inprogress

[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 738db56..d952277 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
@@ -27,9 +27,9 @@ module Evoruby
   class MsaProcessor
 
     PRG_NAME       = "msa_pro"
-    PRG_DATE       = "130411"
+    PRG_DATE       = "131112"
     PRG_DESC       = "processing of multiple sequence alignments"
-    PRG_VERSION    = "1.07"
+    PRG_VERSION    = "1.08"
     COPYRIGHT      = "2008-2010 Christian M Zmasek"
     CONTACT        = "phylosoft@gmail.com"
     WWW            = "www.phylosoft.org"
@@ -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()
@@ -484,8 +484,32 @@ module Evoruby
             Util.print_message( PRG_NAME, "Gap-proportion of processed alignment: " + gp.to_s )
             log << "Gap-proportion of processed alignment: " +  gp.to_s + ld
           else
-            Util.print_warning_message( PRG_NAME, "output is not aligned" )
-            log << "output is not aligned" + ld
+            min = 0
+            max = 0
+            sum = 0
+            first = true
+            for s in 0 ... msa.get_number_of_seqs
+              seq = msa.get_sequence( s )
+              l = seq.get_length
+              sum += l
+              if l > max
+                max = l
+              end
+              if first || l < min
+                min = l
+              end
+              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, "Shortest sequence                    : " + min.to_s )
+            log <<  "Shortest sequence                    : " + min.to_s + ld
+            Util.print_message( PRG_NAME, "Longest sequence                     : " + max.to_s )
+            log <<  "Longest sequence                     : " + max.to_s + ld
+            Util.print_message( PRG_NAME, "Average length                       : " + avg.to_s )
+            log <<  "Average length                       : " + avg.to_s + ld
+
           end
         end
 
@@ -535,13 +559,15 @@ module Evoruby
           w.set_exception_if_name_too_long( @die_if_name_too_long )
         end
 
-
         begin
           io.write_to_file( msa, output, w )
         rescue Exception => e
           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
         end
 
+        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' )
           f.print( log )