15 @@
 
   # Return the linker of param
   def get_linker(linker)
     return @linkers[linker]
   end
+
+  # Return the ab of param
+  def get_ab_adapter(adapter)
+    return @ab_adapters[adapter]
+  end
+
 
   def get_plugin
     plugin='General'
     # puts caller(2)[1]
     at = caller(2)[1]