[BioRuby-cvs] bioruby/lib/bio/io fastacmd.rb,1.11,1.12

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv5385/lib/bio/io

Modified Files:
	fastacmd.rb 
Log Message:
* Changes due to the reconstruction of Bio::Command.
* Attrute 'errorlog' is removed.


Index: fastacmd.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/fastacmd.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** fastacmd.rb	21 Mar 2006 12:18:14 -0000	1.11
--- fastacmd.rb	14 Jul 2006 14:30:09 -0000	1.12
***************
*** 69,73 ****
  
    include Enumerable
-   include Bio::Command::Tools
  
    # Database file path.
--- 69,72 ----
***************
*** 77,82 ****
    attr_accessor :fastacmd
  
-   attr_accessor :errorlog
- 
    # This method provides a handle to a BLASTable database, which you can then
    # use to retrieve sequences.
--- 76,79 ----
***************
*** 136,142 ****
  
      cmd = [ @fastacmd, '-d', @database, '-s', entry_id ]
!     call_command_local(cmd) do |inn, out|
!       inn.close_write
!       Bio::FlatFile.new(Bio::FastaFormat, out).to_a
      end
    end
--- 133,139 ----
  
      cmd = [ @fastacmd, '-d', @database, '-s', entry_id ]
!     Bio::Command.call_command(cmd) do |io|
!       io.close_write
!       Bio::FlatFile.new(Bio::FastaFormat, io).to_a
      end
    end
***************
*** 151,157 ****
    def each_entry
      cmd = [ @fastacmd, '-d', @database, '-D', 'T' ]
!     call_command_local(cmd) do |inn, out|
!       inn.close_write
!       Bio::FlatFile.open(Bio::FastaFormat, out) do |f|
          f.each_entry do |entry|
            yield entry
--- 148,154 ----
    def each_entry
      cmd = [ @fastacmd, '-d', @database, '-D', 'T' ]
!     Bio::Command.call_command(cmd) do |io|
!       io.close_write
!       Bio::FlatFile.open(Bio::FastaFormat, io) do |f|
          f.each_entry do |entry|
            yield entry