[Bioperl-guts-l] bioperl-live/Bio/Tools AlignFactory.pm, 1.8, 1.9 AnalysisResult.pm, 1.18, 1.19 BPbl2seq.pm, 1.29, 1.30 BPlite.pm, 1.42, 1.43 BPpsilite.pm, 1.26, 1.27 Blast.pm, 1.38, 1.39 Blat.pm, 1.8, 1.9 CodonTable.pm, 1.37, 1.38 Coil.pm, 1.7, 1.8 ECnumber.pm, 1.12, 1.13 EPCR.pm, 1.18, 1.19 ERPIN.pm, 1.6, 1.7 ESTScan.pm, 1.14, 1.15 Eponine.pm, 1.13, 1.14 Est2Genome.pm, 1.17, 1.18 Fgenesh.pm, 1.14, 1.15 FootPrinter.pm, 1.9, 1.10 GFF.pm, 1.58, 1.59 Gel.pm, 1.11, 1.12 Geneid.pm, 1.5, 1.6 Genemark.pm, 1.17, 1.18 Genewise.pm, 1.25, 1.26 Genomewise.pm, 1.6, 1.7 Genscan.pm, 1.30, 1.31 Glimmer.pm, 1.5, 1.6 Grail.pm, 1.11, 1.12 GuessSeqFormat.pm, 1.15, 1.16 HMM.pm, 1.8, 1.9 Hmmpfam.pm, 1.9, 1.10 IUPAC.pm, 1.30, 1.31 Lucy.pm, 1.15, 1.16 MZEF.pm, 1.14, 1.15 OddCodes.pm, 1.20, 1.21 Primer3.pm, 1.21, 1.22 Prints.pm, 1.13, 1.14 Profile.pm, 1.8, 1.9 Promoterwise.pm, 1.9, 1.10 PrositeScan.pm, 1.2, 1.3 Pseudowise.pm, 1.10, 1.11 QRNA.pm, 1.5, 1.6 RNAMotif.pm, 1.12, 1.13 RandomDistFunctions.pm, 1.7, 1.8 RepeatMasker.pm, 1.11, 1.12 RestrictionEnzyme.pm, 1.35, 1.36 Seg.pm, 1.10, 1.11 SeqAn! al.pm, 1.19, 1.20 SeqPattern.pm, 1.23, 1.24 SeqStats.pm, 1.31, 1.32 SeqWords.pm, 1.17, 1.18 SiRNA.pm, 1.13, 1.14 Sigcleave.pm, 1.22, 1.23 Signalp.pm, 1.9, 1.10 WWW.pm, 1.18, 1.19 dpAlign.pm, 1.18, 1.19 ipcress.pm, 1.9, 1.10 isPcr.pm, 1.9, 1.10 pICalculator.pm, 1.11, 1.12 pSW.pm, 1.27, 1.28 tRNAscanSE.pm, 1.5, 1.6

Senduran Balasubramaniam sendu at dev.open-bio.org
Tue Sep 26 18:03:19 EDT 2006


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

Modified Files:
	AlignFactory.pm AnalysisResult.pm BPbl2seq.pm BPlite.pm 
	BPpsilite.pm Blast.pm Blat.pm CodonTable.pm Coil.pm 
	ECnumber.pm EPCR.pm ERPIN.pm ESTScan.pm Eponine.pm 
	Est2Genome.pm Fgenesh.pm FootPrinter.pm GFF.pm Gel.pm 
	Geneid.pm Genemark.pm Genewise.pm Genomewise.pm Genscan.pm 
	Glimmer.pm Grail.pm GuessSeqFormat.pm HMM.pm Hmmpfam.pm 
	IUPAC.pm Lucy.pm MZEF.pm OddCodes.pm Primer3.pm Prints.pm 
	Profile.pm Promoterwise.pm PrositeScan.pm Pseudowise.pm 
	QRNA.pm RNAMotif.pm RandomDistFunctions.pm RepeatMasker.pm 
	RestrictionEnzyme.pm Seg.pm SeqAnal.pm SeqPattern.pm 
	SeqStats.pm SeqWords.pm SiRNA.pm Sigcleave.pm Signalp.pm 
	WWW.pm dpAlign.pm ipcress.pm isPcr.pm pICalculator.pm pSW.pm 
	tRNAscanSE.pm 
Log Message:
use base, return true

Index: Blast.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Blast.pm,v
retrieving revision 1.38
retrieving revision 1.39
diff -C2 -d -r1.38 -r1.39
*** Blast.pm	24 Sep 2006 15:36:32 -0000	1.38
--- Blast.pm	26 Sep 2006 22:03:17 -0000	1.39
***************
*** 21,27 ****
  package Bio::Tools::Blast;
  use strict;
- use Exporter;
  
- use Bio::Tools::SeqAnal;
  use Bio::Root::Global     qw(:std);
  use Bio::Root::Utilities  qw(:obj);
--- 21,25 ----
***************
*** 29,36 ****
  require 5.002;
  
! use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS
              $ID $Blast @Blast_programs $Revision $Newline);
  
! @ISA        = qw( Bio::Tools::SeqAnal Exporter);
  @EXPORT     = qw();
  @EXPORT_OK  = qw($Blast);
--- 27,34 ----
  require 5.002;
  
! use vars qw(@EXPORT @EXPORT_OK %EXPORT_TAGS
              $ID $Blast @Blast_programs $Revision $Newline);
  
! use base qw(Bio::Tools::SeqAnal Exporter);
  @EXPORT     = qw();
  @EXPORT_OK  = qw($Blast);

Index: Geneid.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Geneid.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Geneid.pm	4 Jul 2006 22:23:24 -0000	1.5
--- Geneid.pm	26 Sep 2006 22:03:17 -0000	1.6
***************
*** 75,83 ****
  package Bio::Tools::Geneid;
  
! use vars qw(@ISA $SOURCE_TAG);
  use strict;
  
- use Bio::Root::Root;
- use Bio::Root::IO;
  use Bio::Tools::AnalysisResult;
  use Bio::SeqFeature::Generic;
--- 75,81 ----
  package Bio::Tools::Geneid;
  
! use vars qw($SOURCE_TAG);
  use strict;
  
  use Bio::Tools::AnalysisResult;
  use Bio::SeqFeature::Generic;
***************
*** 86,90 ****
  use Bio::SeqFeature::Gene::GeneStructure;
  
! @ISA = qw(Bio::Root::Root Bio::Root::IO);
  $SOURCE_TAG = 'geneid';
  
--- 84,88 ----
  use Bio::SeqFeature::Gene::GeneStructure;
  
! use base qw(Bio::Root::Root Bio::Root::IO);
  $SOURCE_TAG = 'geneid';
  

