From e85ab3ff25098befde19f6f0839292f68739b785 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Wed, 8 Jul 2009 09:22:22 +0000 Subject: [PATCH] use warnings added to perl modules git-svn-id: http://biopieces.googlecode.com/svn/trunk@559 74ccb610-7750-0410-82ae-013aeee3265d --- code_perl/Maasha/Align.pm | 1 + code_perl/Maasha/AlignTwoSeq.pm | 1 + code_perl/Maasha/Berkeley_DB.pm | 1 + code_perl/Maasha/Blast.pm | 1 + code_perl/Maasha/C_bitarray.pm | 1 + code_perl/Maasha/C_code.pm | 1 + code_perl/Maasha/Calc.pm | 1 + code_perl/Maasha/Common.pm | 1 + code_perl/Maasha/Config.pm | 1 + code_perl/Maasha/DumpFunc.pm | 1 + code_perl/Maasha/EMBL.pm | 1 + code_perl/Maasha/Fasta.pm | 1 + code_perl/Maasha/Filesys.pm | 1 + code_perl/Maasha/GFF.pm | 1 + code_perl/Maasha/Gwiki.pm | 1 + code_perl/Maasha/Match.pm | 1 + code_perl/Maasha/Matrix.pm | 1 + code_perl/Maasha/NCBI.pm | 1 + code_perl/Maasha/Patscan.pm | 1 + code_perl/Maasha/Plot.pm | 1 + code_perl/Maasha/SQL.pm | 1 + code_perl/Maasha/Seq.pm | 1 + code_perl/Maasha/Stockholm.pm | 1 + code_perl/Maasha/TwoBit.pm | 1 + code_perl/Maasha/UCSC.pm | 1 + code_perl/Maasha/UCSC/BED.pm | 1 + code_perl/Maasha/UCSC/PSL.pm | 1 + code_perl/Maasha/UCSC/Wiggle.pm | 1 + 28 files changed, 28 insertions(+) diff --git a/code_perl/Maasha/Align.pm b/code_perl/Maasha/Align.pm index 344bcad..55b4c2f 100644 --- a/code_perl/Maasha/Align.pm +++ b/code_perl/Maasha/Align.pm @@ -28,6 +28,7 @@ package Maasha::Align; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use IPC::Open2; diff --git a/code_perl/Maasha/AlignTwoSeq.pm b/code_perl/Maasha/AlignTwoSeq.pm index 00caff6..94f438a 100644 --- a/code_perl/Maasha/AlignTwoSeq.pm +++ b/code_perl/Maasha/AlignTwoSeq.pm @@ -28,6 +28,7 @@ package Maasha::AlignTwoSeq; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use Storable qw( dclone ); diff --git a/code_perl/Maasha/Berkeley_DB.pm b/code_perl/Maasha/Berkeley_DB.pm index 08cf6c8..b5aadc9 100644 --- a/code_perl/Maasha/Berkeley_DB.pm +++ b/code_perl/Maasha/Berkeley_DB.pm @@ -29,6 +29,7 @@ package Maasha::Berkeley_DB; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use Maasha::Common; diff --git a/code_perl/Maasha/Blast.pm b/code_perl/Maasha/Blast.pm index 923fccd..c5d70c3 100644 --- a/code_perl/Maasha/Blast.pm +++ b/code_perl/Maasha/Blast.pm @@ -28,6 +28,7 @@ package Maasha::Blast; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Storable qw( dclone ); use Data::Dumper; diff --git a/code_perl/Maasha/C_bitarray.pm b/code_perl/Maasha/C_bitarray.pm index 50ffcab..d14a248 100644 --- a/code_perl/Maasha/C_bitarray.pm +++ b/code_perl/Maasha/C_bitarray.pm @@ -29,6 +29,7 @@ package Maasha::C_bitarray; +use warnings; use strict; use vars qw ( @ISA @EXPORT ); diff --git a/code_perl/Maasha/C_code.pm b/code_perl/Maasha/C_code.pm index 0e17dad..4b248e9 100644 --- a/code_perl/Maasha/C_code.pm +++ b/code_perl/Maasha/C_code.pm @@ -28,6 +28,7 @@ package Maasha::C_code; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use vars qw ( @ISA @EXPORT ); diff --git a/code_perl/Maasha/Calc.pm b/code_perl/Maasha/Calc.pm