bioperl-live/Bio

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Current directory:[bioperl] / bioperl-live / Bio
Files shown:47
File Rev. Age Author Last log entry
(dir) Align/        
(dir) AlignIO/        
(dir) AnnSeqIO/        
(dir) Annotation/        
(dir) Assembly/        
(dir) Attic/   [show contents]        
(dir) Biblio/        
(dir) Cluster/        
(dir) ClusterIO/        
(dir) CodonUsage/        
(dir) Coordinate/        
(dir) DB/        
(dir) Das/        
(dir) Event/        
(dir) Expression/        
(dir) Factory/        
(dir) FeatureIO/        
(dir) Graph/        
(dir) Graphics/        
(dir) Index/        
(dir) LiveSeq/        
(dir) Location/        
(dir) Map/        
(dir) MapIO/        
(dir) Matrix/        
(dir) Microarray/        
(dir) MolEvol/        
(dir) Ontology/        
(dir) OntologyIO/        
(dir) Phenotype/        
(dir) PhyloNetwork/        
(dir) PopGen/        
(dir) Population/        
(dir) Restriction/        
(dir) Root/        
(dir) Search/        
(dir) SearchIO/        
(dir) Seq/        
(dir) SeqEvolution/        
(dir) SeqFeature/        
(dir) SeqFeatureProducer/        
(dir) SeqIO/        
(dir) Structure/        
(dir) Symbol/        
(dir) Taxonomy/        
(dir) Tools/        
(dir) Tree/        
(dir) TreeIO/        
(dir) Variation/        
(file) AlignIO.pm (graph)   1.50  21 months  cjfields  add xmfa write_aln() method, stk and xmfa file extensions for guessing format
(file) AnalysisI.pm (graph)   1.14  14 months  sendu  removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"
(file) AnalysisParserI.pm (graph)   1.13  22 months  sendu  use base, return true
(file) AnalysisResultI.pm (graph)   1.11  22 months  sendu  use base, return true
(file) AnnotatableI.pm (graph)   1.18  11 months  cjfields  Shouldn't use Carp, use throw/warn instead
(file) AnnotationCollectionI.pm (graph)   1.20  22 months  sendu  use base, return true
(file) AnnotationI.pm (graph)   1.15  11 months  cjfields  * Annotation : explain display_text() more explicitly; remove commented out over...
(file) Biblio.pm (graph)   1.20  14 months  sendu  removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"
(file) ClusterI.pm (graph)   1.8  22 months  tseemann  Removed empty CONTRIBUTORS sections in POD.
(file) ClusterIO.pm (graph)   1.19  22 months  sendu  use base, return true
(file) DBLinkContainerI.pm (graph)   1.13  22 months  sendu  use base, return true
(file) DasI.pm (graph)   1.20  22 months  sendu  use base, return true
(file) DescribableI.pm (graph)   1.11  22 months  sendu  use base, return true
(file) FeatureHolderI.pm (graph)   1.12  22 months  sendu  use base, return true
(file) FeatureIO.pm (graph)   1.22  14 months  sendu  removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"
(file) Graphics.pm (graph)   1.18  22 months  lstein  Fixed synopsis so that it works!
(file) HandlerBaseI.pm (graph)   1.2  16 months  sendu  author is Chris Fields
(file) IdCollectionI.pm (graph)   1.8  22 months  sendu  use base, return true
(file) IdentifiableI.pm (graph)   1.13  22 months  sendu  use base, return true
(file) LocatableSeq.pm (graph)   1.45  12 months  sendu  end() now allows getting and setting of 0, allowing the representation of gaps-o...
(file) LocationI.pm (graph)   1.26  22 months  sendu  use base, return true
(file) MapIO.pm (graph)   1.12  14 months  sendu  removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"
(file) OntologyIO.pm (graph)   1.14  22 months  sendu  use base, return true
(file) ParameterBaseI.pm (graph)   1.2  12 months  cjfields  forogt to commit docs
(file) Perl.pm (graph)   1.28  22 months  sendu  use base, return true
(file) PhyloNetwork.pm (graph)   1.1  8 months  jason  Initial commit of Phylogenetic Network code from Gabriel Valiente and Gabriel Ca...
(file) PrimarySeq.pm (graph)   1.102  13 months  sendu  removed pointless print of 0-length string
(file) PrimarySeqI.pm (graph)   1.70  17 months  nathan  added POD for deprecated moltype() method.
(file) PullParserI.pm (graph)   1.14  13 months  sendu  cleaned up to avoid warnings
(file) Range.pm (graph)   1.30  10 months  cjfields  typo
(file) RangeI.pm (graph)   1.53  18 months  dave_messina  Adding Stephen Montgomery's subtract method to RangeI (Bug 2207)
(file) SearchDist.pm (graph)   1.22  22 months  sendu  use base, return true
(file) SearchIO.pm (graph)   1.45  8 months  cjfields  Several fixes * bug 2409 * code to pull out the GI if present * resolve most of ...
(file) Seq.pm (graph)   1.94  14 months  sendu  removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"
(file) SeqAnalysisParserI.pm (graph)   1.17  22 months  sendu  use base, return true
(file) SeqFeatureI.pm (graph)   1.74  9 months  jason  Don't we need to include Bio::Tools::GFF
(file) SeqI.pm (graph)   1.31  22 months  sendu  use base, return true
(file) SeqIO.pm (graph)   1.99  8 months  heikki  correct syntax in the example; doc formatting
(file) SeqUtils.pm (graph)   1.38  14 months  sendu  removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"
(file) SimpleAlign.pm (graph)   1.144  8 months  cjfields  Related to Albert's fix
(file) SimpleAnalysisI.pm (graph)   1.11  22 months  tseemann  Removed unused "use vars ($Revision); $Revision = ...."
(file) Species.pm (graph)   1.50  14 months  sendu  removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"
(file) Taxon.pm (graph)   1.9  14 months  sendu  revert last change: its not supposed to access the db to find descendents
(file) Taxonomy.pm (graph)   1.13  14 months  sendu  removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"
(file) TreeIO.pm (graph)   1.23  14 months  sendu  removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"
(file) UpdateableSeqI.pm (graph)   1.8  22 months  sendu  use base, return true
(file) WebAgent.pm (graph)   1.18  21 months  sendu  warning in sleep was only supposed to happen when verbose; changed to debug()
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