typos and clarifications on documentation

Build.PL

@@ -33,8 +33,27 @@ my $build = Module::Build->new(
     ],
     create_makefile_pl => 'passthrough',
     build_class        => 'Module::Build',
-    );
-
+    meta_merge => {
+        resources => {
+            homepage => 'http://gmod.org/',
+            ## Oddly, the specs for resources mention a bugtracker
+            ## and repository that are hash references.  However,
+            ## those seem to be ignored by Module::Build at the
+            ## moment.  The documented values are here commented for
+            ## this is sorted out.
+#            bugtracker => {
+#                web => 'https://github.com/GMOD/Bio-Graphics/issues',
+#            },
+#            repository => {
+#                url => 'https://github.com/GMOD/Bio-Graphics.git',
+#                web => 'https://github.com/GMOD/Bio-Graphics',
+#                type => 'git',
+#            },
+            bugtracker => 'https://github.com/GMOD/Bio-Graphics/issues',
+            repository => 'https://github.com/GMOD/Bio-Graphics.git',
+        },
+    },
+);
 
 $build->create_build_script;
 exit 0;

README

@@ -92,7 +92,7 @@ Note that this modules depends on Bio::Perl, GD and the
 Text::Parsewords module.
 
 A good tutorial on this module can be found at
-http://www.bioperl.org/wiki/HOWTO:Graphics.
+http://bioperl.org/howtos/BioGraphics_HOWTO.html
 
 BUILDING AND INSTALLING
 

eg/testit.pl

@@ -1,7 +1,8 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
 
 use lib '.','..','./blib/lib','../blib/lib';
 use strict;
+use warnings;
 
 use Bio::Graphics::Panel;
 use Bio::Graphics::Feature;

eg/testit2.pl

@@ -1,7 +1,8 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
 
 use lib './lib','../lib','./blib/lib','../blib/lib';
 use strict;
+use warnings;
 
 use Bio::Graphics::Panel;
 use Bio::Graphics::Feature;

eg/testit3.pl

@@ -1,7 +1,8 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
 
 use lib '.','..','./blib/lib','../blib/lib';
 use strict;
+use warnings;
 
 use Bio::Graphics::Panel;
 use Bio::Graphics::Feature;

lib/Bio/Graphics.pm

@@ -99,25 +99,6 @@ L<Ace::Sequence>,
 L<GD>
 L<glyph_help.pl>
 
-=head1 FEEDBACK
-
-=head2 Mailing Lists
-
-User feedback is an integral part of the evolution of this and other
-Bioperl modules. Send your comments and suggestions preferably to
-the Bioperl mailing list.  Your participation is much appreciated.
-
-  bioperl-l@bioperl.org                  - General discussion
-  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
-
-=head2 Reporting Bugs
-
-Report bugs to the Bioperl bug tracking system to help us keep track
-of the bugs and their resolution. Bug reports can be submitted via the
-web:
-
-  http://bugzilla.open-bio.org/
-
 =head1 AUTHOR
 
 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.

lib/Bio/Graphics/ConfiguratorI.pm

@@ -1,5 +1,3 @@
-# BioPerl module for Bio::Graphics::ConfiguratorI
-#
 # Cared for by Robert Hubley <rhubley@systemsbiology.org>
 #
 # Copyright Robert Hubley
@@ -29,25 +27,6 @@ up into sections and tags.  This is essentially a multi-level map
 section which is referenced when no section is passed to the
 ConfiguratorI methods.
 
-=head1 FEEDBACK
-
-=head2 Mailing Lists
-
-User feedback is an integral part of the evolution of this and other
-Bioperl modules. Send your comments and suggestions preferably to
-the Bioperl mailing list.  Your participation is much appreciated.
-
-  bioperl-l@bioperl.org                  - General discussion
-  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
-
-=head2 Reporting Bugs
-
-Report bugs to the Bioperl bug tracking system to help us keep track
-of the bugs and their resolution. Bug reports can be submitted via the
-web:
-
-  http://bugzilla.open-bio.org/
-
 =head1 AUTHOR - Robert Hubley
 
 Email rhubley@systemsbiology.org

lib/Bio/Graphics/Feature.pm

@@ -260,7 +260,7 @@ sub factory {
            called the accession_number. For sequences from established
            databases, the implementors should try to use the correct
            accession number. Notice that primary_id() provides the
-           unique id for the implemetation, allowing multiple objects
+           unique id for the implementation, allowing multiple objects
            to have the same accession number in a particular implementation.
 
