[Bioperl-guts-l] bioperl-live/Bio/SearchIO EventHandlerI.pm, 1.13, 1.14 FastHitEventBuilder.pm, 1.13, 1.14 IteratedSearchResultEventBuilder.pm, 1.11, 1.12 SearchResultEventBuilder.pm, 1.42, 1.43 SearchWriterI.pm, 1.10, 1.11 axt.pm, 1.10, 1.11 blast.pm, 1.105, 1.106 blasttable.pm, 1.8, 1.9 blastxml.pm, 1.37, 1.38 exonerate.pm, 1.17, 1.18 fasta.pm, 1.50, 1.51 hmmer.pm, 1.35, 1.36 hmmer_pull.pm, 1.4, 1.5 megablast.pm, 1.8, 1.9 psl.pm, 1.13, 1.14 sim4.pm, 1.13, 1.14 waba.pm, 1.16, 1.17 wise.pm, 1.6, 1.7

Senduran Balasubramaniam sendu at dev.open-bio.org
Tue Sep 26 18:03:15 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/SearchIO
In directory dev.open-bio.org:/tmp/cvs-serv29288/Bio/SearchIO

Modified Files:
	EventHandlerI.pm FastHitEventBuilder.pm 
	IteratedSearchResultEventBuilder.pm 
	SearchResultEventBuilder.pm SearchWriterI.pm axt.pm blast.pm 
	blasttable.pm blastxml.pm exonerate.pm fasta.pm hmmer.pm 
	hmmer_pull.pm megablast.pm psl.pm sim4.pm waba.pm wise.pm 
Log Message:
use base, return true

Index: blasttable.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/blasttable.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** blasttable.pm	20 Sep 2006 05:53:51 -0000	1.8
--- blasttable.pm	26 Sep 2006 22:03:13 -0000	1.9
***************
*** 63,69 ****
  
  package Bio::SearchIO::blasttable;
! use vars qw(@ISA %MAPPING %MODEMAP $DEFAULT_WRITER_CLASS $DefaultProgramName);
  use strict;
- use Bio::SearchIO;
  use Bio::Search::Result::ResultFactory;
  use Bio::Search::Hit::HitFactory;
--- 63,68 ----
  
  package Bio::SearchIO::blasttable;
! use vars qw(%MAPPING %MODEMAP $DEFAULT_WRITER_CLASS $DefaultProgramName);
  use strict;
  use Bio::Search::Result::ResultFactory;
  use Bio::Search::Hit::HitFactory;
***************
*** 119,123 ****
  	     );
  
! @ISA = qw(Bio::SearchIO );
  
  =head2 new
--- 118,122 ----
  	     );
  
! use base qw(Bio::SearchIO);
  
  =head2 new

Index: blast.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/blast.pm,v
retrieving revision 1.105
retrieving revision 1.106
diff -C2 -d -r1.105 -r1.106
*** blast.pm	26 Sep 2006 15:24:07 -0000	1.105
--- blast.pm	26 Sep 2006 22:03:13 -0000	1.106
***************
*** 130,134 ****
  use Bio::SearchIO::IteratedSearchResultEventBuilder;
  use strict;
! use vars qw(@ISA %MAPPING %MODEMAP
    $DEFAULT_BLAST_WRITER_CLASS
    $MAX_HSP_OVERLAP
--- 130,134 ----
  use Bio::SearchIO::IteratedSearchResultEventBuilder;
  use strict;
! use vars qw(%MAPPING %MODEMAP
    $DEFAULT_BLAST_WRITER_CLASS
    $MAX_HSP_OVERLAP
***************
*** 138,144 ****
  );
  
- use Bio::SearchIO;
  
! @ISA = qw(Bio::SearchIO );
  
  BEGIN {
--- 138,143 ----
  );
  
  
! use base qw(Bio::SearchIO);
  
  BEGIN {

Index: megablast.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/megablast.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** megablast.pm	20 Sep 2006 05:53:51 -0000	1.8
--- megablast.pm	26 Sep 2006 22:03:13 -0000	1.9
***************
*** 93,100 ****
  package Bio::SearchIO::megablast;
  use strict;
! use vars qw(@ISA %MAPPING %MODEMAP $DEFAULT_BLAST_WRITER_CLASS);
! use Bio::SearchIO;
  
! @ISA = qw(Bio::SearchIO );
  
  BEGIN {
--- 93,99 ----
  package Bio::SearchIO::megablast;
  use strict;
! use vars qw(%MAPPING %MODEMAP $DEFAULT_BLAST_WRITER_CLASS);
  
! use base qw(Bio::SearchIO);
  
  BEGIN {
***************
*** 513,514 ****
--- 512,515 ----
  
  sub report_count { shift->result_count }
+ 
+ 1;