index 51f841f..b894168 100644 --- a/code_perl/Maasha/Calc.pm +++ b/code_perl/Maasha/Calc.pm @@ -28,6 +28,7 @@ package Maasha::Calc; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use Storable qw( dclone ); diff --git a/code_perl/Maasha/Common.pm b/code_perl/Maasha/Common.pm index 9f4170c..dbe43b7 100644 --- a/code_perl/Maasha/Common.pm +++ b/code_perl/Maasha/Common.pm @@ -29,6 +29,7 @@ package Maasha::Common; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Carp; use Data::Dumper; diff --git a/code_perl/Maasha/Config.pm b/code_perl/Maasha/Config.pm index 6795431..30e8bb1 100644 --- a/code_perl/Maasha/Config.pm +++ b/code_perl/Maasha/Config.pm @@ -28,6 +28,7 @@ package Maasha::Config; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use vars qw( @ISA @EXPORT ); diff --git a/code_perl/Maasha/DumpFunc.pm b/code_perl/Maasha/DumpFunc.pm index 799d97b..e79bdaf 100644 --- a/code_perl/Maasha/DumpFunc.pm +++ b/code_perl/Maasha/DumpFunc.pm @@ -28,6 +28,7 @@ package Maasha::DumpFunc; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Class::Inspector; use vars qw ( @ISA @EXPORT ); diff --git a/code_perl/Maasha/EMBL.pm b/code_perl/Maasha/EMBL.pm index 0cd6267..bd465f4 100644 --- a/code_perl/Maasha/EMBL.pm +++ b/code_perl/Maasha/EMBL.pm @@ -28,6 +28,7 @@ package Maasha::EMBL; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use Storable qw( dclone ); diff --git a/code_perl/Maasha/Fasta.pm b/code_perl/Maasha/Fasta.pm index 55a17b5..795efa6 100644 --- a/code_perl/Maasha/Fasta.pm +++ b/code_perl/Maasha/Fasta.pm @@ -28,6 +28,7 @@ package Maasha::Fasta; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use Maasha::Common; diff --git a/code_perl/Maasha/Filesys.pm b/code_perl/Maasha/Filesys.pm index b545609..e8e40a7 100644 --- a/code_perl/Maasha/Filesys.pm +++ b/code_perl/Maasha/Filesys.pm @@ -29,6 +29,7 @@ package Maasha::Filesys; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use IO::File; use Storable; diff --git a/code_perl/Maasha/GFF.pm b/code_perl/Maasha/GFF.pm index 154dad8..dec68bd 100644 --- a/code_perl/Maasha/GFF.pm +++ b/code_perl/Maasha/GFF.pm @@ -29,6 +29,7 @@ package Maasha::GFF; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use Maasha::Common; diff --git a/code_perl/Maasha/Gwiki.pm b/code_perl/Maasha/Gwiki.pm index 267f960..60987d7 100644 --- a/code_perl/Maasha/Gwiki.pm +++ b/code_perl/Maasha/Gwiki.pm @@ -28,6 +28,7 @@ package Maasha::Gwiki; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use Term::ANSIColor; diff --git a/code_perl/Maasha/Match.pm b/code_perl/Maasha/Match.pm index 7d6e0c0..9d315b7 100644 --- a/code_perl/Maasha/Match.pm +++ b/code_perl/Maasha/Match.pm @@ -28,6 +28,7 @@ package Maasha::Match; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use Storable qw( dclone ); diff --git a/code_perl/Maasha/Matrix.pm b/code_perl/Maasha/Matrix.pm index 74df868..641a9c2 100644 --- a/code_perl/Maasha/Matrix.pm +++ b/code_perl/Maasha/Matrix.pm @@ -28,6 +28,7 @@ package Maasha::Matrix; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use Storable qw( dclone ); diff --git