- Update to 2.15

Changelog: http://search.cpan.org/src/LDS/Bio-Graphics-2.15/Changes

PR:		ports/152189
Submitted by:	Gea-Suan Lin <gslin@gslin.org>

3 files changed, 201 insertions, 196 deletions

diff --git a/biology/p5-Bio-Graphics/Makefile b/biology/p5-Bio-Graphics/Makefile
index 364424cc49f0..f4fe2966cbd2 100644
--- a/biology/p5-Bio-Graphics/Makefile
+++ b/biology/p5-Bio-Graphics/Makefile
@@ -6,120 +6,121 @@
 #
 
 PORTNAME=	Bio-Graphics
-PORTVERSION=	2.14
+PORTVERSION=	2.15
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
-MASTER_SITE_SUBDIR=	../../authors/id/L/LD/LDS
 PKGNAMEPREFIX=	p5-
 
 MAINTAINER=	perl@FreeBSD.org
 COMMENT=	Generate GD Images of Bio::Seq Objects
 
-BUILD_DEPENDS=	p5-GD>=2.3:${PORTSDIR}/graphics/p5-GD \
+RUN_DEPENDS=	p5-Bio-SCF>=1.01:${PORTSDIR}/biology/p5-Bio-SCF \
+		p5-GD>=2.3:${PORTSDIR}/graphics/p5-GD \
 		p5-GD-SVG>=0.32:${PORTSDIR}/graphics/p5-GD-SVG \
 		p5-Statistics-Descriptive>=2.6:${PORTSDIR}/math/p5-Statistics-Descriptive \
-		p5-bioperl>=1.6.0:${PORTSDIR}/biology/p5-bioperl \
-		p5-Bio-SCF>=1.01:${PORTSDIR}/biology/p5-Bio-SCF
-RUN_DEPENDS=	${BUILD_DEPENDS}
+		p5-bioperl>=1.6.0:${PORTSDIR}/biology/p5-bioperl
 
 PERL_MODBUILD=	YES
 
-MAN1=	contig_draw.pl.1 feature_draw.pl.1 \
-	frend.pl.1 search_overview.pl.1
+MAN1=		contig_draw.pl.1 \
+		feature_draw.pl.1 \
+		frend.pl.1 \
+		search_overview.pl.1
 
