diff --git a/Build.PL b/Build.PL index e89c025..fdd6735 100755 --- a/Build.PL +++ b/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; diff --git a/Changes b/Changes old mode 100755 new mode 100644 diff --git a/DISCLAIMER.txt b/DISCLAIMER.txt old mode 100755 new mode 100644 diff --git a/README b/README old mode 100755 new mode 100644 index f0a99a2..cd7f61c --- a/README +++ b/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 diff --git a/README.bioperl b/README.bioperl old mode 100755 new mode 100644 diff --git a/eg/feature_data.gff b/eg/feature_data.gff old mode 100755 new mode 100644 diff --git a/eg/feature_data.txt b/eg/feature_data.txt old mode 100755 new mode 100644 diff --git a/eg/testit.pl b/eg/testit.pl old mode 100755 new mode 100644 index f389e08..dcea5dd --- a/eg/testit.pl +++ b/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; diff --git a/eg/testit2.pl b/eg/testit2.pl old mode 100755 new mode 100644 index 8c2aa89..ac4552e --- a/eg/testit2.pl +++ b/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; diff --git a/eg/testit3.pl b/eg/testit3.pl old mode 100755 new mode 100644 index 3ad5017..0a6dcdf --- a/eg/testit3.pl +++ b/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; diff --git a/lib/Bio/Graphics.pm b/lib/Bio/Graphics.pm old mode 100755 new mode 100644 index 3fb5a68..b71bc42 --- a/lib/Bio/Graphics.pm +++ b/lib/Bio/Graphics.pm @@ -99,25 +99,6 @@ L, L L -=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 Elstein@cshl.orgE. diff --git a/lib/Bio/Graphics/ConfiguratorI.pm b/lib/Bio/Graphics/ConfiguratorI.pm old mode 100755 new mode 100644 index 06fecd9..05bb903 --- a/lib/Bio/Graphics/ConfiguratorI.pm +++ b/lib/Bio/Graphics/ConfiguratorI.pm @@ -1,5 +1,3 @@ -# BioPerl module for Bio::Graphics::ConfiguratorI -# # Cared for by Robert Hubley # # 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 diff --git a/lib/Bio/Graphics/DrawTransmembrane.pm b/lib/Bio/Graphics/DrawTransmembrane.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Feature.pm b/lib/Bio/Graphics/Feature.pm old mode 100755 new mode 100644 index db9444d..d869d9c --- a/lib/Bio/Graphics/Feature.pm +++ b/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 diff --git a/lib/Bio/Graphics/FeatureBase.pm b/lib/Bio/Graphics/FeatureBase.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/FeatureDir.pm b/lib/Bio/Graphics/FeatureDir.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/FeatureFile.pm b/lib/Bio/Graphics/FeatureFile.pm old mode 100755 new mode 100644 index 002715f..8c3b52b --- a/lib/Bio/Graphics/FeatureFile.pm +++ b/lib/Bio/Graphics/FeatureFile.pm @@ -314,7 +314,7 @@ object. Arguments are -name=Evalue 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 + will evaluate "sub {}" options in a L environment with minimum permissions. Subroutines will be able to access and interrogate Bio::DB::SeqFeature objects and perform basic Perl diff --git a/lib/Bio/Graphics/FeatureFile/Iterator.pm b/lib/Bio/Graphics/FeatureFile/Iterator.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph.pm b/lib/Bio/Graphics/Glyph.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/Factory.pm b/lib/Bio/Graphics/Glyph/Factory.pm old mode 100755 new mode 100644 index 1661255..00f4eed --- a/lib/Bio/Graphics/Glyph/Factory.pm +++ b/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 diff --git a/lib/Bio/Graphics/Glyph/alignment.pm b/lib/Bio/Graphics/Glyph/alignment.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/allele_tower.pm b/lib/Bio/Graphics/Glyph/allele_tower.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/anchored_arrow.pm b/lib/Bio/Graphics/Glyph/anchored_arrow.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/arrow.pm b/lib/Bio/Graphics/Glyph/arrow.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/box.pm b/lib/Bio/Graphics/Glyph/box.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/broken_line.pm b/lib/Bio/Graphics/Glyph/broken_line.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/cds.pm b/lib/Bio/Graphics/Glyph/cds.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/christmas_arrow.pm b/lib/Bio/Graphics/Glyph/christmas_arrow.