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[jalview.git]
/
forester
/
ruby
/
evoruby
/
lib
/
evo
/
tool
/
phylogenies_decorator.rb
diff --git
a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index
c9f37ae
..
b2d5a87
100644
(file)
--- a/
forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/
forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@
-166,7
+166,8
@@
module Evoruby
log << counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile + NL
phylogeny_id = get_id( phylogeny_file )
log << counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile + NL
phylogeny_id = get_id( phylogeny_file )
-
+ puts "id:" + phylogeny_id
+
ids_mapfile_name = nil
domains_mapfile_name = nil
seqs_file_name = nil
ids_mapfile_name = nil
domains_mapfile_name = nil
seqs_file_name = nil
@@
-242,27
+243,19
@@
module Evoruby
def get_file( files_in_dir, phylogeny_id, suffix_pattern )
matching_files = Array.new
def get_file( files_in_dir, phylogeny_id, suffix_pattern )
matching_files = Array.new
- matching_suffix_files = Array.new
+
files_in_dir.each { | file |
if ( !File.directory?( file ) &&
file !~ /^\./ &&
file !~ /^00/ &&
files_in_dir.each { | file |
if ( !File.directory?( file ) &&
file !~ /^\./ &&
file !~ /^00/ &&
- file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
+ file =~ /^#{phylogeny_id}#{suffix_pattern}$/ )
matching_files << file
end
matching_files << file
end
- if ( !File.directory?( file ) &&
- file !~ /^\./ &&
- file !~ /^00/ &&
- file =~ /#{suffix_pattern}$/ )
- matching_suffix_files << file
- end
}
}
- if matching_files.length < 1 && matching_suffix_files.length == 1
- return matching_suffix_files[ 0 ]
- end
+
- if matching_files.length < 1 && matching_suffix_files.length < 1
+ if matching_files.length < 1
Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
'_] [' + suffix_pattern + '] present in current directory' )
end
Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
'_] [' + suffix_pattern + '] present in current directory' )
end
@@
-284,7
+277,6
@@
module Evoruby
file =~ /^#{phylogeny_id}.+\d$/ )
matching_files << file
end
file =~ /^#{phylogeny_id}.+\d$/ )
matching_files << file
end
-
}
if matching_files.length < 1
}
if matching_files.length < 1