Table of Contents - bio-gff3-0.9.1 Documentation
Pages
Classes and Modules
- Bio
- Bio::GFF
- Bio::GFF::FastaReader
- Bio::GFF::GFF3
- Bio::GFF::GFF3::BioRubyFileRecord
- Bio::GFF::GFF3::FastParserFileRecord
- Bio::GFF::GFF3::FileIterator
- Bio::GFFbrowser
- Bio::GFFbrowser::Block
- Bio::GFFbrowser::Block::GffBlockParser
- Bio::GFFbrowser::Digest
- Bio::GFFbrowser::Digest::InMemory
- Bio::GFFbrowser::Digest::LruCache
- Bio::GFFbrowser::Digest::LruCacheHelpers
- Bio::GFFbrowser::Digest::LruCacheHelpers::LruRec
- Bio::GFFbrowser::Digest::LruCacheHelpers::SeekLinkedRecs
- Bio::GFFbrowser::Digest::LruCacheHelpers::SeekRec
- Bio::GFFbrowser::Digest::LruCacheHelpers::SeekRecList
- Bio::GFFbrowser::Digest::LruTracker
- Bio::GFFbrowser::Digest::NoCache
- Bio::GFFbrowser::Digest::NoCacheHelpers
- Bio::GFFbrowser::Digest::NoCacheHelpers::SeekLinkedRecs
- Bio::GFFbrowser::Digest::NoCacheHelpers::SeekRec
- Bio::GFFbrowser::Digest::NoCacheHelpers::SeekRecList
- Bio::GFFbrowser::Digest::Parser
- Bio::GFFbrowser::FastLineParser
- Bio::GFFbrowser::FastLineRecord
- Bio::GFFbrowser::FastaRecord
- Bio::GFFbrowser::FastaWriter
- Bio::GFFbrowser::GFF3
- Bio::GFFbrowser::GFF3ParseFile
- Bio::GFFbrowser::Helpers
- Bio::GFFbrowser::Helpers::Counter
- Bio::GFFbrowser::Helpers::Gff3Component
- Bio::GFFbrowser::Helpers::Gff3Features
- Bio::GFFbrowser::Helpers::Gff3Sequence
- Bio::GFFbrowser::Helpers::LinkedRecs
- Bio::GFFbrowser::Helpers::Logger
- Bio::GFFbrowser::Helpers::Record
- Bio::GFFbrowser::Helpers::Section
- Bio::GFFbrowser::Helpers::Sections
- Bio::GFFbrowser::Helpers::Validate
- Bio::GFFbrowser::Record
- LRUHash
Methods
- ::fetch — Bio::GFFbrowser::Digest::LruCacheHelpers::SeekRec
- ::fetch — Bio::GFFbrowser::Digest::NoCacheHelpers::SeekRec
- ::formatID — Bio::GFFbrowser::Helpers::Record
- ::new — Bio::GFFbrowser::Block::GffBlockParser
- ::new — Bio::GFFbrowser::Digest::InMemory
- ::new — Bio::GFFbrowser::Digest::LruCacheHelpers::SeekRecList
- ::new — Bio::GFFbrowser::Digest::LruTracker
- ::new — Bio::GFFbrowser::Digest::LruCache
- ::new — Bio::GFFbrowser::Digest::NoCacheHelpers::SeekRecList
- ::new — Bio::GFFbrowser::Digest::NoCache
- ::new — Bio::GFF::FastaReader
- ::new — Bio::GFF::GFF3::BioRubyFileRecord
- ::new — Bio::GFF::GFF3::FastParserFileRecord
- ::new — Bio::GFF::GFF3::FileIterator
- ::new — Bio::GFFbrowser::GFF3
- ::new — Bio::GFFbrowser::FastaRecord
- ::new — Bio::GFFbrowser::GFF3ParseFile
- ::new — Bio::GFFbrowser::FastLineRecord
- ::new — Bio::GFFbrowser::Helpers::Section
- ::new — Bio::GFFbrowser::FastaWriter
- ::new — LRUHash
- ::sort — Bio::GFFbrowser::Helpers::Sections
- #& — Bio::GFFbrowser::Helpers::Section
