Bio-Graphics 2.40
- Released by
- CJFIELDS
- Version
- Release Date
- 2016-12-16
- Kwalitee
- 131.25
- Core Kwalitee
- 84.38
- LINKS
Bio-Graphics 2.40 Latest
Kwalitee Issues
- buildtool_not_executable
-
Change the permissions of Build.PL/Makefile.PL to not-executable.
- has_human_readable_license
-
Add a section called "LICENSE" to the documentation, or add a file named LICENSE to the distribution.
- has_license_in_source_file
-
Add =head1 LICENSE and the text of the license to the main module in your code.
- use_strict
-
Add 'use strict' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules are strictly written.
Error: Bio::Graphics::FeatureFile::Iterator, Bio::Graphics::GDWrapper, Bio::Graphics::Glyph::fb_shmiggle, Bio::Graphics::Glyph::read_pair
- no_pod_errors
-
Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.
Error: Bio-Graphics-2.40/lib/Bio/Graphics/FeatureDir.pm -- Around line 160: '=item' outside of any '=over' Around line 272: =cut found outside a pod block. Skipping to next block. Around line 274: You forgot a '=back' before '=head1'
- meta_yml_declares_perl_version
-
If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.
- has_known_license_in_source_file
-
Add =head1 LICENSE and/or the proper text of the well-known license to the main module in your code.
- use_warnings
-
Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.
Error: Bio::Graphics, Bio::Graphics::ConfiguratorI, Bio::Graphics::Feature, Bio::Graphics::FeatureBase, Bio::Graphics::FeatureFile, Bio::Graphics::FeatureFile::Iterator, Bio::Graphics::GDWrapper, Bio::Graphics::Glyph, Bio::Graphics::Glyph::Factory, Bio::Graphics::Glyph::alignment, Bio::Graphics::Glyph::allele_tower, Bio::Graphics::Glyph::anchored_arrow, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::box, Bio::Graphics::Glyph::broken_line, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::christmas_arrow, Bio::Graphics::Glyph::cross, Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::dashed_line, Bio::Graphics::Glyph::decorated_gene, Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::dumbbell, Bio::Graphics::Glyph::ellipse, Bio::Graphics::Glyph::ex, Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::fb_shmiggle, Bio::Graphics::Glyph::fixedwidth, Bio::Graphics::Glyph::flag, Bio::Graphics::Glyph::gene, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments, Bio::Graphics::Glyph::group, Bio::Graphics::Glyph::hat, Bio::Graphics::Glyph::heat_map, Bio::Graphics::Glyph::heat_map_ideogram, Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::hidden, Bio::Graphics::Glyph::hybrid_plot, Bio::Graphics::Glyph::ideogram, Bio::Graphics::Glyph::image, Bio::Graphics::Glyph::lightning, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::merge_parts, Bio::Graphics::Glyph::merged_alignment, Bio::Graphics::Glyph::minmax, Bio::Graphics::Glyph::operon, Bio::Graphics::Glyph::oval, Bio::Graphics::Glyph::pairplot, Bio::Graphics::Glyph::pentagram, Bio::Graphics::Glyph::phylo_align, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::point_glyph, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::processed_transcript, Bio::Graphics::Glyph::protein, Bio::Graphics::Glyph::ragged_ends, Bio::Graphics::Glyph::rainbow_gene, Bio::Graphics::Glyph::read_pair, Bio::Graphics::Glyph::redgreen_box, Bio::Graphics::Glyph::redgreen_segment, Bio::Graphics::Glyph::repeating_shape, Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::saw_teeth, Bio::Graphics::Glyph::scale, Bio::Graphics::Glyph::segmented_keyglyph, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::smoothing, Bio::Graphics::Glyph::so_transcript, Bio::Graphics::Glyph::span, Bio::Graphics::Glyph::spectrogram, Bio::Graphics::Glyph::splice_site, Bio::Graphics::Glyph::stackedplot, Bio::Graphics::Glyph::ternary_plot, Bio::Graphics::Glyph::text_in_box, Bio::Graphics::Glyph::three_letters, Bio::Graphics::Glyph::tic_tac_toe, Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::topoview, Bio::Graphics::Glyph::trace, Bio::Graphics::Glyph::track, Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle, Bio::Graphics::Glyph::two_bolts, Bio::Graphics::Glyph::vista_plot, Bio::Graphics::Glyph::wave, Bio::Graphics::Glyph::weighted_arrow, Bio::Graphics::Glyph::whiskerplot, Bio::Graphics::Glyph::wiggle_box, Bio::Graphics::Glyph::wiggle_data, Bio::Graphics::Glyph::wiggle_density, Bio::Graphics::Glyph::wiggle_whiskers, Bio::Graphics::Glyph::wiggle_xyplot, Bio::Graphics::Glyph::xyplot, Bio::Graphics::Layout, Bio::Graphics::Panel, Bio::Graphics::Pictogram, Bio::Graphics::RendererI, Bio::Graphics::Util, Bio::Graphics::Wiggle::Loader
- consistent_version
-
Split the distribution, or fix the version numbers to make them consistent (use the highest version number to avoid version downgrade).