Index: RepeatMasker.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/RepeatMasker.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** RepeatMasker.pm	21 Sep 2006 14:51:39 -0000	1.11
--- RepeatMasker.pm	26 Sep 2006 22:03:17 -0000	1.12
***************
*** 66,77 ****
  
  package Bio::Tools::RepeatMasker;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  use Bio::SeqFeature::FeaturePair;
- use Bio::Root::IO;
  
! @ISA = qw(Bio::Root::Root Bio::Root::IO );
  
  =head2 new
--- 66,74 ----
  
  package Bio::Tools::RepeatMasker;
  use strict;
  
  use Bio::SeqFeature::FeaturePair;
  
! use base qw(Bio::Root::Root Bio::Root::IO);
  
  =head2 new

Index: Est2Genome.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Est2Genome.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** Est2Genome.pm	4 Jul 2006 22:23:24 -0000	1.17
--- Est2Genome.pm	26 Sep 2006 22:03:17 -0000	1.18
***************
*** 79,83 ****
  
  package Bio::Tools::Est2Genome;
- use vars qw(@ISA);
  use strict;
  
--- 79,82 ----
***************
*** 85,89 ****
  
  use Bio::Root::Root;
- use Bio::Tools::AnalysisResult;
  use Bio::SeqFeature::Gene::Exon;
  use Bio::SeqFeature::Gene::Transcript;
--- 84,87 ----
***************
*** 92,96 ****
  use Bio::SeqFeature::SimilarityPair;
  
! @ISA = qw(Bio::Tools::AnalysisResult );
  
  =head2 new
--- 90,94 ----
  use Bio::SeqFeature::SimilarityPair;
  
! use base qw(Bio::Tools::AnalysisResult);
  
  =head2 new

Index: Prints.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Prints.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** Prints.pm	4 Jul 2006 22:23:24 -0000	1.13
--- Prints.pm	26 Sep 2006 22:03:17 -0000	1.14
***************
*** 59,70 ****
  
  package Bio::Tools::Prints;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  use Bio::SeqFeature::FeaturePair;
- use Bio::Root::IO;
  use Bio::SeqFeature::Generic;
! @ISA = qw(Bio::Root::Root Bio::Root::IO);
  
  
--- 59,67 ----
  
  package Bio::Tools::Prints;
  use strict;
  
  use Bio::SeqFeature::FeaturePair;
  use Bio::SeqFeature::Generic;
! use base qw(Bio::Root::Root Bio::Root::IO);
  
  

Index: SeqWords.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/SeqWords.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** SeqWords.pm	4 Jul 2006 22:23:24 -0000	1.17
--- SeqWords.pm	26 Sep 2006 22:03:17 -0000	1.18
***************
*** 121,130 ****
  
  package Bio::Tools::SeqWords;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  
! @ISA = qw(Bio::Root::Root);
  
  sub new {
--- 121,128 ----
  
  package Bio::Tools::SeqWords;
  use strict;
  
  
! use base qw(Bio::Root::Root);
  
  sub new {

Index: Genscan.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Genscan.pm,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** Genscan.pm	20 Sep 2006 05:53:52 -0000	1.30
--- Genscan.pm	26 Sep 2006 22:03:17 -0000	1.31
***************
*** 92,105 ****
  
  package Bio::Tools::Genscan;
- use vars qw(@ISA);
  use strict;
  use Symbol;
  
  use Bio::Root::Root;
- use Bio::Tools::AnalysisResult;
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  
! @ISA = qw(Bio::Tools::AnalysisResult);
  
  my %ExonTags = ('Init' => 'Initial',
--- 92,103 ----
  
  package Bio::Tools::Genscan;
  use strict;
  use Symbol;
  
  use Bio::Root::Root;
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  
! use base qw(Bio::Tools::AnalysisResult);
  
  my %ExonTags = ('Init' => 'Initial',

Index: dpAlign.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/dpAlign.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** dpAlign.pm	4 Jul 2006 22:23:24 -0000	1.18
--- dpAlign.pm	26 Sep 2006 22:03:17 -0000	1.19
***************
*** 187,194 ****
  package Bio::Tools::dpAlign;
  
- use Bio::Tools::AlignFactory;
  use Bio::SimpleAlign;
  
! @ISA = qw(Bio::Tools::AlignFactory);
  
  $VERSION = '0.70';
--- 187,193 ----
  package Bio::Tools::dpAlign;
  
  use Bio::SimpleAlign;
  
! use base qw(Bio::Tools::AlignFactory);
  
  $VERSION = '0.70';

Index: Seg.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Seg.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Seg.pm	4 Jul 2006 22:23:24 -0000	1.10
--- Seg.pm	26 Sep 2006 22:03:17 -0000	1.11
***************
*** 62,73 ****
  
  package Bio::Tools::Seg;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  use Bio::SeqFeature::FeaturePair;
- use Bio::Root::IO;
  use Bio::SeqFeature::Generic;
! @ISA = qw(Bio::Root::Root Bio::Root::IO);
  
  =head2 new
--- 62,70 ----
  
  package Bio::Tools::Seg;
  use strict;
  
  use Bio::SeqFeature::FeaturePair;
  use Bio::SeqFeature::Generic;
! use base qw(Bio::Root::Root Bio::Root::IO);
  
  =head2 new

Index: Promoterwise.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Promoterwise.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** Promoterwise.pm	20 Sep 2006 04:00:57 -0000	1.9
--- Promoterwise.pm	26 Sep 2006 22:03:17 -0000	1.10
***************
*** 80,92 ****
  
  package Bio::Tools::Promoterwise;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  use Bio::SeqFeature::FeaturePair;
  use Bio::SeqFeature::Generic;
- use Bio::Root::IO;
  
! @ISA = qw(Bio::Root::Root Bio::Root::IO );
  
  =head2 new
--- 80,89 ----
  
  package Bio::Tools::Promoterwise;
  use strict;
  
  use Bio::SeqFeature::FeaturePair;
  use Bio::SeqFeature::Generic;
  
! use base qw(Bio::Root::Root Bio::Root::IO);
  
  =head2 new

Index: SeqPattern.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/SeqPattern.pm,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** SeqPattern.pm	24 Sep 2006 15:36:32 -0000	1.23
--- SeqPattern.pm	26 Sep 2006 22:03:17 -0000	1.24
***************
*** 198,203 ****
  package Bio::Tools::SeqPattern;
  
! use Bio::Root::Root;
! @ISA = qw(Bio::Root::Root);
  use strict;
  use vars qw ($ID);
--- 198,202 ----
  package Bio::Tools::SeqPattern;
  
! use base qw(Bio::Root::Root);
  use strict;
  use vars qw ($ID);