-MAN3=	Bio::Graphics.3 \
-	Bio::Graphics::Glyph::transcript2.3 \
-	Bio::Graphics::Glyph::extending_arrow.3 \
-	Bio::Graphics::Wiggle.3 \
-	Bio::Graphics::ConfiguratorI.3 \
-	Bio::Graphics::DrawTransmembrane.3 \
-	Bio::Graphics::Feature.3 \
-	Bio::Graphics::FeatureBase.3 \
-	Bio::Graphics::FeatureDir.3 \
-	Bio::Graphics::FeatureFile.3 \
-	Bio::Graphics::FeatureFile::Iterator.3 \
-	Bio::Graphics::Glyph.3 \
-	Bio::Graphics::Glyph::Factory.3 \
-	Bio::Graphics::Glyph::alignment.3 \
-	Bio::Graphics::Glyph::allele_tower.3 \
-	Bio::Graphics::Glyph::anchored_arrow.3 \
-	Bio::Graphics::Glyph::arrow.3 \
-	Bio::Graphics::Glyph::box.3 \
-	Bio::Graphics::Glyph::broken_line.3 \
-	Bio::Graphics::Glyph::cds.3 \
-	Bio::Graphics::Glyph::christmas_arrow.3 \
-	Bio::Graphics::Glyph::crossbox.3 \
-	Bio::Graphics::Glyph::dashed_line.3 \
-	Bio::Graphics::Glyph::diamond.3 \
-	Bio::Graphics::Glyph::dna.3 \
-	Bio::Graphics::Glyph::dot.3 \
-	Bio::Graphics::Glyph::dumbbell.3 \
-	Bio::Graphics::Glyph::ellipse.3 \
-	Bio::Graphics::Glyph::ex.3 \
-	Bio::Graphics::Glyph::fixedwidth.3 \
-	Bio::Graphics::Glyph::flag.3 \
-	Bio::Graphics::Glyph::gene.3 \
-	Bio::Graphics::Glyph::generic.3 \
-	Bio::Graphics::Glyph::graded_segments.3 \
-	Bio::Graphics::Glyph::group.3 \
-	Bio::Graphics::Glyph::hat.3 \
-	Bio::Graphics::Glyph::heat_map.3 \
-	Bio::Graphics::Glyph::heat_map_ideogram.3 \
-	Bio::Graphics::Glyph::heterogeneous_segments.3 \
-	Bio::Graphics::Glyph::hidden.3 \
-	Bio::Graphics::Glyph::hybrid_plot.3 \
-	Bio::Graphics::Glyph::ideogram.3 \
-	Bio::Graphics::Glyph::image.3 \
-	Bio::Graphics::Glyph::lightning.3 \
-	Bio::Graphics::Glyph::line.3 \
-	Bio::Graphics::Glyph::merge_parts.3 \
-	Bio::Graphics::Glyph::merged_alignment.3 \
-	Bio::Graphics::Glyph::minmax.3 \
-	Bio::Graphics::Glyph::oval.3 \
-	Bio::Graphics::Glyph::pentagram.3 \
-	Bio::Graphics::Glyph::pairplot.3 \
-	Bio::Graphics::Glyph::phylo_align.3 \
-	Bio::Graphics::Glyph::pinsertion.3 \
-	Bio::Graphics::Glyph::primers.3 \
-	Bio::Graphics::Glyph::processed_transcript.3 \
-	Bio::Graphics::Glyph::protein.3 \
-	Bio::Graphics::Glyph::ragged_ends.3 \
-	Bio::Graphics::Glyph::rainbow_gene.3 \
-	Bio::Graphics::Glyph::redgreen_box.3 \
-	Bio::Graphics::Glyph::redgreen_segment.3 \
-	Bio::Graphics::Glyph::repeating_shape.3 \
-	Bio::Graphics::Glyph::rndrect.3 \
-	Bio::Graphics::Glyph::ruler_arrow.3 \
-	Bio::Graphics::Glyph::saw_teeth.3 \
-	Bio::Graphics::Glyph::segmented_keyglyph.3 \
-	Bio::Graphics::Glyph::segments.3 \
-	Bio::Graphics::Glyph::so_transcript.3 \
-	Bio::Graphics::Glyph::span.3 \
-	Bio::Graphics::Glyph::spectrogram.3 \
-	Bio::Graphics::Glyph::splice_site.3 \
-	Bio::Graphics::Glyph::stackedplot.3 \
-	Bio::Graphics::Glyph::ternary_plot.3 \
-	Bio::Graphics::Glyph::text_in_box.3 \
-	Bio::Graphics::Glyph::three_letters.3 \
-	Bio::Graphics::Glyph::tic_tac_toe.3 \
-	Bio::Graphics::Glyph::toomany.3 \
-	Bio::Graphics::Glyph::trace.3 \
-	Bio::Graphics::Glyph::track.3 \
-	Bio::Graphics::Glyph::transcript.3 \
-	Bio::Graphics::Glyph::translation.3 \
-	Bio::Graphics::Glyph::triangle.3 \
-	Bio::Graphics::Glyph::two_bolts.3 \
-	Bio::Graphics::Glyph::wave.3 \
-	Bio::Graphics::Glyph::weighted_arrow.3 \
-	Bio::Graphics::Glyph::whiskerplot.3 \
-	Bio::Graphics::Glyph::wiggle_box.3 \
-	Bio::Graphics::Glyph::wiggle_density.3 \
-	Bio::Graphics::Glyph::wiggle_xyplot.3 \
-	Bio::Graphics::Glyph::xyplot.3 \
-	Bio::Graphics::Panel.3 \
-	Bio::Graphics::Pictogram.3 \
-	Bio::Graphics::RendererI.3 \
-	Bio::Graphics::Util.3 \
-	Bio::Graphics::Wiggle::Loader.3
+MAN3=		Bio::Graphics.3 \
+		Bio::Graphics::Glyph::transcript2.3 \
