typo

[jalview.git] / forester / ruby / evoruby / lib / evo / tool / msa_processor.rb

diff --git a/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb b/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
index e27e416..d952277 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
@@ -301,8 +301,8 @@ module Evoruby
         Util.print_message( PRG_NAME, "Gap-proportion of original alignment : " + gp.to_s )
         log << "Gap-proportion of original alignment : " +  gp.to_s + ld
       else
-        Util.print_message( PRG_NAME, "the input is not aligned" )
-        log << "The input is not aligned" + ld
+        Util.print_message( PRG_NAME, "Input is not aligned" )
+        log << "Input is not aligned" + ld
       end
 
       all_names = Set.new()
@@ -501,8 +501,8 @@ module Evoruby
               first = false
             end
             avg = sum / msa.get_number_of_seqs
-            Util.print_message( PRG_NAME, "output is not aligned" )
-            log << "output is not aligned" + ld
+            Util.print_message( PRG_NAME, "Output is not aligned" )
+            log << "Output is not aligned" + ld
             Util.print_message( PRG_NAME, "Shortest sequence                    : " + min.to_s )
             log <<  "Shortest sequence                    : " + min.to_s + ld
             Util.print_message( PRG_NAME, "Longest sequence                     : " + max.to_s )
@@ -565,7 +565,8 @@ module Evoruby
           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
         end
 
-        Util.print_message( PRG_NAME, "Number of sequences in output        : " + msa.get_length.to_s )
+        Util.print_message( PRG_NAME, "Number of sequences in output        : " + msa.get_number_of_seqs.to_s )
+        log << "Number of sequences in output        : " + msa.get_number_of_seqs.to_s + ld
 
         begin
           f = File.open( output + LOG_SUFFIX, 'a' )