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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
4e26acb
..
6006729
100644
(file)
--- a/
forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/
forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@
-24,7
+24,7
@@
module Evoruby
#DECORATOR_OPTIONS_SEQ_NAMES = '-r=1 -mdn'
#DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -sn'
#DECORATOR_OPTIONS_SEQ_NAMES = '-r=1 -mdn'
#DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -sn'
- DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -c -tc'
+ DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -c -tc -mp -or'
# -mdn is a hidden expert option to rename e.g. "6_ORYLA3" to "6_[3]_ORYLA"
#DECORATOR_OPTIONS_SEQ_NAMES = '-sn -r=1'
#DECORATOR_OPTIONS_DOMAINS = '-r=1'
# -mdn is a hidden expert option to rename e.g. "6_ORYLA3" to "6_[3]_ORYLA"
#DECORATOR_OPTIONS_SEQ_NAMES = '-sn -r=1'
#DECORATOR_OPTIONS_DOMAINS = '-r=1'
@@
-271,6
+271,7
@@
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 ) &&
files_in_dir.each { | file |
if ( !File.directory?( file ) &&
@@
-279,11
+280,22
@@
module Evoruby
file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
matching_files << file
end
file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
matching_files << file
end
+ if ( !File.directory?( file ) &&
+ file !~ /^\./ &&
+ file !~ /^00/ &&
+ file =~ /#{suffix_pattern}$/ )
+ matching_suffix_files << file
+ end
}
}
- if matching_files.length < 1
+ 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
Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
'_] [' + suffix_pattern + '] present in current directory' )
Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
'_] [' + suffix_pattern + '] present in current directory' )
- elsif matching_files.length > 1
+ 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
Util.fatal_error( PRG_NAME, 'more than one file matching [' + phylogeny_id +
'_] [' + suffix_pattern + '] present in current directory' )
end
@@
-296,7
+308,7
@@
module Evoruby
puts( " " + PRG_NAME + ".rb [options] <suffix of intrees to be decorated> <suffix for decorated outtrees> " )
puts()
puts( " options: -" + IDS_ONLY_OPTION + ": decorate with sequence/species names only" )
puts( " " + PRG_NAME + ".rb [options] <suffix of intrees to be decorated> <suffix for decorated outtrees> " )
puts()
puts( " options: -" + IDS_ONLY_OPTION + ": decorate with sequence/species names only" )
- puts( " -" + DOMAINS_ONLY_OPTION + ": decorate with domain structures" )
+ puts( " -" + DOMAINS_ONLY_OPTION + ": decorate with domain structures only" )
puts()
end
end # class PhylogenyiesDecorator
puts()
end
end # class PhylogenyiesDecorator