Index: RandomDistFunctions.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/RandomDistFunctions.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** RandomDistFunctions.pm	4 Jul 2006 22:23:24 -0000	1.7
--- RandomDistFunctions.pm	26 Sep 2006 22:03:17 -0000	1.8
***************
*** 75,87 ****
  package Bio::Tools::RandomDistFunctions;
  require Exporter;
! use vars qw(@ISA %LOADED @EXPORT_OK); 
! use strict;
  
  #use Math::BigFloat lib => 'GMP,Bit::Vector';
  #use Math::BigInt lib  => 'GMP,Bit::Vector';
  use POSIX;
- use Bio::Root::Root;
  
! @ISA = qw(Bio::Root::Root);
  
  =head2 birth_distribution
--- 75,85 ----
  package Bio::Tools::RandomDistFunctions;
  require Exporter;
! use vars qw(%LOADED @EXPORT_OK); use strict;
  
  #use Math::BigFloat lib => 'GMP,Bit::Vector';
  #use Math::BigInt lib  => 'GMP,Bit::Vector';
  use POSIX;
  
! use base qw(Bio::Root::Root);
  
  =head2 birth_distribution

Index: SeqStats.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/SeqStats.pm,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** SeqStats.pm	21 Sep 2006 22:20:50 -0000	1.31
--- SeqStats.pm	26 Sep 2006 22:03:17 -0000	1.32
***************
*** 205,213 ****
  package Bio::Tools::SeqStats;
  use strict;
! use vars qw(@ISA %Alphabets %Alphabets_strict $amino_weights
  	    $rna_weights $dna_weights %Weights $amino_hydropathicity);
  use Bio::Seq;
! use Bio::Root::Root;
! @ISA = qw(Bio::Root::Root);
  
  BEGIN {
--- 205,212 ----
  package Bio::Tools::SeqStats;
  use strict;
! use vars qw(%Alphabets %Alphabets_strict $amino_weights
  	    $rna_weights $dna_weights %Weights $amino_hydropathicity);
  use Bio::Seq;
! use base qw(Bio::Root::Root);
  
  BEGIN {
***************
*** 873,874 ****
--- 872,875 ----
      return 1;
  }
+ 
+ 1;

Index: Coil.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Coil.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** Coil.pm	21 Sep 2006 14:51:39 -0000	1.7
--- Coil.pm	26 Sep 2006 22:03:17 -0000	1.8
***************
*** 64,75 ****
  
  package Bio::Tools::Coil;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  use Bio::SeqFeature::FeaturePair;
- use Bio::Root::IO;
  use Bio::SeqFeature::Generic;
! @ISA = qw(Bio::Root::Root Bio::Root::IO);
  
  
--- 64,72 ----
  
  package Bio::Tools::Coil;
  use strict;
  
  use Bio::SeqFeature::FeaturePair;
  use Bio::SeqFeature::Generic;
! use base qw(Bio::Root::Root Bio::Root::IO);
  
  

Index: EPCR.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/EPCR.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** EPCR.pm	4 Jul 2006 22:23:24 -0000	1.18
--- EPCR.pm	26 Sep 2006 22:03:17 -0000	1.19
***************
*** 77,89 ****
  
  package Bio::Tools::EPCR;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
- use Bio::SeqAnalysisParserI;
  use Bio::SeqFeature::FeaturePair;
  use Bio::SeqFeature::Generic;
  
! @ISA = qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::Root::IO );
  
  =head2 new
--- 77,86 ----
  
  package Bio::Tools::EPCR;
  use strict;
  
  use Bio::SeqFeature::FeaturePair;
  use Bio::SeqFeature::Generic;
  
! use base qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::Root::IO);
  
  =head2 new

Index: RestrictionEnzyme.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/RestrictionEnzyme.pm,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** RestrictionEnzyme.pm	4 Jul 2006 22:23:24 -0000	1.35
--- RestrictionEnzyme.pm	26 Sep 2006 22:03:17 -0000	1.36
***************
*** 170,179 ****
  use strict;
  
- use Bio::Root::Root;
- use Exporter;
  
! use vars qw (@ISA @EXPORT_OK %EXPORT_TAGS $ID  @RE_available $Revision);
  
! @ISA         = qw(Bio::Root::Root Exporter);
  @EXPORT_OK   = qw(@RE_available);
  %EXPORT_TAGS = ( std => [qw(@RE_available)] );
--- 170,177 ----
  use strict;
  
  
! use vars qw (@EXPORT_OK %EXPORT_TAGS $ID @RE_available $Revision);
  
! use base qw(Bio::Root::Root Exporter);
  @EXPORT_OK   = qw(@RE_available);
  %EXPORT_TAGS = ( std => [qw(@RE_available)] );

Index: ipcress.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/ipcress.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** ipcress.pm	20 Sep 2006 05:53:52 -0000	1.9
--- ipcress.pm	26 Sep 2006 22:03:17 -0000	1.10
***************
*** 83,93 ****
  
  package Bio::Tools::ipcress;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  use Bio::SeqFeature::Generic;
  
! @ISA = qw(Bio::Root::Root);
  
  =head2 new
--- 83,91 ----
  
  package Bio::Tools::ipcress;
  use strict;
  
  use Bio::SeqFeature::Generic;
  
! use base qw(Bio::Root::Root);
  
  =head2 new

Index: Primer3.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Primer3.pm,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** Primer3.pm	19 Sep 2006 05:31:53 -0000	1.21
--- Primer3.pm	26 Sep 2006 22:03:17 -0000	1.22
***************
*** 116,129 ****
  package Bio::Tools::Primer3;
  
- use vars qw(@ISA);
  use strict;
  use Bio::Seq;
  use Bio::Seq::PrimedSeq;
  use Bio::SeqFeature::Primer;
- use Bio::Root::Root;
- use Bio::Root::IO;
  use Clone qw(clone);
  
! use vars qw($AUTOLOAD @PRIMER3_PARAMS @ISA %OK_FIELD $ID);
  
  BEGIN {
--- 116,126 ----
  package Bio::Tools::Primer3;
  
  use strict;
  use Bio::Seq;
  use Bio::Seq::PrimedSeq;
  use Bio::SeqFeature::Primer;
  use Clone qw(clone);
  
! use vars qw($AUTOLOAD @PRIMER3_PARAMS %OK_FIELD $ID);
  
  BEGIN {
***************
*** 134,138 ****
  
  
! @ISA = qw(Bio::Root::Root Bio::Root::IO);
  
  
--- 131,135 ----
  
  
! use base qw(Bio::Root::Root Bio::Root::IO);
  
  

Index: QRNA.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/QRNA.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** QRNA.pm	4 Jul 2006 22:23:24 -0000	1.5
--- QRNA.pm	26 Sep 2006 22:03:17 -0000	1.6
***************
*** 116,128 ****
  
  package Bio::Tools::QRNA;
! use vars qw(@ISA @Models);
  use strict;
  