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/cross.pm b/lib/Bio/Graphics/Glyph/cross.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/crossbox.pm b/lib/Bio/Graphics/Glyph/crossbox.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/dashed_line.pm b/lib/Bio/Graphics/Glyph/dashed_line.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/decorated_transcript.pm b/lib/Bio/Graphics/Glyph/decorated_transcript.pm index 77ab3b5..8415099 100644 --- a/lib/Bio/Graphics/Glyph/decorated_transcript.pm +++ b/lib/Bio/Graphics/Glyph/decorated_transcript.pm @@ -17,7 +17,7 @@ use base sub my_descripton { return <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 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. diff --git a/lib/Bio/Graphics/Glyph/diamond.pm b/lib/Bio/Graphics/Glyph/diamond.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/dna.pm b/lib/Bio/Graphics/Glyph/dna.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/dot.pm b/lib/Bio/Graphics/Glyph/dot.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/dumbbell.pm b/lib/Bio/Graphics/Glyph/dumbbell.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/ellipse.pm b/lib/Bio/Graphics/Glyph/ellipse.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/ex.pm b/lib/Bio/Graphics/Glyph/ex.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/extending_arrow.pm b/lib/Bio/Graphics/Glyph/extending_arrow.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/fb_shmiggle.pm b/lib/Bio/Graphics/Glyph/fb_shmiggle.pm index 5db8f8e..430ad37 100644 --- a/lib/Bio/Graphics/Glyph/fb_shmiggle.pm +++ b/lib/Bio/Graphics/Glyph/fb_shmiggle.pm @@ -611,7 +611,7 @@ order of the initial subsets names.

-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. diff --git a/lib/Bio/Graphics/Glyph/fixedwidth.pm b/lib/Bio/Graphics/Glyph/fixedwidth.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/flag.pm b/lib/Bio/Graphics/Glyph/flag.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/gene.pm b/lib/Bio/Graphics/Glyph/gene.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/generic.pm b/lib/Bio/Graphics/Glyph/generic.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/graded_segments.pm b/lib/Bio/Graphics/Glyph/graded_segments.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/group.pm b/lib/Bio/Graphics/Glyph/group.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/hat.pm b/lib/Bio/Graphics/Glyph/hat.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/heat_map.pm b/lib/Bio/Graphics/Glyph/heat_map.pm old mode 100755 new mode 100644 index 516a5ad..02ab26b --- a/lib/Bio/Graphics/Glyph/heat_map.pm +++ b/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 diff --git a/lib/Bio/Graphics/Glyph/heat_map_ideogram.pm b/lib/Bio/Graphics/Glyph/heat_map_ideogram.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/heterogeneous_segments.pm b/lib/Bio/Graphics/Glyph/heterogeneous_segments.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/hidden.pm b/lib/Bio/Graphics/Glyph/hidden.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/hybrid_plot.pm b/lib/Bio/Graphics/Glyph/hybrid_plot.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/ideogram.pm b/lib/Bio/Graphics/Glyph/ideogram.pm old mode 100755 new mode 100644 index 65868c0..04d9595 --- a/lib/Bio/Graphics/Glyph/ideogram.pm +++ b/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; diff --git a/lib/Bio/Graphics/Glyph/image.pm b/lib/Bio/Graphics/Glyph/image.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/lightning.pm b/lib/Bio/Graphics/Glyph/lightning.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/line.pm b/lib/Bio/Graphics/Glyph/line.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/merge_parts.pm b/lib/Bio/Graphics/Glyph/merge_parts.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/merged_alignment.pm b/lib/Bio/Graphics/Glyph/merged_alignment.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/minmax.pm b/lib/Bio/Graphics/Glyph/minmax.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/operon.pm b/lib/Bio/Graphics/Glyph/operon.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/oval.pm b/lib/Bio/Graphics/Glyph/oval.