Index: wise.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/wise.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** wise.pm	4 Jul 2006 22:23:21 -0000	1.6
--- wise.pm	26 Sep 2006 22:03:13 -0000	1.7
***************
*** 64,74 ****
  
  package Bio::SearchIO::wise;
! use vars qw(@ISA %MAPPING %MODEMAP $DEFAULT_WRITER_CLASS);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
! use Bio::SearchIO;
! @ISA = qw(Bio::SearchIO);
  
  %MODEMAP = ('WiseOutput' => 'result',
--- 64,73 ----
  
  package Bio::SearchIO::wise;
! use vars qw(%MAPPING %MODEMAP $DEFAULT_WRITER_CLASS);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
! use base qw(Bio::SearchIO);
  
  %MODEMAP = ('WiseOutput' => 'result',

Index: sim4.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/sim4.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** sim4.pm	4 Jul 2006 22:23:21 -0000	1.13
--- sim4.pm	26 Sep 2006 22:03:13 -0000	1.14
***************
*** 78,89 ****
  
  use strict;
! use vars qw(@ISA $DEFAULTFORMAT %ALIGN_TYPES
              %MAPPING %MODEMAP $DEFAULT_WRITER_CLASS);
  
  use POSIX;
- use Bio::SearchIO;
  use Bio::SearchIO::SearchResultEventBuilder;
  
! @ISA = qw(Bio::SearchIO );
  
  $DEFAULTFORMAT = 'SIM4';
--- 78,88 ----
  
  use strict;
! use vars qw($DEFAULTFORMAT %ALIGN_TYPES
              %MAPPING %MODEMAP $DEFAULT_WRITER_CLASS);
  
  use POSIX;
  use Bio::SearchIO::SearchResultEventBuilder;
  
! use base qw(Bio::SearchIO);
  
  $DEFAULTFORMAT = 'SIM4';

Index: blastxml.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/blastxml.pm,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** blastxml.pm	25 Aug 2006 17:23:47 -0000	1.37
--- blastxml.pm	26 Sep 2006 22:03:13 -0000	1.38
***************
*** 103,107 ****
  
  package Bio::SearchIO::blastxml;
! use vars qw(@ISA $DTD %MAPPING %MODEMAP $DEBUG);
  use strict;
  
--- 103,107 ----
  
  package Bio::SearchIO::blastxml;
! use vars qw($DTD %MAPPING %MODEMAP $DEBUG);
  use strict;
  
***************
*** 110,114 ****
  
  use Bio::Root::Root;
- use Bio::SearchIO;
  use XML::SAX;
  use HTML::Entities;
--- 110,113 ----
***************
*** 189,193 ****
  
  
! @ISA = qw(Bio::SearchIO );
  
  =head2 new
--- 188,192 ----
  
  
! use base qw(Bio::SearchIO);
  
  =head2 new

Index: exonerate.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/exonerate.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** exonerate.pm	4 Jul 2006 22:23:20 -0000	1.17
--- exonerate.pm	26 Sep 2006 22:03:13 -0000	1.18
***************
*** 104,111 ****
  package Bio::SearchIO::exonerate;
  use strict;
! use vars qw(@ISA @STATES %MAPPING %MODEMAP $DEFAULT_WRITER_CLASS $MIN_INTRON);
! use Bio::SearchIO;
  
! @ISA = qw(Bio::SearchIO );
  
  %MODEMAP = ( 'ExonerateOutput' => 'result',
--- 104,110 ----
  package Bio::SearchIO::exonerate;
  use strict;
! use vars qw(@STATES %MAPPING %MODEMAP $DEFAULT_WRITER_CLASS $MIN_INTRON);
  
! use base qw(Bio::SearchIO);
  
  %MODEMAP = ( 'ExonerateOutput' => 'result',

Index: axt.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/axt.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** axt.pm	16 Sep 2006 17:25:27 -0000	1.10
--- axt.pm	26 Sep 2006 22:03:13 -0000	1.11
***************
*** 71,81 ****
  
  package Bio::SearchIO::axt;
! use vars qw(@ISA %MODEMAP %MAPPING @STATES $GAPCHAR);
  use strict;
  
- use Bio::SearchIO;
  use Bio::Search::Result::ResultFactory;
  use Bio::Search::HSP::HSPFactory;
! @ISA = qw(Bio::SearchIO );
  
  use POSIX;
--- 71,80 ----
  
  package Bio::SearchIO::axt;
! use vars qw(%MODEMAP %MAPPING @STATES $GAPCHAR);
  use strict;
  
  use Bio::Search::Result::ResultFactory;
  use Bio::Search::HSP::HSPFactory;
! use base qw(Bio::SearchIO);
  
  use POSIX;