- use Bio::Root::IO;
  use Bio::SeqFeature::Generic;
  use Bio::SeqFeature::FeaturePair;
- use Bio::SeqAnalysisParserI;
  
! @ISA = qw(Bio::Root::IO Bio::SeqAnalysisParserI);
  @Models = qw(OTH COD RNA);
  
--- 116,126 ----
  
  package Bio::Tools::QRNA;
! use vars qw(@Models);
  use strict;
  
  use Bio::SeqFeature::Generic;
  use Bio::SeqFeature::FeaturePair;
  
! use base qw(Bio::Root::IO Bio::SeqAnalysisParserI);
  @Models = qw(OTH COD RNA);
  

Index: Lucy.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Lucy.pm,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Lucy.pm	4 Jul 2006 22:23:24 -0000	1.15
--- Lucy.pm	26 Sep 2006 22:03:17 -0000	1.16
***************
*** 155,165 ****
  package Bio::Tools::Lucy;
  
! use vars qw($AUTOLOAD @ISA @ATTR %OK_FIELD);
  use strict;
  use Bio::PrimarySeq;
- use Bio::Root::Root;
- use Bio::Root::IO;
  
! @ISA = qw(Bio::Root::Root Bio::Root::IO);
  @ATTR = qw(seqfile qualfile stderrfile infofile lucy_verbose fwd_desig rev_desig adv_stderr); 
  foreach my $attr (@ATTR) {
--- 155,163 ----
  package Bio::Tools::Lucy;
  
! use vars qw($AUTOLOAD @ATTR %OK_FIELD);
  use strict;
  use Bio::PrimarySeq;
  
! use base qw(Bio::Root::Root Bio::Root::IO);
  @ATTR = qw(seqfile qualfile stderrfile infofile lucy_verbose fwd_desig rev_desig adv_stderr); 
  foreach my $attr (@ATTR) {

Index: tRNAscanSE.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/tRNAscanSE.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** tRNAscanSE.pm	15 Aug 2006 18:43:37 -0000	1.5
--- tRNAscanSE.pm	26 Sep 2006 22:03:17 -0000	1.6
***************
*** 68,78 ****
  
  package Bio::Tools::tRNAscanSE;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Tools::AnalysisResult;
  use Bio::SeqFeature::Generic;
  
! @ISA = qw(Bio::Tools::AnalysisResult );
  
  use vars qw($GeneTag $SrcTag $ExonTag);
--- 68,76 ----
  
  package Bio::Tools::tRNAscanSE;
  use strict;
  
  use Bio::SeqFeature::Generic;
  
! use base qw(Bio::Tools::AnalysisResult);
  
  use vars qw($GeneTag $SrcTag $ExonTag);

Index: isPcr.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/isPcr.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** isPcr.pm	4 Jul 2006 22:23:24 -0000	1.9
--- isPcr.pm	26 Sep 2006 22:03:17 -0000	1.10
***************
*** 83,95 ****
  
  package Bio::Tools::isPcr;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  use Bio::SeqIO;
  use Bio::SeqFeature::Generic;
  
  
! @ISA = qw(Bio::Root::Root);
  
  
--- 83,93 ----
  
  package Bio::Tools::isPcr;
  use strict;
  
  use Bio::SeqIO;
  use Bio::SeqFeature::Generic;
  
  
! use base qw(Bio::Root::Root);
  
  

Index: BPlite.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/BPlite.pm,v
retrieving revision 1.42
retrieving revision 1.43
diff -C2 -d -r1.42 -r1.43
*** BPlite.pm	7 Jun 2006 09:54:54 -0000	1.42
--- BPlite.pm	26 Sep 2006 22:03:17 -0000	1.43
***************
*** 174,186 ****
  
  use strict;
- use vars qw(@ISA);
  
- use Bio::Root::Root;
- use Bio::Root::IO;
  use Bio::Tools::BPlite::Sbjct; # we want to use Sbjct
- use Bio::SeqAnalysisParserI;
  use Symbol;
  
! @ISA = qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::Root::IO);
  
  # new comes from a RootI now
--- 174,182 ----
  
  use strict;
  
  use Bio::Tools::BPlite::Sbjct; # we want to use Sbjct
  use Symbol;
  
! use base qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::Root::IO);
  
  # new comes from a RootI now

Index: WWW.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/WWW.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** WWW.pm	24 Sep 2006 15:36:32 -0000	1.18
--- WWW.pm	26 Sep 2006 22:03:17 -0000	1.19
***************
*** 19,28 ****
  package Bio::Tools::WWW;
  use strict;
! use Bio::Root::Root;
! use Exporter      ();
! use vars qw(@ISA @EXPORT_OK %EXPORT_TAGS $ID  $BioWWW $Revision
  	    $AUTHORITY);
  $AUTHORITY = 'nobody at localhost';
! @ISA         = qw( Bio::Root::Root Exporter);
  @EXPORT_OK   = qw($BioWWW);
  %EXPORT_TAGS = ( obj => [qw($BioWWW)],
--- 19,26 ----
  package Bio::Tools::WWW;
  use strict;
! use vars qw(@EXPORT_OK %EXPORT_TAGS $ID $BioWWW $Revision
  	    $AUTHORITY);
  $AUTHORITY = 'nobody at localhost';
! use base qw(Bio::Root::Root Exporter);
  @EXPORT_OK   = qw($BioWWW);
  %EXPORT_TAGS = ( obj => [qw($BioWWW)],

Index: Fgenesh.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Fgenesh.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** Fgenesh.pm	26 Sep 2006 00:55:52 -0000	1.14
--- Fgenesh.pm	26 Sep 2006 22:03:17 -0000	1.15
***************
*** 92,105 ****
  
  package Bio::Tools::Fgenesh;
- use vars qw(@ISA);
  use strict;
  use Symbol;
  
  use Bio::Root::Root;
- use Bio::Tools::AnalysisResult;
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  
! @ISA = qw(Bio::Tools::AnalysisResult);
  
  my %ExonTags = ('CDSf' => 'Initial',
--- 92,103 ----
  
  package Bio::Tools::Fgenesh;
  use strict;
  use Symbol;
  
  use Bio::Root::Root;
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  
! use base qw(Bio::Tools::AnalysisResult);
  
  my %ExonTags = ('CDSf' => 'Initial',

Index: GFF.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/GFF.pm,v
retrieving revision 1.58
retrieving revision 1.59
diff -C2 -d -r1.58 -r1.59
*** GFF.pm	13 Jul 2006 21:19:27 -0000	1.58
--- GFF.pm	26 Sep 2006 22:03:17 -0000	1.59
***************
*** 133,146 ****
  package Bio::Tools::GFF;
  
! use vars qw(@ISA $HAS_HTML_ENTITIES);
  use strict;
  