+		Bio::Graphics::Glyph::extending_arrow.3 \
+		Bio::Graphics::Wiggle.3 \
+		Bio::Graphics::ConfiguratorI.3 \
+		Bio::Graphics::DrawTransmembrane.3 \
+		Bio::Graphics::Feature.3 \
+		Bio::Graphics::FeatureBase.3 \
+		Bio::Graphics::FeatureDir.3 \
+		Bio::Graphics::FeatureFile.3 \
+		Bio::Graphics::FeatureFile::Iterator.3 \
+		Bio::Graphics::Glyph.3 \
+		Bio::Graphics::Glyph::Factory.3 \
+		Bio::Graphics::Glyph::alignment.3 \
+		Bio::Graphics::Glyph::allele_tower.3 \
+		Bio::Graphics::Glyph::anchored_arrow.3 \
+		Bio::Graphics::Glyph::arrow.3 \
+		Bio::Graphics::Glyph::box.3 \
+		Bio::Graphics::Glyph::broken_line.3 \
+		Bio::Graphics::Glyph::cds.3 \
+		Bio::Graphics::Glyph::christmas_arrow.3 \
+		Bio::Graphics::Glyph::crossbox.3 \
+		Bio::Graphics::Glyph::dashed_line.3 \
+		Bio::Graphics::Glyph::diamond.3 \
+		Bio::Graphics::Glyph::dna.3 \
+		Bio::Graphics::Glyph::dot.3 \
+		Bio::Graphics::Glyph::dumbbell.3 \
+		Bio::Graphics::Glyph::ellipse.3 \
+		Bio::Graphics::Glyph::ex.3 \
+		Bio::Graphics::Glyph::fixedwidth.3 \
+		Bio::Graphics::Glyph::flag.3 \
+		Bio::Graphics::Glyph::gene.3 \
+		Bio::Graphics::Glyph::generic.3 \
+		Bio::Graphics::Glyph::graded_segments.3 \
+		Bio::Graphics::Glyph::group.3 \
+		Bio::Graphics::Glyph::hat.3 \
+		Bio::Graphics::Glyph::heat_map.3 \
+		Bio::Graphics::Glyph::heat_map_ideogram.3 \
+		Bio::Graphics::Glyph::heterogeneous_segments.3 \
+		Bio::Graphics::Glyph::hidden.3 \
+		Bio::Graphics::Glyph::hybrid_plot.3 \
+		Bio::Graphics::Glyph::ideogram.3 \
+		Bio::Graphics::Glyph::image.3 \
+		Bio::Graphics::Glyph::lightning.3 \
+		Bio::Graphics::Glyph::line.3 \
+		Bio::Graphics::Glyph::merge_parts.3 \
+		Bio::Graphics::Glyph::merged_alignment.3 \
+		Bio::Graphics::Glyph::minmax.3 \
+		Bio::Graphics::Glyph::oval.3 \
+		Bio::Graphics::Glyph::pairplot.3 \
+		Bio::Graphics::Glyph::pentagram.3 \
+		Bio::Graphics::Glyph::phylo_align.3 \
+		Bio::Graphics::Glyph::pinsertion.3 \
+		Bio::Graphics::Glyph::primers.3 \
+		Bio::Graphics::Glyph::processed_transcript.3 \
+		Bio::Graphics::Glyph::protein.3 \
+		Bio::Graphics::Glyph::ragged_ends.3 \
+		Bio::Graphics::Glyph::rainbow_gene.3 \
+		Bio::Graphics::Glyph::redgreen_box.3 \
+		Bio::Graphics::Glyph::redgreen_segment.3 \
+		Bio::Graphics::Glyph::repeating_shape.3 \
+		Bio::Graphics::Glyph::rndrect.3 \
+		Bio::Graphics::Glyph::ruler_arrow.3 \
+		Bio::Graphics::Glyph::saw_teeth.3 \
+		Bio::Graphics::Glyph::segmented_keyglyph.3 \
+		Bio::Graphics::Glyph::segments.3 \
+		Bio::Graphics::Glyph::so_transcript.3 \
+		Bio::Graphics::Glyph::span.3 \
+		Bio::Graphics::Glyph::spectrogram.3 \
+		Bio::Graphics::Glyph::splice_site.3 \
+		Bio::Graphics::Glyph::stackedplot.3 \
+		Bio::Graphics::Glyph::ternary_plot.3 \
+		Bio::Graphics::Glyph::text_in_box.3 \
+		Bio::Graphics::Glyph::three_letters.3 \
+		Bio::Graphics::Glyph::tic_tac_toe.3 \
+		Bio::Graphics::Glyph::toomany.3 \
+		Bio::Graphics::Glyph::trace.3 \
+		Bio::Graphics::Glyph::track.3 \
+		Bio::Graphics::Glyph::transcript.3 \
+		Bio::Graphics::Glyph::translation.3 \
+		Bio::Graphics::Glyph::triangle.3 \
+		Bio::Graphics::Glyph::two_bolts.3 \
+		Bio::Graphics::Glyph::vista_plot.3 \
+		Bio::Graphics::Glyph::wave.3 \
+		Bio::Graphics::Glyph::weighted_arrow.3 \
+		Bio::Graphics::Glyph::whiskerplot.3 \
+		Bio::Graphics::Glyph::wiggle_box.3 \
+		Bio::Graphics::Glyph::wiggle_density.3 \
+		Bio::Graphics::Glyph::wiggle_xyplot.3 \
+		Bio::Graphics::Glyph::xyplot.3 \
+		Bio::Graphics::Panel.3 \
+		Bio::Graphics::Pictogram.3 \
+		Bio::Graphics::RendererI.3 \
+		Bio::Graphics::Util.3 \
+		Bio::Graphics::Wiggle::Loader.3
 
