Table of Contents - bio-bigbio-0.1.6 Documentation
Pages
Classes and Modules
- Bio
- Bio::Big
- Bio::Big::Environment
- Bio::Big::FastaEmitter
- Bio::Big::FrameCodonHelpers
- Bio::Big::FrameCodonHelpers::CreateShortFrame
- Bio::Big::FrameCodonHelpers::FrameCodonSequence
- Bio::Big::FrameCodonHelpers::TrackSequenceTrait
- Bio::Big::OrfEmitter
- Bio::Big::PhylipReader
- Bio::Big::ShortFrameState
- Bio::Big::ShortReversedFrameState
- Bio::Big::TranslationAdapter
- BlastClust
- FastaIndex
- FastaPairedReader
- FastaPairedRecord
- FastaPairedWriter
- FastaReader
- FastaRecord
- FastaWriter
- Indexer
- Nucleotide
- Nucleotide::Translate
- Nucleotide::TranslationTable
- ORF
- ORFaminoacids
- ORFnucleotides
- ORFsequence
- PredictORF
Methods
- ::create_left — Bio::Big::FrameCodonHelpers::CreateShortFrame
- ::create_right — Bio::Big::FrameCodonHelpers::CreateShortFrame
- ::emit — FastaReader
- ::emit_fastarecord — FastaReader
- ::emit_seq — Bio::Big::PhylipReader
- ::new — BlastClust
- ::new — Bio::Big::FastaEmitter
- ::new — Bio::Big::FrameCodonHelpers::FrameCodonSequence
- ::new — Bio::Big::ShortFrameState
- ::new — Bio::Big::ShortReversedFrameState
- ::new — Bio::Big::OrfEmitter
- ::new — FastaPairedReader
- ::new — FastaPairedWriter
- ::new — FastaReader
- ::new — FastaRecord
- ::new — FastaPairedRecord
- ::new — FastaWriter
- ::new — ORFsequence
- ::new — ORFnucleotides
- ::new — ORF
- ::new — PredictORF
- ::new — Nucleotide::Translate
- ::pre_translate — Bio::Big::TranslationAdapter
- ::translate — Bio::Big::TranslationAdapter
- ::translation_table — Bio::Big::TranslationAdapter
- ::update_reversed_sequence_pos — Bio::Big::FrameCodonHelpers::TrackSequenceTrait
- ::update_sequence_pos — Bio::Big::FrameCodonHelpers::TrackSequenceTrait
- #<=> — ORF
- #[] — Bio::Big::FrameCodonHelpers::FrameCodonSequence
- #aa_6_frames — Nucleotide::Translate
- #aa_forward_frames — Nucleotide::Translate
- #close — FastaPairedWriter
- #close — FastaReader
- #close — FastaWriter
- #digest_tag — FastaReader
- #each — BlastClust
- #each — Bio::Big::FrameCodonHelpers::FrameCodonSequence
- #each — FastaReader
- #emit_forward — Bio::Big::OrfEmitter
- #emit_reverse — Bio::Big::OrfEmitter
- #emit_seq — Bio::Big::FastaEmitter
- #emit_seq — Bio::Big::OrfEmitter
- #first — FastaReader
- #fullseq — ORFnucleotides
- #get — FastaPairedReader
- #get — FastaReader
- #get_by_index — FastaReader
- #get_codon_orfs1 — Bio::Big::ShortFrameState
- #get_codon_orfs2 — Bio::Big::ShortFrameState
- #get_rec — FastaReader
- #get_startstop_orfs — Bio::Big::ShortFrameState
- #get_stopstop_orfs — Bio::Big::ShortFrameState
- #id — FastaPairedRecord
- #indexed? — FastaReader
- #indexer_get — Indexer
- #indexer_get_by_index — Indexer
- #indexer_set — Indexer
- #indexer_use — Indexer
- #longest_startstop — PredictORF
- #parse_each — FastaReader
- #rpos — Bio::Big::FrameCodonHelpers::FrameCodonSequence
- #seq — ORFnucleotides
- #shift — Bio::Big::FrameCodonHelpers::FrameCodonSequence
- #size — Bio::Big::FrameCodonHelpers::FrameCodonSequence
- #size — FastaReader
- #split — Bio::Big::ShortFrameState
- #startstop — PredictORF
- #stopstop — PredictORF
- #tag_digest — Bio::Big::FastaEmitter
- #to_fasta — FastaRecord
- #to_fastarec — ORF
- #to_s — ORFnucleotides
- #to_seq — Bio::Big::FrameCodonHelpers::FrameCodonSequence
- #write — FastaPairedWriter
- #write — FastaWriter