- #<=> — Bio::GFFbrowser::Helpers::Section
- #[] — Bio::GFFbrowser::Digest::LruCacheHelpers::SeekRecList
- #[] — Bio::GFFbrowser::Digest::LruTracker
- #[] — Bio::GFFbrowser::Digest::NoCacheHelpers::SeekRecList
- #[] — Bio::GFF::FastaReader
- #[] — LRUHash
- #[]= — Bio::GFFbrowser::Digest::LruCacheHelpers::SeekRecList
- #[]= — Bio::GFFbrowser::Digest::LruTracker
- #[]= — Bio::GFFbrowser::Digest::NoCacheHelpers::SeekRecList
- #[]= — LRUHash
- #add — Bio::GFFbrowser::Digest::LruCacheHelpers::SeekLinkedRecs
- #add — Bio::GFFbrowser::Digest::NoCacheHelpers::SeekLinkedRecs
- #add — Bio::GFF::FastaReader
- #add — Bio::GFFbrowser::Helpers::Counter
- #add — Bio::GFFbrowser::Helpers::LinkedRecs
- #assemble — Bio::GFFbrowser::Helpers::Gff3Sequence
- #assembleAA — Bio::GFFbrowser::Helpers::Gff3Sequence
- #assoc — LRUHash
- #attributes — Bio::GFFbrowser::FastLineRecord
- #clear — LRUHash
- #comment — Bio::GFFbrowser::FastLineRecord
- #debug — Bio::GFFbrowser::Helpers::Logger
- #delete — LRUHash
- #delete_if — LRUHash
- #delete_oldest — LRUHash
- #description — Bio::GFFbrowser::Helpers::Gff3Sequence
- #display — Bio::GFFbrowser::Digest::LruTracker
- #each — Bio::GFFbrowser::Digest::LruCacheHelpers::SeekRecList
- #each — Bio::GFFbrowser::Digest::NoCacheHelpers::SeekRecList
- #each — Bio::GFF::FastaReader
- #each — LRUHash
- #each_CDS — Bio::GFFbrowser::Digest::Parser
- #each_CDS_seq — Bio::GFFbrowser::Block::GffBlockParser
- #each_CDS_seq — Bio::GFFbrowser::Digest::Parser
- #each_exon — Bio::GFFbrowser::Digest::Parser
- #each_exon_seq — Bio::GFFbrowser::Block::GffBlockParser
- #each_exon_seq — Bio::GFFbrowser::Digest::Parser
- #each_gene — Bio::GFFbrowser::Digest::Parser
- #each_gene_seq — Bio::GFFbrowser::Block::GffBlockParser
- #each_gene_seq — Bio::GFFbrowser::Digest::Parser
- #each_item — Bio::GFFbrowser::Digest::InMemory
- #each_item — Bio::GFFbrowser::Digest::LruCache
- #each_item — Bio::GFFbrowser::Digest::NoCache
- #each_key — LRUHash
- #each_mRNA — Bio::GFFbrowser::Digest::Parser
- #each_mRNA_seq — Bio::GFFbrowser::Block::GffBlockParser
- #each_mRNA_seq — Bio::GFFbrowser::Digest::Parser
- #each_node — LRUHash
- #each_pair — LRUHash
- #each_rec — Bio::GFF::GFF3::FileIterator
- #each_seq — Bio::GFFbrowser::Block::GffBlockParser
- #each_sequence — Bio::GFF::GFF3::FileIterator
- #each_value — LRUHash
- #empty? — LRUHash
- #end — Bio::GFFbrowser::FastLineRecord
- #entry_id — Bio::GFFbrowser::FastaRecord
- #entry_id — Bio::GFFbrowser::FastLineRecord
- #error — Bio::GFFbrowser::Helpers::Logger
- #fasta_rec — Bio::GFF::FastaReader
- #feature — Bio::GFFbrowser::FastLineRecord
- #feature_type — Bio::GFFbrowser::FastLineRecord