a/code_perl/Maasha/NCBI.pm b/code_perl/Maasha/NCBI.pm index 41f1756..baafb69 100644 --- a/code_perl/Maasha/NCBI.pm +++ b/code_perl/Maasha/NCBI.pm @@ -28,6 +28,7 @@ package Maasha::NCBI; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use LWP::Simple; diff --git a/code_perl/Maasha/Patscan.pm b/code_perl/Maasha/Patscan.pm index 2fed120..1729488 100644 --- a/code_perl/Maasha/Patscan.pm +++ b/code_perl/Maasha/Patscan.pm @@ -28,6 +28,7 @@ package Maasha::Patscan; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use Maasha::Common; diff --git a/code_perl/Maasha/Plot.pm b/code_perl/Maasha/Plot.pm index cac8536..94d542b 100644 --- a/code_perl/Maasha/Plot.pm +++ b/code_perl/Maasha/Plot.pm @@ -28,6 +28,7 @@ package Maasha::Plot; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use SVG; diff --git a/code_perl/Maasha/SQL.pm b/code_perl/Maasha/SQL.pm index 5ce3927..048fdf7 100644 --- a/code_perl/Maasha/SQL.pm +++ b/code_perl/Maasha/SQL.pm @@ -28,6 +28,7 @@ package Maasha::SQL; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use warnings; diff --git a/code_perl/Maasha/Seq.pm b/code_perl/Maasha/Seq.pm index 85e3911..93e9ba6 100644 --- a/code_perl/Maasha/Seq.pm +++ b/code_perl/Maasha/Seq.pm @@ -28,6 +28,7 @@ package Maasha::Seq; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use POSIX qw( islower ); use Maasha::Common; diff --git a/code_perl/Maasha/Stockholm.pm b/code_perl/Maasha/Stockholm.pm index 45e379c..849c177 100644 --- a/code_perl/Maasha/Stockholm.pm +++ b/code_perl/Maasha/Stockholm.pm @@ -29,6 +29,7 @@ package Maasha::Stockholm; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use Maasha::Common; diff --git a/code_perl/Maasha/TwoBit.pm b/code_perl/Maasha/TwoBit.pm index 1e93c23..a8e7bcf 100644 --- a/code_perl/Maasha/TwoBit.pm +++ b/code_perl/Maasha/TwoBit.pm @@ -29,6 +29,7 @@ package Maasha::TwoBit; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use warnings; use strict; use vars qw( @ISA @EXPORT ); diff --git a/code_perl/Maasha/UCSC.pm b/code_perl/Maasha/UCSC.pm index 5a8ad95..3dcc830 100644 --- a/code_perl/Maasha/UCSC.pm +++ b/code_perl/Maasha/UCSC.pm @@ -28,6 +28,7 @@ package Maasha::UCSC; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use vars qw ( @ISA @EXPORT ); diff --git a/code_perl/Maasha/UCSC/BED.pm b/code_perl/Maasha/UCSC/BED.pm index 3b57757..6bfa590 100644 --- a/code_perl/Maasha/UCSC/BED.pm +++ b/code_perl/Maasha/UCSC/BED.pm @@ -30,6 +30,7 @@ package Maasha::UCSC::BED; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; diff --git a/code_perl/Maasha/UCSC/PSL.pm b/code_perl/Maasha/UCSC/PSL.pm index d0ff611..19f6e71 100644 --- a/code_perl/Maasha/UCSC/PSL.pm +++ b/code_perl/Maasha/UCSC/PSL.pm @@ -30,6 +30,7 @@ package Maasha::UCSC::PSL; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; diff --git a/code_perl/Maasha/UCSC/Wiggle.pm b/code_perl/Maasha/UCSC/Wiggle.pm index 0e512e1..b9a9dd9 100644 --- a/code_perl/Maasha/UCSC/Wiggle.pm +++ b/code_perl/Maasha/UCSC/Wiggle.pm @@ -30,6 +30,7 @@ package Maasha::UCSC::Wiggle; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; -- 2.39.5