 .include <bsd.port.mk>
diff --git a/biology/p5-Bio-Graphics/distinfo b/biology/p5-Bio-Graphics/distinfo
index 5c4b1f21b29b..cdc29eb4ce57 100644
--- a/biology/p5-Bio-Graphics/distinfo
+++ b/biology/p5-Bio-Graphics/distinfo
@@ -1,3 +1,2 @@
-MD5 (Bio-Graphics-2.14.tar.gz) = 8a19807fb3f5c91551066956c17cd933
-SHA256 (Bio-Graphics-2.14.tar.gz) = 78ce70c48ac72ba12d694a1c0e57ff4ef2a2b9d477f828586f4430013acd5d62
-SIZE (Bio-Graphics-2.14.tar.gz) = 780551
+SHA256 (Bio-Graphics-2.15.tar.gz) = bee91112c1e8be1f90215d5d965077fc0c8c8fd3a24da4f28a270fa337266376
+SIZE (Bio-Graphics-2.15.tar.gz) = 856073
diff --git a/biology/p5-Bio-Graphics/pkg-plist b/biology/p5-Bio-Graphics/pkg-plist
index 5cb564388b6c..bf5da506e9ba 100644
--- a/biology/p5-Bio-Graphics/pkg-plist
+++ b/biology/p5-Bio-Graphics/pkg-plist
@@ -1,108 +1,113 @@
-bin/glyph_help.pl
-bin/contig_draw.pl
-bin/feature_draw.pl
-bin/frend.pl
-bin/render_msa.pl
-bin/search_overview.pl
-%%SITE_PERL%%/Bio/Graphics/FeatureFile/Iterator.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/cross.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/phylo_align.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/pairplot.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/rainbow_gene.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/spectrogram.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/ideogram.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/hat.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/heat_map.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/hidden.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/hybrid_plot.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/smoothing.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/stackedplot.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/trace.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/wiggle_density.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/fixedwidth.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/wiggle_box.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/wiggle_whiskers.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/ternary_plot.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/wiggle_minmax.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/wiggle_xyplot.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/heat_map_ideogram.pm
-%%SITE_PERL%%/Bio/Graphics/Wiggle/Loader.pm
+@comment $FreeBSD$
+%%SITE_PERL%%/Bio/Graphics.pm
+%%SITE_PERL%%/Bio/Graphics/ConfiguratorI.pm
 %%SITE_PERL%%/Bio/Graphics/DrawTransmembrane.pm
+%%SITE_PERL%%/Bio/Graphics/Feature.pm
 %%SITE_PERL%%/Bio/Graphics/FeatureBase.pm
 %%SITE_PERL%%/Bio/Graphics/FeatureDir.pm
-%%SITE_PERL%%/Bio/Graphics/RendererI.pm
-%%SITE_PERL%%/Bio/Graphics/Util.pm
-%%SITE_PERL%%/Bio/Graphics/Pictogram.pm
-%%SITE_PERL%%/Bio/Graphics/ConfiguratorI.pm
 %%SITE_PERL%%/Bio/Graphics/FeatureFile.pm
-%%SITE_PERL%%/Bio/Graphics/Feature.pm
-%%SITE_PERL%%/Bio/Graphics/Panel.pm
+%%SITE_PERL%%/Bio/Graphics/FeatureFile/Iterator.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph.pm
-%%SITE_PERL%%/Bio/Graphics.pm
-%%SITE_PERL%%/Bio/Graphics/Wiggle.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/track.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/generic.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/saw_teeth.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/pentagram.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/image.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/christmas_arrow.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/flag.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/Factory.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/alignment.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/allele_tower.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/anchored_arrow.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/arrow.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/box.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/broken_line.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/ellipse.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/cds.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/protein.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/repeating_shape.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/graded_segments.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/merge_parts.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/weighted_arrow.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/splice_site.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/wave.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/xyplot.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/gene.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/ragged_ends.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/segments.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/ex.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/christmas_arrow.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/cross.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/crossbox.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/lightning.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/merged_alignment.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/ruler_arrow.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/rndrect.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/span.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/pinsertion.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/two_bolts.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/primers.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/dashed_line.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/diamond.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/dna.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/dot.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/dumbbell.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/box.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/toomany.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/minmax.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/whiskerplot.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/redgreen_box.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/alignment.