Index: hmmer.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/hmmer.pm,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** hmmer.pm	20 Sep 2006 05:53:51 -0000	1.35
--- hmmer.pm	26 Sep 2006 22:03:13 -0000	1.36
***************
*** 70,83 ****
  package Bio::SearchIO::hmmer;
  
- use vars qw(@ISA);
  use strict;
  
  use Bio::Factory::ObjectFactory;
  
! use vars qw(@ISA %MAPPING %MODEMAP
  );
- use Bio::SearchIO;
  
! @ISA = qw(Bio::SearchIO );
  
  BEGIN {
--- 70,81 ----
  package Bio::SearchIO::hmmer;
  
  use strict;
  
  use Bio::Factory::ObjectFactory;
  
! use vars qw(%MAPPING %MODEMAP
  );
  
! use base qw(Bio::SearchIO);
  
  BEGIN {

Index: SearchResultEventBuilder.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/SearchResultEventBuilder.pm,v
retrieving revision 1.42
retrieving revision 1.43
diff -C2 -d -r1.42 -r1.43
*** SearchResultEventBuilder.pm	19 Sep 2006 08:31:09 -0000	1.42
--- SearchResultEventBuilder.pm	26 Sep 2006 22:03:13 -0000	1.43
***************
*** 64,75 ****
  
  package Bio::SearchIO::SearchResultEventBuilder;
! use vars qw(@ISA %KNOWNEVENTS);
  use strict;
  
- use Bio::Root::Root;
- use Bio::SearchIO::EventHandlerI;
  use Bio::Factory::ObjectFactory;
  
! @ISA = qw(Bio::Root::Root Bio::SearchIO::EventHandlerI);
  
  =head2 new
--- 64,73 ----
  
  package Bio::SearchIO::SearchResultEventBuilder;
! use vars qw(%KNOWNEVENTS);
  use strict;
  
  use Bio::Factory::ObjectFactory;
  
! use base qw(Bio::Root::Root Bio::SearchIO::EventHandlerI);
  
  =head2 new

Index: FastHitEventBuilder.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/FastHitEventBuilder.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** FastHitEventBuilder.pm	11 Aug 2006 16:32:13 -0000	1.13
--- FastHitEventBuilder.pm	26 Sep 2006 22:03:13 -0000	1.14
***************
*** 79,92 ****
  
  package Bio::SearchIO::FastHitEventBuilder;
! use vars qw(@ISA %KNOWNEVENTS);
  use strict;
  
- use Bio::Root::Root;
- use Bio::SearchIO::EventHandlerI;
  use Bio::Search::HSP::HSPFactory;
  use Bio::Search::Hit::HitFactory;
  use Bio::Search::Result::ResultFactory;
  
! @ISA = qw(Bio::Root::Root Bio::SearchIO::EventHandlerI);
  
  =head2 new
--- 79,90 ----
  
  package Bio::SearchIO::FastHitEventBuilder;
! use vars qw(%KNOWNEVENTS);
  use strict;
  
  use Bio::Search::HSP::HSPFactory;
  use Bio::Search::Hit::HitFactory;
  use Bio::Search::Result::ResultFactory;
  
! use base qw(Bio::Root::Root Bio::SearchIO::EventHandlerI);
  
  =head2 new

Index: psl.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/psl.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** psl.pm	4 Jul 2006 22:23:21 -0000	1.13
--- psl.pm	26 Sep 2006 22:03:13 -0000	1.14
***************
*** 68,75 ****
  
  package Bio::SearchIO::psl;
! use vars qw(@ISA %MAPPING %MODEMAP $DEFAULT_WRITER_CLASS $DefaultProgramName);
  
  use strict;
- use Bio::SearchIO;
  use Bio::Search::HSP::HSPFactory;
  use Bio::Search::Hit::HitFactory;
--- 68,74 ----
  
  package Bio::SearchIO::psl;
! use vars qw(%MAPPING %MODEMAP $DEFAULT_WRITER_CLASS $DefaultProgramName);
  
  use strict;
  use Bio::Search::HSP::HSPFactory;
  use Bio::Search::Hit::HitFactory;
***************
*** 126,130 ****
  	     );
  
! @ISA = qw(Bio::SearchIO );
  
  =head2 new
--- 125,129 ----
  	     );
  
! use base qw(Bio::SearchIO);
  
  =head2 new

Index: hmmer_pull.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/hmmer_pull.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** hmmer_pull.pm	20 Sep 2006 10:20:02 -0000	1.4
--- hmmer_pull.pm	26 Sep 2006 22:03:13 -0000	1.5
***************
*** 75,85 ****
  package Bio::SearchIO::hmmer_pull;
  
- use vars qw(@ISA);
  use strict;
  
- use Bio::SearchIO;
- use Bio::PullParserI;
  
! @ISA = qw(Bio::SearchIO Bio::PullParserI);
  
  =head2 new
--- 75,82 ----
  package Bio::SearchIO::hmmer_pull;
  
  use strict;
  