- use Bio::Root::IO;
- use Bio::SeqAnalysisParserI;
  use Bio::Seq::SeqFactory;
  use Bio::LocatableSeq;
  use Bio::SeqFeature::Generic;
  
! @ISA = qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::Root::IO);
  
  =head2 new
--- 133,144 ----
  package Bio::Tools::GFF;
  
! use vars qw($HAS_HTML_ENTITIES);
  use strict;
  
  use Bio::Seq::SeqFactory;
  use Bio::LocatableSeq;
  use Bio::SeqFeature::Generic;
  
! use base qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::Root::IO);
  
  =head2 new

Index: AlignFactory.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/AlignFactory.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** AlignFactory.pm	20 Nov 2001 02:09:40 -0000	1.8
--- AlignFactory.pm	26 Sep 2006 22:03:17 -0000	1.9
***************
*** 39,47 ****
  
  package Bio::Tools::AlignFactory;
- use vars qw(@ISA);
  use strict;
  
! use Bio::Root::Root;
! @ISA = qw(Bio::Root::Root);
  
  BEGIN {
--- 39,45 ----
  
  package Bio::Tools::AlignFactory;
  use strict;
  
! use base qw(Bio::Root::Root);
  
  BEGIN {

Index: Profile.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Profile.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** Profile.pm	4 Jul 2006 22:23:24 -0000	1.8
--- Profile.pm	26 Sep 2006 22:03:17 -0000	1.9
***************
*** 56,68 ****
  
  package Bio::Tools::Profile;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  use Bio::SeqFeature::FeaturePair;
- use Bio::Root::IO;
  use Bio::SeqFeature::Generic;
  
! @ISA = qw(Bio::Root::Root Bio::Root::IO );
  
  
--- 56,65 ----
  
  package Bio::Tools::Profile;
  use strict;
  
  use Bio::SeqFeature::FeaturePair;
  use Bio::SeqFeature::Generic;
  
! use base qw(Bio::Root::Root Bio::Root::IO);
  
  

Index: Signalp.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Signalp.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** Signalp.pm	21 Sep 2006 14:51:39 -0000	1.9
--- Signalp.pm	26 Sep 2006 22:03:17 -0000	1.10
***************
*** 66,77 ****
  
  package Bio::Tools::Signalp;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  use Bio::SeqFeature::FeaturePair;
- use Bio::Root::IO;
  use Bio::SeqFeature::Generic;
! @ISA = qw(Bio::Root::Root Bio::Root::IO );
  
  
--- 66,74 ----
  
  package Bio::Tools::Signalp;
  use strict;
  
  use Bio::SeqFeature::FeaturePair;
  use Bio::SeqFeature::Generic;
! use base qw(Bio::Root::Root Bio::Root::IO);
  
  

Index: Genomewise.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Genomewise.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Genomewise.pm	4 Jul 2006 22:23:24 -0000	1.6
--- Genomewise.pm	26 Sep 2006 22:03:17 -0000	1.7
***************
*** 71,78 ****
  
  package Bio::Tools::Genomewise;
! use vars qw(@ISA $Srctag);
  use strict;
  
- use Bio::Tools::Genewise;
  use Bio::Tools::AnalysisResult;
  use Bio::SeqFeature::Generic;
--- 71,77 ----
  
  package Bio::Tools::Genomewise;
! use vars qw($Srctag);
  use strict;
  
  use Bio::Tools::AnalysisResult;
  use Bio::SeqFeature::Generic;
***************
*** 82,86 ****
  use Bio::SeqFeature::Gene::GeneStructure;
  
! @ISA = qw(Bio::Tools::Genewise);
  
  $Srctag = 'genomewise';
--- 81,85 ----
  use Bio::SeqFeature::Gene::GeneStructure;
  
! use base qw(Bio::Tools::Genewise);
  
  $Srctag = 'genomewise';

Index: CodonTable.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/CodonTable.pm,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** CodonTable.pm	15 Aug 2006 04:59:01 -0000	1.37
--- CodonTable.pm	26 Sep 2006 22:03:17 -0000	1.38
***************
*** 173,187 ****
  
  package Bio::Tools::CodonTable;
! use vars qw(@ISA @NAMES @TABLES @STARTS $TRCOL $CODONS %IUPAC_DNA 
! 	    $CODONGAP $GAP
  	    %IUPAC_AA %THREELETTERSYMBOLS $VALID_PROTEIN $TERMINATOR);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
- use Bio::Root::Root;
  use Bio::Tools::IUPAC;
  use Bio::SeqUtils;
  
! @ISA = qw(Bio::Root::Root);
  
  
--- 173,185 ----
  
  package Bio::Tools::CodonTable;
! use vars qw(@NAMES @TABLES @STARTS $TRCOL $CODONS %IUPAC_DNA 	    $CODONGAP $GAP
  	    %IUPAC_AA %THREELETTERSYMBOLS $VALID_PROTEIN $TERMINATOR);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  use Bio::Tools::IUPAC;
  use Bio::SeqUtils;
  
! use base qw(Bio::Root::Root);
  
  

Index: Eponine.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Eponine.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** Eponine.pm	4 Jul 2006 22:23:24 -0000	1.13
--- Eponine.pm	26 Sep 2006 22:03:17 -0000	1.14
***************
*** 78,89 ****
  
  package Bio::Tools::Eponine;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Tools::AnalysisResult;
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  
! @ISA = qw(Bio::Tools::AnalysisResult);
  
  sub _initialize_state {
--- 78,87 ----
  
  package Bio::Tools::Eponine;
  use strict;
  
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  
! use base qw(Bio::Tools::AnalysisResult);
  
  sub _initialize_state {

Index: Blat.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Blat.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** Blat.pm	21 Sep 2006 14:51:39 -0000	1.8
--- Blat.pm	26 Sep 2006 22:03:17 -0000	1.9
***************
*** 55,66 ****
  
  package Bio::Tools::Blat;
- use vars qw(@ISA);
  use strict;
  use Bio::SeqFeature::Generic;
- use Bio::Root::Root;
  use Bio::SeqFeature::FeaturePair;
- use Bio::Root::IO;
  use Bio::SeqFeature::Generic;
! @ISA = qw(Bio::Root::Root Bio::Root::IO );
  
  =head2 new
--- 55,63 ----
  
  package Bio::Tools::Blat;
  use strict;
  use Bio::SeqFeature::Generic;
  use Bio::SeqFeature::FeaturePair;
  use Bio::SeqFeature::Generic;
! use base qw(Bio::Root::Root Bio::Root::IO);
  
  =head2 new

Index: ESTScan.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/ESTScan.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** ESTScan.pm	4 Jul 2006 22:23:24 -0000	1.14
--- ESTScan.pm	26 Sep 2006 22:03:17 -0000	1.15
***************
*** 77,89 ****
  
  package Bio::Tools::ESTScan;
- use vars qw(@ISA);
  use strict;
  use Symbol;
  
  use Bio::Root::Root;
- use Bio::Tools::AnalysisResult;
  use Bio::Tools::Prediction::Exon;
  