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/triangle.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/tic_tac_toe.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/transcript2.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/text_in_box.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/ellipse.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/ex.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/extending_arrow.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/fixedwidth.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/flag.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/gene.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/generic.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/graded_segments.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/group.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/translation.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/three_letters.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/line.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/hat.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/heat_map.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/heat_map_ideogram.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/heterogeneous_segments.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/extending_arrow.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/transcript.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/hidden.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/hybrid_plot.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/ideogram.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/image.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/lightning.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/line.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/merge_parts.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/merged_alignment.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/minmax.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/oval.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/arrow.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/dashed_line.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/dot.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/Factory.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/so_transcript.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/pairplot.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/pentagram.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/phylo_align.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/pinsertion.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/primers.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/processed_transcript.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/segmented_keyglyph.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/anchored_arrow.pm
-%%SITE_PERL%%/Bio/Graphics/Glyph/allele_tower.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/protein.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/ragged_ends.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/rainbow_gene.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/read_pair.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/redgreen_box.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/redgreen_segment.pm
-@dirrm %%SITE_PERL%%/Bio/Graphics/FeatureFile
-@dirrm %%SITE_PERL%%/Bio/Graphics/Wiggle
-@dirrm %%SITE_PERL%%/Bio/Graphics/Glyph
+%%SITE_PERL%%/Bio/Graphics/Glyph/repeating_shape.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/rndrect.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/ruler_arrow.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/saw_teeth.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/segmented_keyglyph.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/segments.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/smoothing.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/so_transcript.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/span.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/spectrogram.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/splice_site.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/stackedplot.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/ternary_plot.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/text_in_box.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/three_letters.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/tic_tac_toe.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/toomany.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/trace.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/track.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/transcript.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/transcript2.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/translation.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/triangle.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/two_bolts.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/vista_plot.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/wave.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/weighted_arrow.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/whiskerplot.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/wiggle_box.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/wiggle_density.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/wiggle_minmax.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/wiggle_whiskers.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/wiggle_xyplot.pm
+%%SITE_PERL%%/Bio/Graphics/Glyph/xyplot.pm
+%%SITE_PERL%%/Bio/Graphics/Layout.pm
+%%SITE_PERL%%/Bio/Graphics/Panel.pm
+%%SITE_PERL%%/Bio/Graphics/Pictogram.pm
+%%SITE_PERL%%/Bio/Graphics/RendererI.pm
+%%SITE_PERL%%/Bio/Graphics/Util.pm
+%%SITE_PERL%%/Bio/Graphics/Wiggle.pm
+%%SITE_PERL%%/Bio/Graphics/Wiggle/Loader.pm
+bin/contig_draw.pl
+bin/feature_draw.pl
+bin/frend.pl
+bin/glyph_help.pl
+bin/render_msa.pl
+bin/search_overview.pl
+@dirrmtry %%SITE_PERL%%/Bio/Graphics/Wiggle
+@dirrmtry %%SITE_PERL%%/Bio/Graphics/Glyph
+@dirrmtry %%SITE_PERL%%/Bio/Graphics/FeatureFile
 @dirrmtry %%SITE_PERL%%/Bio/Graphics
+@dirrmtry %%SITE_PERL%%/Bio