From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 14 Sep 2012 02:31:02 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=4ba9da76a3e7e0861fcd80cc55eaea79573d623d;p=jalview.git

in progress
---

diff --git a/forester/ruby/evoruby/lib/evo/apps/domain_sequence_extractor_new.rb b/forester/ruby/evoruby/lib/evo/apps/domain_sequence_extractor_new.rb
index 098cf05..f6335ea 100644
--- a/forester/ruby/evoruby/lib/evo/apps/domain_sequence_extractor_new.rb
+++ b/forester/ruby/evoruby/lib/evo/apps/domain_sequence_extractor_new.rb
@@ -114,10 +114,10 @@ module Evoruby
       end
 
       add_species = false
-      if cla.is_option_set? ADD_SPECIES 
+      if cla.is_option_set? ADD_SPECIES
         add_species = true
       end
-      
+
       if ( add_domain_number_as_letter && add_domain_number_as_digit )
         puts( "attempt to add domain number as letter and digit at the same time" )
         print_help
@@ -223,7 +223,7 @@ module Evoruby
           add_domain_number_as_digit,
           add_domain_number_as_letter,
           trim,
-           add_species,
+          add_species,
           log )
       rescue ArgumentError, IOError, StandardError => e
         Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
diff --git a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb
index 3bf3fb7..c7d8146 100644
--- a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb
+++ b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb
@@ -37,7 +37,7 @@ module Evoruby
         add_domain_number_as_digit,
         add_domain_number_as_letter,
         trim_name,
-         add_species,
+        add_species,
         log )
 
       Util.check_file_for_readability( hmmsearch_output )
@@ -82,8 +82,8 @@ module Evoruby
             if domain_id != target_name
               next
             end
-            
-            
+
+
             sequence = $4
             number   = $10.to_i
             out_of   = $11.to_i
@@ -227,7 +227,7 @@ module Evoruby
         add_domain_number_as_digit,
         add_domain_number_as_letter,
         trim_name,
-        add_species      )
+        add_species )
       if ( number < 1 || out_of < 1 || number > out_of )
         error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s
         raise ArgumentError, error_msg
@@ -247,11 +247,11 @@ module Evoruby
       end
       # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
       seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )
-      
+
       orig_name = seq.get_name
-      
+
       seq.set_name( orig_name.split[ 0 ] )
-      
+
       if add_position
         seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
       end
@@ -272,18 +272,18 @@ module Evoruby
         elsif ( add_domain_number )
           seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
         end
-        
+
         if add_species
           a = orig_name.rindex "["
           b = orig_name.rindex "]"
           unless a && b
-               error_msg = "species not found in " + orig_name
-               raise StandardError, error_msg
+            error_msg = "species not found in " + orig_name
+            raise StandardError, error_msg
           end
           species = orig_name[ a .. b ]
           seq.set_name( seq.get_name + " [" + species + "]" )
-        end  
-          
+        end
+
       end
 
       # if ( seq.get_name.length > 10 )