! @ISA = qw(Bio::Tools::AnalysisResult);
  
  sub _initialize_state {
--- 77,87 ----
  
  package Bio::Tools::ESTScan;
  use strict;
  use Symbol;
  
  use Bio::Root::Root;
  use Bio::Tools::Prediction::Exon;
  
! use base qw(Bio::Tools::AnalysisResult);
  
  sub _initialize_state {

Index: Hmmpfam.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Hmmpfam.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** Hmmpfam.pm	21 Sep 2006 14:51:39 -0000	1.9
--- Hmmpfam.pm	26 Sep 2006 22:03:17 -0000	1.10
***************
*** 56,67 ****
  
  package Bio::Tools::Hmmpfam;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  use Bio::SeqFeature::FeaturePair;
- use Bio::Root::IO;
  use Bio::SeqFeature::Generic;
! @ISA = qw(Bio::Root::Root Bio::Root::IO );
  
  
--- 56,64 ----
  
  package Bio::Tools::Hmmpfam;
  use strict;
  
  use Bio::SeqFeature::FeaturePair;
  use Bio::SeqFeature::Generic;
! use base qw(Bio::Root::Root Bio::Root::IO);
  
  

Index: IUPAC.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/IUPAC.pm,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** IUPAC.pm	19 Sep 2006 05:31:53 -0000	1.30
--- IUPAC.pm	26 Sep 2006 22:03:17 -0000	1.31
***************
*** 134,138 ****
  
  use strict;
! use vars qw(@ISA %IUP %IUB %REV_IUB $AUTOLOAD);
  
  BEGIN {
--- 134,138 ----
  
  use strict;
! use vars qw(%IUP %IUB %REV_IUB $AUTOLOAD);
  
  BEGIN {
***************
*** 204,209 ****
  
  }
! use Bio::Root::Root;
! @ISA = qw(Bio::Root::Root);
  
  =head2 new
--- 204,208 ----
  
  }
! use base qw(Bio::Root::Root);
  
  =head2 new

Index: Glimmer.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Glimmer.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Glimmer.pm	20 Sep 2006 02:11:55 -0000	1.5
--- Glimmer.pm	26 Sep 2006 22:03:17 -0000	1.6
***************
*** 104,115 ****
  
  package Bio::Tools::Glimmer;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Tools::AnalysisResult;
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  
! @ISA = qw(Bio::Tools::AnalysisResult);
  
  sub _initialize_state {
--- 104,113 ----
  
  package Bio::Tools::Glimmer;
  use strict;
  
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  
! use base qw(Bio::Tools::AnalysisResult);
  
  sub _initialize_state {

Index: BPbl2seq.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/BPbl2seq.pm,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** BPbl2seq.pm	4 Jul 2006 22:23:24 -0000	1.29
--- BPbl2seq.pm	26 Sep 2006 22:03:17 -0000	1.30
***************
*** 125,137 ****
  
  use strict;
- use vars qw(@ISA);
  use Bio::Tools::BPlite;
- use Bio::Root::Root;
- use Bio::Root::IO;
  use Bio::Tools::BPlite::Sbjct; # we want to use Sbjct
- use Bio::SeqAnalysisParserI;
  use Symbol;
  
! @ISA = qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::Root::IO);
  
  #@ISA = qw(Bio::Tools::BPlite);
--- 125,133 ----
  
  use strict;
  use Bio::Tools::BPlite;
  use Bio::Tools::BPlite::Sbjct; # we want to use Sbjct
  use Symbol;
  
! use base qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::Root::IO);
  
  #@ISA = qw(Bio::Tools::BPlite);

Index: BPpsilite.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/BPpsilite.pm,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** BPpsilite.pm	4 Jul 2006 22:23:24 -0000	1.26
--- BPpsilite.pm	26 Sep 2006 22:03:17 -0000	1.27
***************
*** 143,154 ****
  
  use strict;
- use vars qw(@ISA);
  use Bio::Tools::BPlite::Iteration; #
  use Bio::Tools::BPlite::Sbjct; #   Debug code
- use Bio::Root::Root; # root interface to inherit from
- use Bio::Root::IO;
  use Bio::Tools::BPlite; 
  
! @ISA = qw(Bio::Root::Root Bio::Root::IO);
  
  sub new {
--- 143,151 ----
  
  use strict;
  use Bio::Tools::BPlite::Iteration; #
  use Bio::Tools::BPlite::Sbjct; #   Debug code
  use Bio::Tools::BPlite; 
  
! use base qw(Bio::Root::Root Bio::Root::IO);
  
  sub new {

Index: SiRNA.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/SiRNA.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** SiRNA.pm	4 Jul 2006 22:23:24 -0000	1.13
--- SiRNA.pm	26 Sep 2006 22:03:17 -0000	1.14
***************
*** 129,138 ****
  use Bio::Seq::RichSeq;
  use Bio::SeqFeature::Generic;
- use Bio::Root::Root;
  use Bio::SeqFeature::SiRNA::Oligo;
  use Bio::SeqFeature::SiRNA::Pair;
  
  
! our @ISA = qw(Bio::Root::Root);
  
  
--- 129,137 ----
  use Bio::Seq::RichSeq;
  use Bio::SeqFeature::Generic;
  use Bio::SeqFeature::SiRNA::Oligo;
  use Bio::SeqFeature::SiRNA::Pair;
  
  
! use base qw(Bio::Root::Root);
  
  

Index: Grail.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Grail.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** Grail.pm	4 Jul 2006 22:23:24 -0000	1.11
--- Grail.pm	26 Sep 2006 22:03:17 -0000	1.12
***************
*** 84,97 ****
  
  package Bio::Tools::Grail;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
- use Bio::Root::IO;
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  use Symbol;
  
! @ISA = qw(Bio::Root::IO Bio::Root::Root);
  
  sub new {
--- 84,94 ----
  
  package Bio::Tools::Grail;
  use strict;
  
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  use Symbol;
  
! use base qw(Bio::Root::IO Bio::Root::Root);
  
  sub new {

Index: Genewise.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Genewise.pm,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** Genewise.pm	4 Jul 2006 22:23:24 -0000	1.25
--- Genewise.pm	26 Sep 2006 22:03:17 -0000	1.26
***************
*** 70,79 ****
  
  package Bio::Tools::Genewise;
! use vars qw(@ISA $Srctag);
  use strict;
  use Symbol;
  