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/pairplot.pm b/lib/Bio/Graphics/Glyph/pairplot.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/pentagram.pm b/lib/Bio/Graphics/Glyph/pentagram.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/phylo_align.pm b/lib/Bio/Graphics/Glyph/phylo_align.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/pinsertion.pm b/lib/Bio/Graphics/Glyph/pinsertion.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/primers.pm b/lib/Bio/Graphics/Glyph/primers.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/processed_transcript.pm b/lib/Bio/Graphics/Glyph/processed_transcript.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/protein.pm b/lib/Bio/Graphics/Glyph/protein.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/ragged_ends.pm b/lib/Bio/Graphics/Glyph/ragged_ends.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/rainbow_gene.pm b/lib/Bio/Graphics/Glyph/rainbow_gene.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/read_pair.pm b/lib/Bio/Graphics/Glyph/read_pair.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/redgreen_box.pm b/lib/Bio/Graphics/Glyph/redgreen_box.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/redgreen_segment.pm b/lib/Bio/Graphics/Glyph/redgreen_segment.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/repeating_shape.pm b/lib/Bio/Graphics/Glyph/repeating_shape.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/rndrect.pm b/lib/Bio/Graphics/Glyph/rndrect.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/ruler_arrow.pm b/lib/Bio/Graphics/Glyph/ruler_arrow.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/saw_teeth.pm b/lib/Bio/Graphics/Glyph/saw_teeth.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/scale.pm b/lib/Bio/Graphics/Glyph/scale.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/segmented_keyglyph.pm b/lib/Bio/Graphics/Glyph/segmented_keyglyph.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/segments.pm b/lib/Bio/Graphics/Glyph/segments.pm old mode 100755 new mode 100644 index 49df27e..4d524f4 --- a/lib/Bio/Graphics/Glyph/segments.pm +++ b/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 diff --git a/lib/Bio/Graphics/Glyph/smoothing.pm b/lib/Bio/Graphics/Glyph/smoothing.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/so_transcript.pm b/lib/Bio/Graphics/Glyph/so_transcript.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/span.pm b/lib/Bio/Graphics/Glyph/span.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/spectrogram.pm b/lib/Bio/Graphics/Glyph/spectrogram.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/splice_site.pm b/lib/Bio/Graphics/Glyph/splice_site.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/stackedplot.pm b/lib/Bio/Graphics/Glyph/stackedplot.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/ternary_plot.pm b/lib/Bio/Graphics/Glyph/ternary_plot.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/text_in_box.pm b/lib/Bio/Graphics/Glyph/text_in_box.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/three_letters.pm b/lib/Bio/Graphics/Glyph/three_letters.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/tic_tac_toe.pm b/lib/Bio/Graphics/Glyph/tic_tac_toe.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/toomany.pm b/lib/Bio/Graphics/Glyph/toomany.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/topoview.pm b/lib/Bio/Graphics/Glyph/topoview.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/trace.pm b/lib/Bio/Graphics/Glyph/trace.pm old mode 100755 new mode 100644 index 6d77269..8781a3c --- a/lib/Bio/Graphics/Glyph/trace.pm +++ b/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 for an explaination of how to align the trace with the +See the L 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 diff --git a/lib/Bio/Graphics/Glyph/track.pm b/lib/Bio/Graphics/Glyph/track.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/transcript.pm b/lib/Bio/Graphics/Glyph/transcript.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/transcript2.pm b/lib/Bio/Graphics/Glyph/transcript2.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/translation.pm b/lib/Bio/Graphics/Glyph/translation.