Error: 1.0,2.40
- meta_yml_has_repository_resource
-
Add a 'repository' resource to the META.yml via 'meta_add' accessor (for Module::Build) or META_ADD parameter (for ExtUtils::MakeMaker).
- has_separate_license_file
-
This is not a critical issue. Currently mainly informative for the CPANTS authors. It might be removed later.
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::Graphics | Generate GD images of Bio::Seq objects | 2.40 | metacpan |
| Bio::Graphics::ConfiguratorI | A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag->value semantics (ie. of Bio::AnnotationCollectionI) for object-representation information (eg. foreground color), and for general interface preferences (eg. image width in gbrowse). | metacpan | |
| Bio::Graphics::DrawTransmembrane | draw a cartoon of an Alpha-helical transmembrane protein. | metacpan | |
| Bio::Graphics::Feature | A simple feature object for use with Bio::Graphics::Panel | metacpan | |
| Bio::Graphics::FeatureBase | Compatibility module | metacpan | |
| Bio::Graphics::FeatureDir | A directory of feature files and conf files | metacpan | |
| Bio::Graphics::FeatureFile | A set of Bio::Graphics features, stored in a file | metacpan | |
| Bio::Graphics::FeatureFile::Iterator | Iterator across a Bio::Graphics::FeatureFile | metacpan | |
| Bio::Graphics::FileSplitter | metacpan | ||
| Bio::Graphics::GDWrapper | metacpan | ||
| Bio::Graphics::Glyph | Base class for Bio::Graphics::Glyph objects | metacpan | |
| Bio::Graphics::Glyph::Factory | Factory for Bio::Graphics::Glyph objects | metacpan | |
| Bio::Graphics::Glyph::alignment | The "alignment" glyph | metacpan | |
| Bio::Graphics::Glyph::allele_tower | The "allele_tower" glyph | metacpan | |
| Bio::Graphics::Glyph::anchored_arrow | The "anchored_arrow" glyph | metacpan | |
| Bio::Graphics::Glyph::arrow | the "arrow" glyph | metacpan | |
| Bio::Graphics::Glyph::box | The "box" glyph | metacpan | |
| Bio::Graphics::Glyph::broken_line | The "broken line" glyph | metacpan | |
| Bio::Graphics::Glyph::cds | The "cds" glyph | metacpan | |
| Bio::Graphics::Glyph::christmas_arrow | The "christmas arrow" glyph | metacpan | |
| Bio::Graphics::Glyph::cross | metacpan | ||
| Bio::Graphics::Glyph::crossbox | The "crossbox" glyph | metacpan | |
| Bio::Graphics::Glyph::dashed_line | The "dashed line" glyph | metacpan | |
| Bio::Graphics::Glyph::decorated_gene | A GFF3-compatible gene glyph with protein decorations | metacpan | |
| Bio::Graphics::Glyph::decorated_transcript | draws processed transcript with protein decorations | metacpan | |
| Bio::Graphics::Glyph::diamond | The "diamond" glyph | metacpan | |
| Bio::Graphics::Glyph::dna | The "dna" glyph | metacpan | |
| Bio::Graphics::Glyph::dot | The "dot" glyph | metacpan | |
| Bio::Graphics::Glyph::dumbbell | A glyph that draws a "dumbbell" with the same shapes on both ends. | metacpan | |
| Bio::Graphics::Glyph::ellipse | The "ellipse" glyph | metacpan | |
| Bio::Graphics::Glyph::ex | the "ex", or "crossed box" glyph | metacpan | |
| Bio::Graphics::Glyph::extending_arrow | The "extending arrow" glyph | metacpan | |
