inprogress

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

diff --git a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
index 1563a82..a1baafb 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
@@ -304,7 +304,8 @@ module Evoruby
                 fs_e_value_threshold,
                 hmm_for_protein_output,
                 i_e_value_threshold,
-                true )
+                false,
+                species )
             end
             hmmscan_results_per_protein.clear
           end
@@ -319,12 +320,14 @@ module Evoruby
           end
         end
       end
+    
       if !hmm_for_protein_output.empty? && !hmmscan_results_per_protein.empty?
         process_hmmscan_results_per_protein( hmmscan_results_per_protein,
           fs_e_value_threshold,
           hmm_for_protein_output,
           i_e_value_threshold,
-          true )
+          false,
+          species )
       end
 
       outfile.flush()
@@ -355,7 +358,10 @@ module Evoruby
         fs_e_value_threshold,
         hmm_for_protein_output,
         i_e_value_threshold,
-        uniprotkb )
+        uniprotkb,
+        species      )
+      
+    
 
       dc = 0
       # filter according to i-Evalue threshold
@@ -363,6 +369,10 @@ module Evoruby
       hmmscan_results_per_protein_filtered = []
 
       hmmscan_results_per_protein.each do | r |
+        
+        puts r.model
+         puts r.fs_e_value
+        
         if r.model == hmm_for_protein_output
           if r.fs_e_value > fs_e_value_threshold
             return
@@ -401,12 +411,13 @@ module Evoruby
         s << r.model + " "
       end
       s << "\t"
-      e = UniprotKB::get_entry_by_id( process_id( own.query ) )
+      puts s
+      #e = UniprotKB::get_entry_by_id( process_id( own.query ) )
 
-      if e != nil
-        s << uniprot_annotation( e )
-       # s << "\uniprot_annotationt"
-      end
+      #if e != nil
+      #  s << uniprot_annotation( e )
+      # # s << "\uniprot_annotationt"
+      #end
 
       overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )