From: cmzmasek <chris.zma@outlook.com>
Date: Fri, 28 Apr 2017 01:32:23 +0000 (-0700)
Subject: in progress...
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=46089d65925eac47d07e5b0f592ae185e8d8ba6f;p=jalview.git

in progress...
---

diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index 4606e9c..a811899 100644
--- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@ -21,7 +21,6 @@ module Evoruby
 
     DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -mp -or'
     DECORATOR_OPTIONS_DOMAINS   = '-p -t'
-    IDS_MAPFILE_SUFFIX          = '.nim'
     DOMAINS_MAPFILE_SUFFIX      = '.dff'
     SLEEP_TIME                  = 0.01
     REMOVE_NI                   = true
@@ -208,7 +207,7 @@ module Evoruby
           domains_mapfile_name = nil
           seqs_file_name = nil
 
-          ids_mapfile_name = get_file( files, phylogeny_id, IDS_MAPFILE_SUFFIX )
+          ids_mapfile_name = get_file( ".", phylogeny_id, Constants::ID_MAP_FILE_SUFFIX )
 
           begin
             Util.check_file_for_readability( ids_mapfile_name )
@@ -221,7 +220,7 @@ module Evoruby
           log << "Ids mapfile: " + ids_mapfile_name + NL
 
           unless no_seqs_files
-            seqs_file_name = get_seq_file( files, phylogeny_id )
+            seqs_file_name = get_file( ".", phylogeny_id, Constants::ID_NORMALIZED_FASTA_FILE_SUFFIX )
             begin
               Util.check_file_for_readability( seqs_file_name  )
             rescue IOError
@@ -234,7 +233,7 @@ module Evoruby
           end
 
           unless no_domains
-            domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
+            domains_mapfile_name = get_file( ".", phylogeny_id, Constants::DOMAINS_TO_FORESTER_OUTFILE_SUFFIX  )
             begin
               Util.check_file_for_readability( domains_mapfile_name )
             rescue IOError
@@ -329,25 +328,27 @@ module Evoruby
     end
 
     def get_id( phylogeny_file_name )
-      if phylogeny_file_name =~ /^(.+?_DA)_/
-        return $1
-      elsif phylogeny_file_name =~ /^(.+?)_/
-        return $1
-      end
-      nil
+      return phylogeny_file_name
+      #if phylogeny_file_name =~ /^(.+?_DA)_/
+      #  return $1
+      #elsif phylogeny_file_name =~ /^(.+?)_/
+      #  return $1
+      #end
+      #nil
     end
 
     def get_file( files_in_dir, phylogeny_id, suffix_pattern )
-      matching_files = Util.get_matching_files( files_in_dir, phylogeny_id, suffix_pattern )
-      if matching_files.length < 1
-        Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
-        '...' + suffix_pattern + '] present in current directory' )
-      end
-      if matching_files.length > 1
-        Util.fatal_error( PRG_NAME, 'more than one file matching [' +
-        phylogeny_id  + '...' + suffix_pattern + '] present in current directory' )
-      end
-      matching_files[ 0 ]
+      Util.get_matching_file( files_in_dir, phylogeny_id, suffix_pattern )
+      #      matching_files = Util.get_matching_files( files_in_dir, phylogeny_id, suffix_pattern )
+      #      if matching_files.length < 1
+      #        Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
+      #        '...' + suffix_pattern + '] present in current directory' )
+      #      end
+      #      if matching_files.length > 1
+      #        Util.fatal_error( PRG_NAME, 'more than one file matching [' +
+      #        phylogeny_id  + '...' + suffix_pattern + '] present in current directory' )
+      #      end
+      #      matching_files[ 0 ]
     end
 
     def get_seq_file( files_in_dir, phylogeny_id )
diff --git a/forester/ruby/evoruby/lib/evo/util/util.rb b/forester/ruby/evoruby/lib/evo/util/util.rb
index 80916ca..df28bc5 100644
--- a/forester/ruby/evoruby/lib/evo/util/util.rb
+++ b/forester/ruby/evoruby/lib/evo/util/util.rb
@@ -4,7 +4,7 @@
 # Copyright::    Copyright (C) 2017 Christian M. Zmasek
 # License::      GNU Lesser General Public License (LGPL)
 #
-# Last modified: 2017/02/07
+# Last modified: 2017/04/27
 
 require 'lib/evo/util/constants'
 
@@ -22,6 +22,72 @@ module Evoruby
       matching_files
     end
 
+    def Util.get_matching_file( dir_name, prefix, suffix )
+      unless Dir.exist? dir_name
+        raise IOError, "directory [#{dir_name}] does not exist"
+      end
+
+      all_files = Dir.entries(dir_name)
+
+      if ( all_files.size <= 2 )
+        raise IOError, "directory [#{dir_name}] is empty"
+      end
+      matching_files = Array.new
+      all_files.each { | file |
+        if  (( !File.directory?( file )) && (file.end_with? suffix))
+          matching_files << file
+        end
+      }
+
+      if ( matching_files.size == 0 )
+        raise IOError, "no files ending with \"" + suffix + "\" found in [" + dir_name + "]"
+      end
+      my_prefix = prefix
+      done = false
+      more_than_one = false
+      the_one = nil;
+
+      loop do
+        puts my_prefix #TODO remove me
+        matches = 0
+        matching_files.each { | file |
+          if file.start_with?( my_prefix )
+            matches += 1
+            if matches > 1
+              the_one = nil
+              break
+            end
+            the_one = file
+          end
+        }
+        if matches > 1
+          more_than_one = true
+          done = true
+        end
+        if matches == 1
+          done = true
+        else
+          if my_prefix.length <= 1
+            raise IOError, "no file matching \"" + removeFileExtension( prefix )
+            + "\" and ending with \"" + suffix + "\" found in [" + dir_name + "]"
+          end
+          my_prefix = my_prefix[ 0 ... ( my_prefix.length - 1 ) ]
+
+        end
+        break if done
+      end
+
+      if more_than_one
+        raise IOError, "multiple files matching \"" +  prefix  +
+        "\" and ending with \"" + suffix + "\" found in [" + dir_name + "]"
+      elsif the_one != nil
+      else
+        raise IOError, "no file matching \"" + prefix  + "\" and ending with \"" +
+        suffix + "\" found in [" + dir_name + "]"
+      end
+      the_one
+    end
+
     def Util.normalize_seq_name( name, length, exception_if_too_long = false )
       if name.length > length
         if exception_if_too_long