[BioRuby] Bio::Blat::Report

[Davide Rambaldi]

Hi, after installing the last version from git (http://github.com/ 
bioruby/bioruby), I have a couple of warnings using my application:

NOTE: the file test.psl I am using for testing is without psl headers

Oni:~/code/Ruby/bioruby tucano$ ./blatanalyzer list blatanalyzerdir/ 
test/test.psl
/usr/local/lib/ruby/site_ruby/1.8/bio/io/flatfile/splitter.rb:81:  
warning: private attribute?
/usr/local/lib/ruby/site_ruby/1.8/bio/io/flatfile/splitter.rb:84:  
warning: private attribute?
/usr/local/lib/ruby/site_ruby/1.8/bio/io/flatfile/splitter.rb:87:  
warning: private attribute?
/usr/local/lib/ruby/site_ruby/1.8/bio/io/flatfile/splitter.rb:90:  
warning: private attribute?
/usr/local/lib/ruby/site_ruby/1.8/bio/io/flatfile/splitter.rb:93:  
warning: private attribute?
/usr/local/lib/ruby/site_ruby/1.8/bio/io/flatfile/splitter.rb:96:  
warning: private attribute?
/usr/local/lib/ruby/site_ruby/1.8/bio/io/flatfile/splitter.rb:270:  
warning: private attribute?
/usr/local/lib/ruby/site_ruby/1.8/bio/appl/blat/report.rb:89:  
warning: instance variable @header_lines not initialized


The previuos version I was using don't give warnings

here the diff of changes in the new git version and in the previous  
report.rb:

diff oldreport.rb /usr/local/lib/ruby/site_ruby/1.8/bio/appl/blat/ 
report.rb

48a49,51
 >       # Splitter for Bio::FlatFile
 >       FLATFILE_SPLITTER = Bio::FlatFile::Splitter::LineOriented
 >
53c56
<       def initialize(text)
---
 >       def initialize(text = '')
57c60
<         text.each do |line|
---
 >         text.each_line do |line|
74c77,115
<         @columns = parse_header(head)
---
 >         @columns = parse_header(head) unless head.empty?
 >       end
 >
 >       # Adds a header line if the header data is not yet given and
 >       # the given line is suitable for header.
 >       # Returns self if adding header line is succeeded.
 >       # Otherwise, returns false (the line is not added).
 >       def add_header_line(line)
 >         return false if defined? @columns
 >         line = line.chomp
 >         case line
 >         when /^\d/
 >           @columns = defined? @header_lines ? parse_header 
(@header_lines) : []
 >           return false
 >         when /\A\-+\s*\z/
 >           @columns = defined? @header_lines ? parse_header 
(@header_lines) : []
 >           return self
 >         else
 >           @header_lines ||= []
 >           @header_lines.push line
 >         end
 >       end
 >
 >       # Adds a line to the entry if the given line is regarded as
 >       # a part of the current entry.
 >       # If the current entry (self) is empty, or the line has the  
same
 >       # query name, the line is added and returns self.
 >       # Otherwise, returns false (the line is not added).
 >       def add_line(line)
 >         if /\A\s*\z/ =~ line then
 >           return @hits.empty? ? self : false
 >         end
 >         hit = Hit.new(line.chomp)
 >         if @hits.empty? or @hits.first.query.name ==  
hit.query.name then
 >           @hits.push hit
 >           return self
 >         else
 >           return false
 >         end

Best Regards

Davide Rambaldi,
Bioinformatics PhD student.
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Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy

[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi  
(homepage)
[i] http://www.semm.it             (PhD school)
[i] http://www.btbs.unimib.it/     (Master)

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