[BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb, 1.16, 1.17 wublast.rb, 1.5, 1.6

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory pub.open-bio.org:/tmp/cvs-serv384/lib/bio/appl/blast

Modified Files:
	format0.rb wublast.rb 
Log Message:
* changed license to Ruby's.
* added a new constant DELIMITER_OVERRUN for Bio::FlatFile.


Index: wublast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/wublast.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** wublast.rb	18 Dec 2005 15:58:39 -0000	1.5
--- wublast.rb	22 Feb 2006 08:46:15 -0000	1.6
***************
*** 3,23 ****
  # 
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ng at bioruby.org>
! # License:: LGPL
! #
! #--
! #  This library is free software; you can redistribute it and/or
! #  modify it under the terms of the GNU Lesser General Public
! #  License as published by the Free Software Foundation; either
! #  version 2 of the License, or (at your option) any later version.
! #
! #  This library is distributed in the hope that it will be useful,
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
! #  Lesser General Public License for more details.
! #
! #  You should have received a copy of the GNU Lesser General Public
! #  License along with this library; if not, write to the Free Software
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
! #++
  #
  #  $Id$
--- 3,7 ----
  # 
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ng at bioruby.org>
! # License:: Ruby's
  #
  #  $Id$
***************
*** 338,341 ****
--- 322,328 ----
          # Delimter of each entry for TBLAST. Bio::FlatFile uses it.
          DELIMITER = RS = "\nTBLAST"
+ 
+         # (Integer) excess read size included in DELIMITER.
+         DELIMITER_OVERRUN = 6 # "TBLAST"
        end #class Report_TBlast
  

Index: format0.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** format0.rb	1 Nov 2005 05:32:23 -0000	1.16
--- format0.rb	22 Feb 2006 08:46:15 -0000	1.17
***************
*** 3,24 ****
  # 
  # Author:: Naohisa GOTO
! # Copyright:: Copyright (C) 2003 GOTO Naohisa <ng at bioruby.org>
! # License:: LGPL
! #
! #--
! #  This library is free software; you can redistribute it and/or
! #  modify it under the terms of the GNU Lesser General Public
! #  License as published by the Free Software Foundation; either
! #  version 2 of the License, or (at your option) any later version.
! #
! #  This library is distributed in the hope that it will be useful,
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
! #  Lesser General Public License for more details.
! #
! #  You should have received a copy of the GNU Lesser General Public
! #  License along with this library; if not, write to the Free Software
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
! #++
  #
  #  $Id$
--- 3,8 ----
  # 
  # Author:: Naohisa GOTO
! # Copyright:: Copyright (C) 2003-2006 GOTO Naohisa <ng at bioruby.org>
! # License:: Ruby's
  #
  #  $Id$
***************
*** 57,60 ****
--- 41,47 ----
          DELIMITER = RS = "\nBLAST"
  
+         # (Integer) excess read size included in DELIMITER.
+         DELIMITER_OVERRUN = 5 # "BLAST"
+ 
          # Opens file by using Bio::FlatFile.open.
          def self.open(filename, *mode)
***************
*** 1202,1205 ****
--- 1189,1195 ----
          # Delimter of each entry for TBLAST. Bio::FlatFile uses it.
          DELIMITER = RS = "\nTBLAST"
+ 
+         # (Integer) excess read size included in DELIMITER.
+         DELIMITER_OVERRUN = 6 # "TBLAST"
        end #class Report_TBlast