            For sequences with no accession number, this method should return

lib/Bio/Graphics/FeatureFile.pm

@@ -314,7 +314,7 @@ object.  Arguments are -name=E<gt>value pairs:
 
    -safe_world     If the -safe option is not set, and -safe_world
                    is set to a true value, then Bio::Graphics::FeatureFile
-                   will evalute "sub {}" options in a L<Safe::World>
+                   will evaluate "sub {}" options in a L<Safe::World>
                    environment with minimum permissions. Subroutines
                    will be able to access and interrogate 
                    Bio::DB::SeqFeature objects and perform basic Perl

lib/Bio/Graphics/Glyph/Factory.pm

@@ -12,25 +12,6 @@ This class is used internally by Bio::Graphics to generate new Glyph
 objects by combining a list of features with the user's desired
 configuration.  It is intended to be used internally by Bio::Graphics.
 
-=head1 FEEDBACK
-
-=head2 Mailing Lists
-
-User feedback is an integral part of the evolution of this and other
-Bioperl modules. Send your comments and suggestions preferably to one
-of the Bioperl mailing lists.  Your participation is much appreciated.
-
-  bioperl-l@bioperl.org                  - General discussion
-  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
-
-=head2 Reporting Bugs
-
-Report bugs to the Bioperl bug tracking system to help us keep track
-the bugs and their resolution.  Bug reports can be submitted via the
-web:
-
-  http://bugzilla.open-bio.org/
-
 =head1 AUTHOR - Lincoln Stein
 
 Email - lstein@cshl.org

lib/Bio/Graphics/Glyph/decorated_transcript.pm

@@ -17,7 +17,7 @@ use base
 sub my_descripton {
   return <<END;
 This glyph extends the functionality of the Bio::Graphics::Glyph::processed_transcript glyph 
-and allows to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)
+and allows one to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)
 on top of gene models. Currently, the glyph can draw decorations in form of colored or outlined boxes 
 inside or around CDS segments. Protein decorations are specified at the 'mRNA' transcript level 
 in protein coordinates. Protein coordinates are automatically mapped to nucleotide coordinates by the glyph. 
@@ -201,7 +201,7 @@ sub decorations {
 	return $feature->get_tag_values(DECORATION_TAG_NAME);
 }
 
-# allows to retrieve additional decorations via callback
+# allows one to retrieve additional decorations via callback
 sub additional_decorations {
 	my $self    = shift;
 	my $feature = $self->feature;
@@ -948,7 +948,7 @@ Bio::Graphics::Glyph::decorated_transcript - draws processed transcript with pro
 =head1 DESCRIPTION
 
 This glyph extends the functionality of the L<Bio::Graphics::Glyph::processed_transcript> glyph 
-and allows to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)
+and allows one to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)
 on top of gene models. Currently, the glyph can draw decorations in form of colored or outlined boxes 
 inside or around CDS segments. Protein decorations are specified at the 'mRNA' transcript level 
 in protein coordinates. Protein coordinates are automatically mapped to nucleotide coordinates by the glyph. 

lib/Bio/Graphics/Glyph/fb_shmiggle.pm

@@ -611,7 +611,7 @@ order of the initial subsets names.
 <br>
 <br>
 
-Setting 'subsetsnames' allows to rename subsets (very important as in most cases
+Setting 'subsetsnames' allows one to rename subsets (very important as in most cases
 workflow names of subsets are unsutable for intelligent data display to end users).
 If setting omitted, initial subsets names will be used for display.
 

lib/Bio/Graphics/Glyph/heat_map.pm

@@ -522,7 +522,7 @@ effective visual heat map is to progress from
 white->red.
 
 For the start_color and end_color options, 140 named webcolors
-and their corresponsing RGB hex codes (listed below) are supported.
+and their corresponding RGB hex codes (listed below) are supported.
 
  steelblue           	#4682B4
  royalblue           	#041690

lib/Bio/Graphics/Glyph/ideogram.pm

@@ -298,7 +298,7 @@ sub draw_telomere {
   $self->wipe(@_);
 
   # For single, unaggregated bands, make the terminal band
-  # a bit wider to accomodate the arc
+  # a bit wider to accommodate the arc
   if ($self->{single}) {
     $x1 -= 5 if $state == 1;
     $x2 += 5 if $state == 0;

lib/Bio/Graphics/Glyph/segments.pm

@@ -1136,7 +1136,7 @@ target (the hit).  For this to work, the feature must implement the
 hit() method, and both the source and the target DNA must be
 available.  If you pass the glyph a series of
 Bio::SeqFeature::SimilarityPair objects, then these criteria will be
-satisified.
+satisfied.
 
 Without additional help, this glyph cannot display gapped alignments
 correctly.  To display gapped alignments, you can use the

lib/Bio/Graphics/Glyph/trace.pm

@@ -733,7 +733,7 @@ filesystem or located at a remote URL (provided that you have the LWP module
 installed).
 
 Until an alignment feature is added to this glyph, the feature start and end
-must correspond exactly with the begining and end of the called sequence.
+must correspond exactly with the beginning and end of the called sequence.
 Meaning that even if the starting sequence is poor and doesn't match the
 sequence, it must still be included.
 