| Bio::Graphics::Glyph::fb_shmiggle | metacpan | ||
| Bio::Graphics::Glyph::fixedwidth | A base class fixed width glyphs | metacpan | |
| Bio::Graphics::Glyph::flag | the "flag" glyph | metacpan | |
| Bio::Graphics::Glyph::gene | A GFF3-compatible gene glyph | metacpan | |
| Bio::Graphics::Glyph::generic | The "generic" glyph | metacpan | |
| Bio::Graphics::Glyph::graded_segments | The "graded_segments" glyph | metacpan | |
| Bio::Graphics::Glyph::group | The "group" glyph | metacpan | |
| Bio::Graphics::Glyph::hat | The "hat" glyph | metacpan | |
| Bio::Graphics::Glyph::heat_map | The "heat_map" glyph | metacpan | |
| Bio::Graphics::Glyph::heat_map_ideogram | The "heat_map_ideogram" glyph | metacpan | |
| Bio::Graphics::Glyph::heterogeneous_segments | The "heterogeneous_segments" glyph | metacpan | |
| Bio::Graphics::Glyph::hidden | The "hidden" glyph | metacpan | |
| Bio::Graphics::Glyph::hybrid_plot | An xyplot plot drawing dual graph using data from two or more wiggle files per track | 1.0 | metacpan |
| Bio::Graphics::Glyph::ideogram | The "ideogram" glyph | metacpan | |
| Bio::Graphics::Glyph::image | A glyph that draws photographs & other images | metacpan | |
| Bio::Graphics::Glyph::lightning | The "lightning" glyph | metacpan | |
| Bio::Graphics::Glyph::line | The "line" glyph | metacpan | |
| Bio::Graphics::Glyph::merge_parts | a base class which suppors semantic zooming of scored alignment features | metacpan | |
| Bio::Graphics::Glyph::merged_alignment | The "merged_alignment" glyph | metacpan | |
| Bio::Graphics::Glyph::minmax | The minmax glyph | metacpan | |
| Bio::Graphics::Glyph::operon | The "polycistronic operon" glyph | metacpan | |
| Bio::Graphics::Glyph::oval | The "oval" glyph | metacpan | |
| Bio::Graphics::Glyph::pairplot | The "pairwise plot" glyph | metacpan | |
| Bio::Graphics::Glyph::pentagram | The "pentagram" glyph | metacpan | |
| Bio::Graphics::Glyph::phylo_align | The "phylogenetic alignment" glyph | metacpan | |
| Bio::Graphics::Glyph::pinsertion | The "Drosophila P-element Insertion" glyph | metacpan | |
| Bio::Graphics::Glyph::point_glyph | metacpan | ||
| Bio::Graphics::Glyph::primers | The "STS primers" glyph | metacpan | |
| Bio::Graphics::Glyph::processed_transcript | The sequence ontology transcript glyph | metacpan | |
| Bio::Graphics::Glyph::protein | The "protein" glyph | metacpan | |
| Bio::Graphics::Glyph::ragged_ends | The "ragged ends" glyph | metacpan | |
| Bio::Graphics::Glyph::rainbow_gene | metacpan | ||
| Bio::Graphics::Glyph::read_pair | metacpan | ||
| Bio::Graphics::Glyph::redgreen_box | The "redgreen_box" glyph | metacpan | |
| Bio::Graphics::Glyph::redgreen_segment | The "redgreen_segments" glyph | metacpan | |
| Bio::Graphics::Glyph::repeating_shape | A glyph that draws the same shape repeatedly. | metacpan | |
| Bio::Graphics::Glyph::rndrect | The "round rect" glyph | metacpan | |
| Bio::Graphics::Glyph::ruler_arrow | glyph for drawing an arrow as ruler (5' and 3' are marked as label) | metacpan | |
| Bio::Graphics::Glyph::saw_teeth | The "saw teeth" glyph | metacpan | |