- use Bio::Root::Root;
- use Bio::Root::IO;
  use Bio::Tools::AnalysisResult;
  use Bio::SeqFeature::Generic;
--- 70,77 ----
  
  package Bio::Tools::Genewise;
! use vars qw($Srctag);
  use strict;
  use Symbol;
  
  use Bio::Tools::AnalysisResult;
  use Bio::SeqFeature::Generic;
***************
*** 83,87 ****
  use Bio::SeqFeature::Gene::GeneStructure;
  
! @ISA = qw(Bio::Root::Root Bio::Root::IO);
  $Srctag = 'genewise';
  
--- 81,85 ----
  use Bio::SeqFeature::Gene::GeneStructure;
  
! use base qw(Bio::Root::Root Bio::Root::IO);
  $Srctag = 'genewise';
  

Index: Pseudowise.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Pseudowise.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Pseudowise.pm	4 Jul 2006 22:23:24 -0000	1.10
--- Pseudowise.pm	26 Sep 2006 22:03:17 -0000	1.11
***************
*** 67,76 ****
  
  package Bio::Tools::Pseudowise;
- use vars qw(@ISA);
  use strict;
  use Symbol;
  
  use Bio::Root::Root;
- use Bio::Tools::AnalysisResult;
  use Bio::SeqFeature::Generic;
  use Bio::SeqFeature::Gene::Exon;
--- 67,74 ----
***************
*** 79,83 ****
  use Bio::SeqFeature::Gene::GeneStructure;
  
! @ISA = qw(Bio::Tools::AnalysisResult);
  
  sub _initialize_state {
--- 77,81 ----
  use Bio::SeqFeature::Gene::GeneStructure;
  
! use base qw(Bio::Tools::AnalysisResult);
  
  sub _initialize_state {

Index: Genemark.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Genemark.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** Genemark.pm	4 Jul 2006 22:23:24 -0000	1.17
--- Genemark.pm	26 Sep 2006 22:03:17 -0000	1.18
***************
*** 97,111 ****
  
  package Bio::Tools::Genemark;
- use vars qw(@ISA);
  use strict;
  use Symbol;
  
  use Bio::Root::Root;
- use Bio::Tools::AnalysisResult;
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  use Bio::Seq;
  
! @ISA = qw(Bio::Tools::AnalysisResult);
  
  sub _initialize_state {
--- 97,109 ----
  
  package Bio::Tools::Genemark;
  use strict;
  use Symbol;
  
  use Bio::Root::Root;
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  use Bio::Seq;
  
! use base qw(Bio::Tools::AnalysisResult);
  
  sub _initialize_state {

Index: ECnumber.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/ECnumber.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** ECnumber.pm	20 Sep 2006 16:29:25 -0000	1.12
--- ECnumber.pm	26 Sep 2006 22:03:17 -0000	1.13
***************
*** 141,145 ****
  
  package Bio::Tools::ECnumber;
- use vars qw( @ISA );
  use strict;
  use Bio::Root::Object;
--- 141,144 ----
***************
*** 149,153 ****
  use constant FALSE   => 0;
  
! @ISA = qw( Bio::Root::Root );
  
  
--- 148,152 ----
  use constant FALSE   => 0;
  
! use base qw(Bio::Root::Root);
  
  

Index: HMM.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/HMM.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** HMM.pm	4 Jul 2006 22:23:24 -0000	1.8
--- HMM.pm	26 Sep 2006 22:03:17 -0000	1.9
***************
*** 128,132 ****
  package Bio::Tools::HMM;
  
! @ISA = qw(Bio::Root::Root);
  
  $VERSION = '0.10';
--- 128,132 ----
  package Bio::Tools::HMM;
  
! use base qw(Bio::Root::Root);
  
  $VERSION = '0.10';

Index: GuessSeqFormat.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/GuessSeqFormat.pm,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** GuessSeqFormat.pm	4 Jul 2006 22:23:24 -0000	1.15
--- GuessSeqFormat.pm	26 Sep 2006 22:03:17 -0000	1.16
***************
*** 225,232 ****
  use warnings;
  
- use Bio::Root::Root;
  
! use vars qw(@ISA);
! @ISA = qw(Bio::Root::Root);
  
  =head1 METHODS
--- 225,230 ----
  use warnings;
  
  
! use base qw(Bio::Root::Root);
  
  =head1 METHODS

Index: Gel.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Gel.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** Gel.pm	4 Jul 2006 22:23:24 -0000	1.11
--- Gel.pm	26 Sep 2006 22:03:17 -0000	1.12
***************
*** 87,97 ****
  
  package Bio::Tools::Gel;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  use Bio::PrimarySeq;
  
! @ISA = qw(Bio::Root::Root);
  
  =head2 new
--- 87,95 ----
  
  package Bio::Tools::Gel;
  use strict;
  
  use Bio::PrimarySeq;
  
! use base qw(Bio::Root::Root);
  
  =head2 new

Index: AnalysisResult.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/AnalysisResult.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** AnalysisResult.pm	19 Sep 2006 05:31:53 -0000	1.18
--- AnalysisResult.pm	26 Sep 2006 22:03:17 -0000	1.19
***************
*** 93,106 ****
  
  package Bio::Tools::AnalysisResult;
- use vars qw(@ISA);
  use strict;
  
! use Bio::Root::Root;
! use Bio::Root::IO;
! use Bio::SeqAnalysisParserI;
! use Bio::AnalysisResultI;
! 
! @ISA = qw(Bio::Root::Root Bio::SeqAnalysisParserI
! 	Bio::AnalysisResultI Bio::Root::IO);
  
  sub new {
--- 93,99 ----
  
  package Bio::Tools::AnalysisResult;
  use strict;
  
! use base qw(Bio::Root::Root Bio::SeqAnalysisParserI Bio::AnalysisResultI Bio::Root::IO);
  
  sub new {

Index: OddCodes.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/OddCodes.pm,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** OddCodes.pm	19 Sep 2006 05:31:53 -0000	1.20
--- OddCodes.pm	26 Sep 2006 22:03:17 -0000	1.21
***************
*** 121,130 ****
  
  package Bio::Tools::OddCodes;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  
! @ISA = qw(Bio::Root::Root);
  
  sub new
--- 121,128 ----
  
  package Bio::Tools::OddCodes;
  use strict;
  
  
! use base qw(Bio::Root::Root);
  
  sub new

Index: Sigcleave.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Sigcleave.pm,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** Sigcleave.pm	4 Jul 2006 22:23:24 -0000	1.22
--- Sigcleave.pm	26 Sep 2006 22:03:17 -0000	1.23
***************
*** 181,188 ****
  package Bio::Tools::Sigcleave;
  
- use Bio::Root::Root;
  use Bio::PrimarySeq;
  
! @ISA = qw(Bio::Root::Root);
  use strict;
  use vars qw ($ID %WeightTable_euc  %WeightTable_pro );
--- 181,187 ----
  package Bio::Tools::Sigcleave;
  
  use Bio::PrimarySeq;
  
