[BioRuby-cvs] bioruby/lib/bio/shell/plugin codon.rb, 1.12, 1.13 emboss.rb, 1.1, 1.2 entry.rb, 1.5, 1.6 flatfile.rb, 1.11, 1.12 keggapi.rb, 1.9, 1.10 midi.rb, 1.6, 1.7 obda.rb, 1.8, 1.9 seq.rb, 1.16, 1.17
Katayama Toshiaki
k at pub.open-bio.org
Thu Feb 9 20:48:55 UTC 2006
Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv19056/shell/plugin
Modified Files:
codon.rb emboss.rb entry.rb flatfile.rb keggapi.rb midi.rb
obda.rb seq.rb
Log Message:
* license is changed to Ruby's
Index: midi.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/midi.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** midi.rb 28 Nov 2005 12:06:18 -0000 1.6
--- midi.rb 9 Feb 2006 20:48:53 -0000 1.7
***************
*** 2,29 ****
# = bio/shell/plugin/midi.rb - Sequence to MIDI converter
#
! # Copyright:: Copyright (C) 2003, 2005
! # Natsuhiro Ichinose <ichinose at genome.ist.i.kyoto-u.ac.jp>,
! # Toshiaki Katayama <k at bioruby.org>
! # License:: LGPL
#
# $Id$
- #
- #--
- #
- # 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
- #
- #++
#
--- 2,11 ----
# = bio/shell/plugin/midi.rb - Sequence to MIDI converter
#
! # Copyright:: Copyright (C) 2003, 2005
! # Natsuhiro Ichinose <ichinose at genome.ist.i.kyoto-u.ac.jp>,
! # Toshiaki Katayama <k at bioruby.org>
! # License:: Ruby's
#
# $Id$
#
Index: emboss.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/emboss.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** emboss.rb 28 Jan 2006 07:22:14 -0000 1.1
--- emboss.rb 9 Feb 2006 20:48:53 -0000 1.2
***************
*** 2,28 ****
# = bio/shell/plugin/emboss.rb - methods to use EMBOSS
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License:: LGPL
#
# $Id$
- #
- #--
- #
- # 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
- #
- #++
#
--- 2,10 ----
# = bio/shell/plugin/emboss.rb - methods to use EMBOSS
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License:: Ruby's
#
# $Id$
#
Index: obda.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/obda.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** obda.rb 30 Nov 2005 02:01:04 -0000 1.8
--- obda.rb 9 Feb 2006 20:48:53 -0000 1.9
***************
*** 2,28 ****
# = bio/shell/plugin/obda.rb - plugin for OBDA
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License:: LGPL
#
# $Id$
- #
- #--
- #
- # 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
- #
- #++
#
--- 2,10 ----
# = bio/shell/plugin/obda.rb - plugin for OBDA
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License: Ruby's
#
# $Id$
#
Index: flatfile.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/flatfile.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** flatfile.rb 30 Nov 2005 01:57:18 -0000 1.11
--- flatfile.rb 9 Feb 2006 20:48:53 -0000 1.12
***************
*** 2,29 ****
# = bio/shell/plugin/flatfile.rb - plugin for flatfile database
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License:: LGPL
#
# $Id$
#
- #--
- #
- # 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
- #
- #++
- #
module Bio::Shell
--- 2,11 ----
# = bio/shell/plugin/flatfile.rb - plugin for flatfile database
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License: Ruby's
#
# $Id$
#
module Bio::Shell
***************
*** 87,92 ****
def flatindex(dbname, *flatfiles)
- dir = Bio::Shell.create_flat_dir(dbname)
begin
print "Creating BioFlat index (#{dir}) ... "
bdb = format = options = nil
--- 69,74 ----
def flatindex(dbname, *flatfiles)
begin
+ dir = Bio::Shell.create_flat_dir(dbname)
print "Creating BioFlat index (#{dir}) ... "
bdb = format = options = nil
Index: keggapi.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/keggapi.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** keggapi.rb 6 Feb 2006 06:17:53 -0000 1.9
--- keggapi.rb 9 Feb 2006 20:48:53 -0000 1.10
***************
*** 2,28 ****
# = bio/shell/plugin/keggapi.rb - plugin for KEGG API
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License:: LGPL
#
# $Id$
- #
- #--
- #
- # 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
- #
- #++
#
--- 2,10 ----
# = bio/shell/plugin/keggapi.rb - plugin for KEGG API
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License:: Ruby's
#
# $Id$
#
Index: seq.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/seq.rb,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** seq.rb 19 Dec 2005 01:20:06 -0000 1.16
--- seq.rb 9 Feb 2006 20:48:53 -0000 1.17
***************
*** 2,29 ****
# = bio/shell/plugin/seq.rb - plugin for biological sequence manipulations
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License:: LGPL
#
# $Id$
#
- #--
- #
- # 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
- #
- #++
- #
module Bio::Shell
--- 2,11 ----
# = bio/shell/plugin/seq.rb - plugin for biological sequence manipulations
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License:: Ruby's
#
# $Id$
#
module Bio::Shell
***************
*** 211,215 ****
pos = self[n, size].rindex(separater)
! if self[n, size].length < size # last line of the folded str
pos = nil
end
--- 193,197 ----
pos = self[n, size].rindex(separater)
! if self[n, size].length < size # last line of the folded str
pos = nil
end
***************
*** 218,222 ****
ary << self[n, pos+separater.length]
n += pos + separater.length
! else # line too long or the last line
ary << self[n, size]
n += size
--- 200,204 ----
ary << self[n, pos+separater.length]
n += pos + separater.length
! else # line too long or the last line
ary << self[n, size]
n += size
Index: codon.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/codon.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** codon.rb 19 Dec 2005 02:34:24 -0000 1.12
--- codon.rb 9 Feb 2006 20:48:53 -0000 1.13
***************
*** 2,28 ****
# = bio/shell/plugin/codon.rb - plugin for the codon table
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License:: LGPL
#
# $Id$
- #
- #--
- #
- # 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
- #
- #++
#
--- 2,10 ----
# = bio/shell/plugin/codon.rb - plugin for the codon table
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License:: Ruby's
#
# $Id$
#
Index: entry.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/entry.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** entry.rb 28 Jan 2006 06:46:43 -0000 1.5
--- entry.rb 9 Feb 2006 20:48:53 -0000 1.6
***************
*** 2,28 ****
# = bio/shell/plugin/entry.rb - extract entry and sequence
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License:: LGPL
#
# $Id$
- #
- #--
- #
- # 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
- #
- #++
#
--- 2,10 ----
# = bio/shell/plugin/entry.rb - extract entry and sequence
#
! # Copyright:: Copyright (C) 2005
! # Toshiaki Katayama <k at bioruby.org>
! # License:: Ruby's
#
# $Id$
#
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