  
! use base qw(Bio::SearchIO Bio::PullParserI);
  
  =head2 new

Index: EventHandlerI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/EventHandlerI.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** EventHandlerI.pm	4 Jul 2006 22:23:20 -0000	1.13
--- EventHandlerI.pm	26 Sep 2006 22:03:13 -0000	1.14
***************
*** 63,73 ****
  
  package Bio::SearchIO::EventHandlerI;
- use vars qw(@ISA);
  use strict;
  use Carp;
  
- use Bio::Event::EventHandlerI;
  
! @ISA = qw (Bio::Event::EventHandlerI);
  
  =head2 start_result
--- 63,71 ----
  
  package Bio::SearchIO::EventHandlerI;
  use strict;
  use Carp;
  
  
! use base qw(Bio::Event::EventHandlerI);
  
  =head2 start_result

Index: IteratedSearchResultEventBuilder.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/IteratedSearchResultEventBuilder.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** IteratedSearchResultEventBuilder.pm	19 Sep 2006 08:31:09 -0000	1.11
--- IteratedSearchResultEventBuilder.pm	26 Sep 2006 22:03:13 -0000	1.12
***************
*** 70,75 ****
  
  package Bio::SearchIO::IteratedSearchResultEventBuilder;
! use vars qw(@ISA %KNOWNEVENTS 
!             $DEFAULT_INCLUSION_THRESHOLD
              $MAX_HSP_OVERLAP
  );
--- 70,74 ----
  
  package Bio::SearchIO::IteratedSearchResultEventBuilder;
! use vars qw(%KNOWNEVENTS             $DEFAULT_INCLUSION_THRESHOLD
              $MAX_HSP_OVERLAP
  );
***************
*** 77,84 ****
  use strict;
  
- use Bio::SearchIO::SearchResultEventBuilder;
  use Bio::Factory::ObjectFactory;
  
! @ISA = qw(Bio::SearchIO::SearchResultEventBuilder);
  
  # e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp)
--- 76,82 ----
  use strict;
  
  use Bio::Factory::ObjectFactory;
  
! use base qw(Bio::SearchIO::SearchResultEventBuilder);
  
  # e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp)

Index: waba.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/waba.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** waba.pm	4 Jul 2006 22:23:21 -0000	1.16
--- waba.pm	26 Sep 2006 22:03:13 -0000	1.17
***************
*** 70,79 ****
  
  package Bio::SearchIO::waba;
! use vars qw(@ISA  %MODEMAP %MAPPING @STATES);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
- use Bio::SearchIO;
  use Bio::Search::Result::ResultFactory;
  use Bio::Search::HSP::HSPFactory;
--- 70,78 ----
  
  package Bio::SearchIO::waba;
! use vars qw(%MODEMAP %MAPPING @STATES);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
  use Bio::Search::Result::ResultFactory;
  use Bio::Search::HSP::HSPFactory;
***************
*** 112,116 ****
  
  
! @ISA = qw(Bio::SearchIO );
  
  =head2 new
--- 111,115 ----
  
  
! use base qw(Bio::SearchIO);
  
  =head2 new

Index: fasta.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/fasta.pm,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** fasta.pm	4 Jul 2006 22:23:20 -0000	1.50
--- fasta.pm	26 Sep 2006 22:03:13 -0000	1.51
***************
*** 72,81 ****
  
  package Bio::SearchIO::fasta;
! use vars qw(@ISA %MODEMAP %MAPPING $IDLENGTH);
  use strict;
  
  # Object preamble - inherits from Bio::Root::RootI
  
- use Bio::SearchIO;
  use Bio::Factory::ObjectFactory;
  use POSIX;
--- 72,80 ----
  
  package Bio::SearchIO::fasta;
! use vars qw(%MODEMAP %MAPPING $IDLENGTH);
  use strict;
  
  # Object preamble - inherits from Bio::Root::RootI
  
  use Bio::Factory::ObjectFactory;
  use POSIX;
***************
*** 156,160 ****
  
  
! @ISA = qw(Bio::SearchIO );
  
  =head2 new
--- 155,159 ----
  
  
! use base qw(Bio::SearchIO);
  
  =head2 new

Index: SearchWriterI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/SearchWriterI.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** SearchWriterI.pm	7 Jun 2006 09:54:53 -0000	1.10
--- SearchWriterI.pm	26 Sep 2006 22:03:13 -0000	1.11
***************
*** 45,51 ****
  package Bio::SearchIO::SearchWriterI;
  
- use Bio::Root::RootI;
  
! @ISA = qw( Bio::Root::RootI );
  
  =head2 to_string
--- 45,50 ----
  package Bio::SearchIO::SearchWriterI;
  
  
! use base qw(Bio::Root::RootI);
  
  =head2 to_string



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