use warnings added to perl modules

git-svn-id: http://biopieces.googlecode.com/svn/trunk@559 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_perl/Maasha/Align.pm b/code_perl/Maasha/Align.pm
index 344bcad6cc45468435e2e1e2b14a34db26cbef3d..55b4c2f9f0f6b9a698aa1278317a1599626479e4 100644 (file)
--- 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 00caff6430d1f15ff79d89bba25732e9663515e4..94f438a2daee0b6a68d7bec8512683c98a23cc4b 100644 (file)
--- 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 08cf6c8d0c5b77db18a2ffed035c843127b7003e..b5aadc9b462c0937aea1c05149718fc4e5ade6f5 100644 (file)
--- 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 923fccd32b2d8bff6da61e744f603ff2d29f9d38..c5d70c30d8153531d1a4e1b5ab396876c5784b3d 100644 (file)
--- 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 50ffcabf202bd20456cec336d143d7b9c8285e1b..d14a2480e385afb33c7aa45cd97ef5ab41b55530 100644 (file)
--- 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 0e17dadd1d52deae0b33c6ad9cd646423815ec5d..4b248e9521cc9261e8e6959743207b2bbc30fd63 100644 (file)
--- 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 51f841f6e251a647ab6a16665ff2dc5811a890e4..b8941688888b08e118a80acd465906581dd33d79 100644 (file)
--- 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 9f4170c01dd6d2769159d6f86b5c40edea69d769..dbe43b759f775ac759aea14a41e1556c7a686345 100644 (file)
--- 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 679543164f671a33b46c59f84120a769c26da1d8..30e8bb1477daf0aea16e3a3d91b29c391cb959d0 100644 (file)
--- 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 799d97b737fa7b6177e9fe95e8f4ca6e8979d062..e79bdaf11ea4890bf6372bed15261b2bf1f064dd 100644 (file)
--- 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 0cd626766cb50e52c89cff8c4ffbe77779aa14f8..bd465f4f998dcea8641dcc5dc1e6568e0a9cb36a 100644 (file)
--- 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 55a17b570e2327011aed2e84189cd229f815ab34..795efa6faa337057ddb9155c96df211692914562 100644 (file)
--- 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 b545609787529c3f991efe13853fd8bd49c68d43..e8e40a703c762c58832b307e3f86e743dac83cc8 100644 (file)
--- 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 154dad83594ae11de55e6a4732757ec19c5617e0..dec68bd6ac97bef905369d268bb240840e9e77c7 100644 (file)
--- 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 267f9603e0b10690c7433b335d0fb9721ad9e6ae..60987d7f646e42c428269adbf348f5c677ea2f76 100644 (file)
--- 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 7d6e0c0395d60ffef7f83bd42760863c0adb63fb..9d315b7d6f84aba42e9e5dbb2fdef5423181341f 100644 (file)
--- 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 74df868ccce1ed11a61b12a41703b5762d9da4aa..641a9c231eb28486a58004a098595bf32fdafe83 100644 (file)
--- 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 41f17562dca65ac80c24f24a4e0f7ce5934683e2..baafb69eabef11913798e016442ae94b7355c098 100644 (file)
--- 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 2fed12052572356cd6705f6528587544e8016f4b..1729488db816411cab307e1967c02e7cfda3189c 100644 (file)
--- 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 cac8536aa5be44c479e5d3040bcf70d0b509b0c0..94d542bb4e389cc1f35df12fa883a695c6ab6d76 100644 (file)
--- 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 5ce392708b94e96979f9894cd65d9497b65a595b..048fdf7c90af45bd62499e91b164d804ffacec28 100644 (file)
--- 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 85e391107a181d52d02bab253af1db48cea869b6..93e9ba6c9f09350d524749f848c637971769b73e 100644 (file)
--- 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 45e379ce3ef7694dbb0ec73edb936e4d855e21bb..849c1778a520e432f71b43d36430777282c6a5e6 100644 (file)
--- 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 1e93c23dbe940d0b790215dee27b0a2b45b1f8dd..a8e7bcf3fa0e1d35e449b2980ecd3ed23f708857 100644 (file)
--- 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 5a8ad956ba122cc05953eefe542151d4ff1f4b9c..3dcc830f23729aafe40dc5a13da19b5bbcc9b1a5 100644 (file)
--- 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 3b57757a05fee6c641a7aba10e891d5b3a67e2b5..6bfa590b364d486f8202ddc454793b24d5fbc21d 100644 (file)
--- 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 d0ff611635e01c8ff9bf6e714af95c30965f1bd6..19f6e71f5ea968d620a1486d2d9f81908f43fdcb 100644 (file)
--- 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 0e512e1beae9d29b47bf048522c040a90e15e61c..b9a9dd9de7b88cee9689dfeda53b602ba8e6d857 100644 (file)
--- 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;