- #fetch — LRUHash
- #fetch — Bio::GFFbrowser::Digest::LruCacheHelpers::LruRec
- #find_component — Bio::GFFbrowser::Helpers::Gff3Component
- #frame — Bio::GFFbrowser::FastLineRecord
- #front — LRUHash
- #get_attribute — Bio::GFFbrowser::FastLineRecord
- #has_key? — LRUHash
- #has_value? — LRUHash
- #id — Bio::GFFbrowser::FastLineRecord
- #include? — LRUHash
- #info — Bio::GFFbrowser::Helpers::Logger
- #inspect — LRUHash
- #intersection — Bio::GFFbrowser::Helpers::Section
- #key — LRUHash
- #key? — LRUHash
- #keys — LRUHash
- #log_sys_info — Bio::GFFbrowser::Helpers::Logger
- #max_size= — LRUHash
- #member? — LRUHash
- #normalize_max — LRUHash
- #parse — Bio::GFFbrowser::Block::GffBlockParser
- #parse — Bio::GFFbrowser::Digest::InMemory
- #parse — Bio::GFFbrowser::Digest::LruCache
- #parse — Bio::GFFbrowser::Digest::NoCache
- #parse — Bio::GFF::FastaReader
- #parse_attributes_fast — Bio::GFFbrowser::FastLineParser
- #parse_block — Bio::GFFbrowser::Block::GffBlockParser
- #parse_line_fast — Bio::GFFbrowser::FastLineParser
- #phase — Bio::GFFbrowser::FastLineRecord
- #put — Bio::GFFbrowser::FastaWriter
- #put_seq — Bio::GFFbrowser::FastaWriter
- #rassoc — LRUHash
- #read_fasta — Bio::GFFbrowser::Digest::Parser
- #remove_node — LRUHash
- #score — Bio::GFFbrowser::FastLineRecord
- #seqid — Bio::GFFbrowser::FastLineRecord
- #seqname — Bio::GFFbrowser::FastLineRecord
- #show_unrecognized_features — Bio::GFFbrowser::Digest::Parser
- #size — LRUHash
- #source — Bio::GFFbrowser::FastLineRecord
- #start — Bio::GFFbrowser::FastLineRecord
- #store — LRUHash
- #store_record — Bio::GFFbrowser::Digest::Parser
- #strand — Bio::GFFbrowser::FastLineRecord
- #to_s — Bio::GFFbrowser::FastaRecord
- #to_s — LRUHash
- #validate_cdss — Bio::GFFbrowser::Helpers::Validate
- #validate_mrnas — Bio::GFFbrowser::Helpers::Validate
- #validate_nonoverlapping — Bio::GFFbrowser::Digest::LruCacheHelpers::SeekLinkedRecs
- #validate_nonoverlapping — Bio::GFFbrowser::Digest::NoCacheHelpers::SeekLinkedRecs
- #validate_nonoverlapping — Bio::GFFbrowser::Helpers::LinkedRecs
- #validate_seqname — Bio::GFFbrowser::Digest::LruCacheHelpers::SeekLinkedRecs
- #validate_seqname — Bio::GFFbrowser::Digest::NoCacheHelpers::SeekLinkedRecs
- #validate_seqname — Bio::GFFbrowser::Helpers::LinkedRecs
- #validate_shared_parent — Bio::GFFbrowser::Digest::LruCacheHelpers::SeekLinkedRecs
- #validate_shared_parent — Bio::GFFbrowser::Digest::NoCacheHelpers::SeekLinkedRecs
- #validate_shared_parent — Bio::GFFbrowser::Helpers::LinkedRecs
- #value? — LRUHash
- #values — LRUHash
- #values_at — LRUHash
- #warn — Bio::GFFbrowser::Helpers::Logger