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/triangle.pm b/lib/Bio/Graphics/Glyph/triangle.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/two_bolts.pm b/lib/Bio/Graphics/Glyph/two_bolts.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/vista_plot.pm b/lib/Bio/Graphics/Glyph/vista_plot.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/wave.pm b/lib/Bio/Graphics/Glyph/wave.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/weighted_arrow.pm b/lib/Bio/Graphics/Glyph/weighted_arrow.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/whiskerplot.pm b/lib/Bio/Graphics/Glyph/whiskerplot.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/wiggle_box.pm b/lib/Bio/Graphics/Glyph/wiggle_box.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/wiggle_data.pm b/lib/Bio/Graphics/Glyph/wiggle_data.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/wiggle_density.pm b/lib/Bio/Graphics/Glyph/wiggle_density.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/wiggle_whiskers.pm b/lib/Bio/Graphics/Glyph/wiggle_whiskers.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/wiggle_xyplot.pm b/lib/Bio/Graphics/Glyph/wiggle_xyplot.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Glyph/xyplot.pm b/lib/Bio/Graphics/Glyph/xyplot.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Layout.pm b/lib/Bio/Graphics/Layout.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Panel.pm b/lib/Bio/Graphics/Panel.pm old mode 100755 new mode 100644 index bab836f..e8aaa34 --- a/lib/Bio/Graphics/Panel.pm +++ b/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 diff --git a/lib/Bio/Graphics/Pictogram.pm b/lib/Bio/Graphics/Pictogram.pm old mode 100755 new mode 100644 index 080b6e8..3af09e0 --- a/lib/Bio/Graphics/Pictogram.pm +++ b/lib/Bio/Graphics/Pictogram.pm @@ -1,5 +1,3 @@ -# BioPerl module for Bio::Graphics::Pictogram -# # Cared for by Shawn Hoon # # 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 diff --git a/lib/Bio/Graphics/RendererI.pm b/lib/Bio/Graphics/RendererI.pm old mode 100755 new mode 100644 index b8bfc6a..fd019ce --- a/lib/Bio/Graphics/RendererI.pm +++ b/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 Epaul@systemsbiology.orgE. diff --git a/lib/Bio/Graphics/Util.pm b/lib/Bio/Graphics/Util.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Wiggle.pm b/lib/Bio/Graphics/Wiggle.pm old mode 100755 new mode 100644 diff --git a/lib/Bio/Graphics/Wiggle/Loader.pm b/lib/Bio/Graphics/Wiggle/Loader.pm old mode 100755 new mode 100644 diff --git a/scripts/bam_coverage_windows.pl b/scripts/bam_coverage_windows.pl old mode 100755 new mode 100644 index f593df3..17afd19 --- a/scripts/bam_coverage_windows.pl +++ b/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; diff --git a/scripts/contig_draw.pl b/scripts/contig_draw.pl old mode 100755 new mode 100644 index db1f520..0ee718d --- a/scripts/contig_draw.pl +++ b/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; diff --git a/scripts/coverage_to_topoview.pl b/scripts/coverage_to_topoview.pl old mode 100755 new mode 100644 index cc432d6..6fb33b8 --- a/scripts/coverage_to_topoview.pl +++ b/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; diff --git a/scripts/feature_draw.pl b/scripts/feature_draw.pl old mode 100755 new mode 100644 index d597ee8..f57900a --- a/scripts/feature_draw.pl +++ b/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; diff --git a/scripts/frend.pl b/scripts/frend.pl old mode 100755 new mode 100644 index 49b48ef..5755c28 --- a/scripts/frend.pl +++ b/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; diff --git a/scripts/glyph_help.pl b/scripts/glyph_help.pl old mode 100755 new mode 100644 diff --git a/scripts/render_msa.pl b/scripts/render_msa.pl old mode 100755 new mode 100644 diff --git a/scripts/search_overview.pl b/scripts/search_overview.pl old mode 100755 new mode 100644 index ef03a48..025478a --- a/scripts/search_overview.pl +++ b/scripts/search_overview.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; diff --git a/t/BioGraphics.t b/t/BioGraphics.t old mode 100755 new mode 100644 diff --git a/t/Wiggle.t b/t/Wiggle.t old mode 100755 new mode 100644