@@ -883,7 +883,7 @@ CVS checkout of Bio::Perl to work properly with the "arrow", "span" and
 
 =head1 BUGS AND LIMITATIONS
 
-See the L<DESCRIPTION> for an explaination of how to align the trace with the
+See the L<DESCRIPTION> for an explanation of how to align the trace with the
 reference.
 
 The trace looks a little off when the feature is on the negative strand of the

lib/Bio/Graphics/Panel.pm

@@ -1710,7 +1710,7 @@ a set of tag/value pairs as follows:
   -auto_pad    If "left" or "right" keys are in use  true
                then setting auto_pad to a true value
                will allow the panel to adjust its
-               width in order to accomodate the
+               width in order to accommodate the
                length of the longest key.
 
   -empty_tracks What to do when a track is empty.    suppress

lib/Bio/Graphics/Pictogram.pm

@@ -1,5 +1,3 @@
-# BioPerl module for Bio::Graphics::Pictogram
-#
 # Cared for by Shawn Hoon <shawnh@fugu-sg.org>
 #
 # Copyright Shawn Hoon
@@ -83,26 +81,6 @@ http://www.cpan.org
 Recommended viewing of the SVG is the plugin available at Adobe:
 http://www.adobe.com/svg
 
-=head1 FEEDBACK
-
-
-=head2 Mailing Lists
-
-User feedback is an integral part of the evolution of this and other
-Bioperl modules. Send your comments and suggestions preferably to one
-of the Bioperl mailing lists. Your participation is much appreciated.
-
-  bioperl-l@bioperl.org                  - General discussion
-  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
-
-=head2 Reporting Bugs
-
-Report bugs to the Bioperl bug tracking system to help us keep track
-the bugs and their resolution.  Bug reports can be submitted via the
-web:
-
-  http://bugzilla.open-bio.org/
-
 =head1 AUTHOR - Shawn Hoon
 
 Email shawnh@fugu-sg.org

lib/Bio/Graphics/RendererI.pm

@@ -20,25 +20,6 @@ Renderer of Bio::SeqFeature::CollectionIs (collections of features)
 onto a Bio::Graphics::Panel using a Bio::Graphics::ConfiguratorI for
 general and track-specific rendering options.
 
-=head1 FEEDBACK
-
-=head2 Mailing Lists
-
-User feedback is an integral part of the evolution of this and other
-Bioperl modules. Send your comments and suggestions preferably to
-the Bioperl mailing list.  Your participation is much appreciated.
-
-  bioperl-l@bioperl.org                  - General discussion
-  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
-
-=head2 Reporting Bugs
-
-Report bugs to the Bioperl bug tracking system to help us keep track
-of the bugs and their resolution. Bug reports can be submitted via the
-web:
-
-  http://bugzilla.open-bio.org/
-
 =head1 AUTHOR
 
 Paul Edlefsen E<lt>paul@systemsbiology.orgE<gt>.

scripts/bam_coverage_windows.pl

@@ -1,5 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
 use strict;
+use warnings;
 use List::Util 'sum';
 use Getopt::Long;
 

scripts/contig_draw.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
 
 =head1 NAME
 
@@ -49,6 +49,7 @@ =head1 AUTHOR Jason Stajich
 =cut
 
 use strict;
+use warnings;
 
 use Bio::Graphics::Panel;
 use Bio::Graphics::Feature;

scripts/coverage_to_topoview.pl

@@ -1,5 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
 use strict;
+use warnings;
 use BerkeleyDB;
 use Data::Dumper;
 use Getopt::Long;

scripts/feature_draw.pl

@@ -1,6 +1,7 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
 
 use strict;
+use warnings;
 use lib './blib/lib','../blib/lib';
 use Bio::Graphics::Panel;
 use Bio::Graphics::Feature;

scripts/frend.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
 
 =head1 NAME
 
@@ -236,6 +236,7 @@ =head1 AUTHOR
 =cut
 
 use strict;
+use warnings;
 use Bio::Graphics::Panel;
 use Bio::Graphics::Feature;
 use Bio::Graphics::FeatureFile;
@@ -259,8 +260,8 @@ =head1 AUTHOR
 print header,start_html('Sequence Feature Renderer');
 print h1('Sequence Feature Renderer');
 
-print p('This is a front end to the Bio::Graphics package, a part of the',
-	a({-href=>'http://www.bioperl.org'},'BioPerl library.'),
+print p('This is a front end to the Bio::Graphics perl module distribution, a part of the',
+	a({-href=>'http://gmod.org/'},'GMOD project.'),
 	  'Cut and paste your sequence annotation data into the text field below, or upload it using the',
 	'upload button.',
 	'The format of the annotation data is explained',a({-href=>'#format'},'below.'));
@@ -319,7 +320,7 @@ =head1 AUTHOR
 
 print_format();
 
-print hr(),a({-href=>'http://www.bioperl.org'},'www.bioperl.org'),end_html();
+print hr(),a({-href=>'http://gmod.org/'},'http://gmod.org/'),end_html();
 
 exit 0;