! use base qw(Bio::Root::Root);
  use strict;
  use vars qw ($ID %WeightTable_euc  %WeightTable_pro );

Index: pSW.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/pSW.pm,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** pSW.pm	4 Jul 2006 22:23:24 -0000	1.27
--- pSW.pm	26 Sep 2006 22:03:17 -0000	1.28
***************
*** 115,119 ****
  
  package Bio::Tools::pSW;
- use vars qw(@ISA);
  use strict;
  no strict ( 'refs');
--- 115,118 ----
***************
*** 129,137 ****
  }
  
- use Bio::Tools::AlignFactory;
  use Bio::SimpleAlign;
  
  
! @ISA = qw(Bio::Tools::AlignFactory);
  
  
--- 128,135 ----
  }
  
  use Bio::SimpleAlign;
  
  
! use base qw(Bio::Tools::AlignFactory);
  
  
***************
*** 417,420 ****
  }
  
!     
! 
--- 415,417 ----
  }
  
! 1;

Index: SeqAnal.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/SeqAnal.pm,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** SeqAnal.pm	24 Sep 2006 15:36:32 -0000	1.19
--- SeqAnal.pm	26 Sep 2006 22:03:17 -0000	1.20
***************
*** 13,23 ****
  package Bio::Tools::SeqAnal;
  
- use Bio::Root::Object ();
  use Bio::Root::Global qw(:std);
  
  use strict;
! use vars qw($ID @ISA);
  
! @ISA        = qw( Bio::Root::Object );
  $ID = 'Bio::Tools::SeqAnal';
  
--- 13,22 ----
  package Bio::Tools::SeqAnal;
  
  use Bio::Root::Global qw(:std);
  
  use strict;
! use vars qw($ID);
  
! use base qw(Bio::Root::Object);
  $ID = 'Bio::Tools::SeqAnal';
  

Index: pICalculator.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/pICalculator.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** pICalculator.pm	21 Sep 2006 14:51:39 -0000	1.11
--- pICalculator.pm	26 Sep 2006 22:03:17 -0000	1.12
***************
*** 103,112 ****
  
  package Bio::Tools::pICalculator;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  
! @ISA = qw(Bio::Root::Root);
  
  # pK values from the DTASelect program from Scripps
--- 103,110 ----
  
  package Bio::Tools::pICalculator;
  use strict;
  
  
! use base qw(Bio::Root::Root);
  
  # pK values from the DTASelect program from Scripps

Index: MZEF.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/MZEF.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** MZEF.pm	4 Jul 2006 22:23:24 -0000	1.14
--- MZEF.pm	26 Sep 2006 22:03:17 -0000	1.15
***************
*** 90,101 ****
  
  package Bio::Tools::MZEF;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Tools::AnalysisResult;
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  
! @ISA = qw(Bio::Tools::AnalysisResult);
  
  sub _initialize_state {
--- 90,99 ----
  
  package Bio::Tools::MZEF;
  use strict;
  
  use Bio::Tools::Prediction::Gene;
  use Bio::Tools::Prediction::Exon;
  
! use base qw(Bio::Tools::AnalysisResult);
  
  sub _initialize_state {

Index: RNAMotif.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/RNAMotif.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** RNAMotif.pm	20 Sep 2006 11:50:09 -0000	1.12
--- RNAMotif.pm	26 Sep 2006 22:03:17 -0000	1.13
***************
*** 140,151 ****
  
  package Bio::Tools::RNAMotif;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Tools::AnalysisResult;
  use Bio::SeqFeature::Generic;
  use Bio::SeqFeature::Collection;
  
! @ISA = qw(Bio::Tools::AnalysisResult );
  
  use vars qw($MotifTag $SrcTag $DescTag);
--- 140,149 ----
  
  package Bio::Tools::RNAMotif;
  use strict;
  
  use Bio::SeqFeature::Generic;
  use Bio::SeqFeature::Collection;
  
! use base qw(Bio::Tools::AnalysisResult);
  
  use vars qw($MotifTag $SrcTag $DescTag);

Index: PrositeScan.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/PrositeScan.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** PrositeScan.pm	8 Sep 2003 12:17:14 -0000	1.2
--- PrositeScan.pm	26 Sep 2006 22:03:17 -0000	1.3
***************
*** 32,44 ****
  
  package Bio::Tools::PrositeScan;
! use vars qw(@ISA @FORMATS);
  use strict;
- use Bio::Root::Root;
- use Bio::Root::IO;
  use Bio::Seq;
  use Bio::SeqFeature::Generic;
  use Bio::SeqFeature::FeaturePair;
  
! @ISA = qw(Bio::Root::Root Bio::Root::IO);
  @FORMATS = qw(SCAN FASTA PSA MSA PFF MATCHLIST);
  
--- 32,42 ----
  
  package Bio::Tools::PrositeScan;
! use vars qw(@FORMATS);
  use strict;
  use Bio::Seq;
  use Bio::SeqFeature::Generic;
  use Bio::SeqFeature::FeaturePair;
  
! use base qw(Bio::Root::Root Bio::Root::IO);
  @FORMATS = qw(SCAN FASTA PSA MSA PFF MATCHLIST);
  

Index: FootPrinter.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/FootPrinter.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** FootPrinter.pm	20 Sep 2006 04:00:57 -0000	1.9
--- FootPrinter.pm	26 Sep 2006 22:03:17 -0000	1.10
***************
*** 66,78 ****
  
  package Bio::Tools::FootPrinter;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  use Bio::SeqFeature::Generic;
  use Bio::PrimarySeq;
- use Bio::Root::IO;
  
! @ISA = qw(Bio::Root::Root Bio::Root::IO );
  
  =head2 new
--- 66,75 ----
  
  package Bio::Tools::FootPrinter;
  use strict;
  
  use Bio::SeqFeature::Generic;
  use Bio::PrimarySeq;
  
! use base qw(Bio::Root::Root Bio::Root::IO);
  
  =head2 new

Index: ERPIN.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/ERPIN.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** ERPIN.pm	20 Sep 2006 10:20:02 -0000	1.6
--- ERPIN.pm	26 Sep 2006 22:03:17 -0000	1.7
***************
*** 93,103 ****
  
  package Bio::Tools::ERPIN;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Tools::AnalysisResult;
  use Bio::SeqFeature::Generic;
  
! @ISA = qw(Bio::Tools::AnalysisResult );
  
  use vars qw($MotifTag $SrcTag $DescTag);
--- 93,101 ----
  
  package Bio::Tools::ERPIN;
  use strict;
  
  use Bio::SeqFeature::Generic;
  
! use base qw(Bio::Tools::AnalysisResult);
  
  use vars qw($MotifTag $SrcTag $DescTag);



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