| Bio::Graphics::Glyph::scale | The "scale" glyph | metacpan | |
| Bio::Graphics::Glyph::segmented_keyglyph | The "segmented_keyglyph" glyph | metacpan | |
| Bio::Graphics::Glyph::segments | The "segments" glyph | metacpan | |
| Bio::Graphics::Glyph::smoothing | metacpan | ||
| Bio::Graphics::Glyph::so_transcript | The sequence ontology transcript glyph | metacpan | |
| Bio::Graphics::Glyph::span | The "span" glyph | metacpan | |
| Bio::Graphics::Glyph::spectrogram | The "spectrogram" glyph | metacpan | |
| Bio::Graphics::Glyph::splice_site | The "splice_site" glyph | metacpan | |
| Bio::Graphics::Glyph::stackedplot | The stackedplot glyph | metacpan | |
| Bio::Graphics::Glyph::ternary_plot | Draw ternary plot data | metacpan | |
| Bio::Graphics::Glyph::text_in_box | The "text in box" glyph | metacpan | |
| Bio::Graphics::Glyph::three_letters | DAS-compatible package to use for drawing a line of groups of three letters | metacpan | |
| Bio::Graphics::Glyph::tic_tac_toe | The "tic-tac-toe" glyph | metacpan | |
| Bio::Graphics::Glyph::toomany | The "too many to show" glyph | metacpan | |
| Bio::Graphics::Glyph::topoview | metacpan | ||
| Bio::Graphics::Glyph::trace | A glyph that visualizes a trace file | metacpan | |
| Bio::Graphics::Glyph::track | The "track" glyph | metacpan | |
| Bio::Graphics::Glyph::transcript | The "transcript" glyph | metacpan | |
| Bio::Graphics::Glyph::transcript2 | The "transcript2" glyph | metacpan | |
| Bio::Graphics::Glyph::translation | The "6-frame translation" glyph | metacpan | |
| Bio::Graphics::Glyph::triangle | The "triangle" glyph | metacpan | |
| Bio::Graphics::Glyph::two_bolts | The "two bolts" glyph | metacpan | |
| Bio::Graphics::Glyph::vista_plot | The "vista_plot" glyph | 1.0 | metacpan |
| Bio::Graphics::Glyph::wave | The "wave" glyph | metacpan | |
| Bio::Graphics::Glyph::weighted_arrow | The "weighted arrow" glyph | metacpan | |
| Bio::Graphics::Glyph::whiskerplot | The whiskerplot glyph | metacpan | |
| Bio::Graphics::Glyph::wiggle_box | A generic box glyph compatible with dense "wig"data | metacpan | |
| Bio::Graphics::Glyph::wiggle_data | metacpan | ||
| Bio::Graphics::Glyph::wiggle_density | A density plot compatible with dense "wig"data | metacpan | |
| Bio::Graphics::Glyph::wiggle_whiskers | metacpan | ||
| Bio::Graphics::Glyph::wiggle_xyplot | An xyplot plot compatible with dense "wig"data | metacpan | |
| Bio::Graphics::Glyph::xyplot | The xyplot glyph | metacpan | |
| Bio::Graphics::Layout | metacpan | ||
| Bio::Graphics::Layout::Contour | metacpan | ||
| Bio::Graphics::Math | metacpan | ||
| Bio::Graphics::Panel | Generate GD images of Bio::Seq objects | metacpan | |
| Bio::Graphics::Pictogram | generate SVG output of Pictogram display for consensus motifs | metacpan | |
| Bio::Graphics::RendererI | A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI. | metacpan | |
| Bio::Graphics::Util | non-object-oriented utilities used in Bio::Graphics modules | metacpan | |
| Bio::Graphics::Wiggle | Binary storage for dense genomic features | 1.0 | metacpan |
| Bio::Graphics::Wiggle::Loader | metacpan |