### Home Classes Methods

### In Files

- lib/bio/shell/core.rb

### Methods

- #check_marshal
- #close_history
- #closing_splash
- #config_color
- #config_echo
- #config_message
- #config_pager
- #config_show
- #config_splash
- #configure
- #create_flat_dir
- #create_real_dir
- #create_save_dir
- #create_save_dir_ask
- #find_flat_dir
- #load_config
- #load_config_file
- #load_history
- #load_history_file
- #load_object
- #load_object_file
- #load_plugin
- #load_plugin_dir
- #load_session
- #open_history
- #opening_splash
- #save_config
- #save_config_file
- #save_history
- #save_history_file
- #save_object
- #save_object_file
- #save_script
- #save_script_file
- #save_session
- #script
- #script_begin
- #script_end
- #splash_message
- #splash_message_action
- #splash_message_action_color
- #splash_message_color
- #store_history

### Included Modules

- Bio::Shell::Core

### Files

- KNOWN_ISSUES.rdoc
- README.rdoc
- README_DEV.rdoc
- RELEASE_NOTES.rdoc
- Changes-1.3.rdoc
- RELEASE_NOTES-1.4.0.rdoc
- RELEASE_NOTES-1.4.1.rdoc
- RELEASE_NOTES-1.4.2.rdoc

### Class/Module Index

Quicksearch

- Bio
- Bio::AAindex
- Bio::AAindex1
- Bio::AAindex2
- Bio::Abif
- Bio::Abif::DirectoryEntry
- Bio::Alignment
- Bio::Alignment::ArrayExtension
- Bio::Alignment::EnumerableExtension
- Bio::Alignment::FactoryTemplate
- Bio::Alignment::FactoryTemplate::FileInFileOut
- Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
- Bio::Alignment::FactoryTemplate::FileInStdoutOut
- Bio::Alignment::FactoryTemplate::Simple
- Bio::Alignment::FactoryTemplate::StdinInFileOut
- Bio::Alignment::FactoryTemplate::WrapInputStdin
- Bio::Alignment::FactoryTemplate::WrapInputTempfile
- Bio::Alignment::FactoryTemplate::WrapOutputStdout
- Bio::Alignment::FactoryTemplate::WrapOutputTempfile
- Bio::Alignment::GAP
- Bio::Alignment::HashExtension
- Bio::Alignment::MultiFastaFormat
- Bio::Alignment::OriginalAlignment
- Bio::Alignment::OriginalPrivate
- Bio::Alignment::Output
- Bio::Alignment::PropertyMethods
- Bio::Alignment::SequenceArray
- Bio::Alignment::SequenceHash
- Bio::Alignment::Site
- Bio::Alignment::SiteMethods
- Bio::AminoAcid
- Bio::AminoAcid::Data
- Bio::Blast
- Bio::Blast::Bl2seq
- Bio::Blast::Bl2seq::Report
- Bio::Blast::Bl2seq::Report::HSP
- Bio::Blast::Bl2seq::Report::Hit
- Bio::Blast::Bl2seq::Report::Iteration
- Bio::Blast::Default
- Bio::Blast::Default::Report
- Bio::Blast::Default::Report::HSP
- Bio::Blast::Default::Report::Hit
- Bio::Blast::Default::Report::Iteration
- Bio::Blast::Default::Report_TBlast
- Bio::Blast::Fastacmd
- Bio::Blast::NCBIOptions
- Bio::Blast::RPSBlast
- Bio::Blast::RPSBlast::RPSBlastSplitter
- Bio::Blast::RPSBlast::Report
- Bio::Blast::RPSBlast::Report::FLATFILE_SPLITTER
- Bio::Blast::RPSBlast::Report::Iteration
- Bio::Blast::Remote
- Bio::Blast::Remote::DDBJ
- Bio::Blast::Remote::DDBJ::Information
- Bio::Blast::Remote::Ddbj
- Bio::Blast::Remote::GenomeNet
- Bio::Blast::Remote::GenomeNet::Information
- Bio::Blast::Remote::Genomenet
- Bio::Blast::Remote::Information
- Bio::Blast::Report
- Bio::Blast::Report::BlastXmlSplitter
- Bio::Blast::Report::FLATFILE_SPLITTER
- Bio::Blast::Report::Hit
- Bio::Blast::Report::Hsp
- Bio::Blast::Report::Iteration
- Bio::Blast::Report_tab
- Bio::Blast::WU
- Bio::Blast::WU::Report
- Bio::Blast::WU::Report::HSP
- Bio::Blast::WU::Report::Hit
- Bio::Blast::WU::Report::Iteration
- Bio::Blast::WU::Report_TBlast
- Bio::Blat
- Bio::Blat::Report
- Bio::Blat::Report::Hit
- Bio::Blat::Report::SegmentPair
- Bio::Blat::Report::SeqDesc
- Bio::ClustalW
- Bio::ClustalW::Report
- Bio::CodonTable
- Bio::ColorScheme
- Bio::Command
- Bio::Command::Tmpdir
- Bio::Command::Tmpdir::Remover
- Bio::ContingencyTable
- Bio::DAS
- Bio::DAS::DNA
- Bio::DAS::DSN
- Bio::DAS::ENTRY_POINT
- Bio::DAS::FEATURE
- Bio::DAS::GFF
- Bio::DAS::GROUP
- Bio::DAS::LINK
- Bio::DAS::SEGMENT
- Bio::DAS::SEQUENCE
- Bio::DAS::TARGET
- Bio::DAS::TYPE
- Bio::DAS::TYPES
- Bio::DB
- Bio::DBGET
- Bio::DDBJ
- Bio::DDBJ::REST
- Bio::DDBJ::REST::Blast
- Bio::DDBJ::REST::ClustalW
- Bio::DDBJ::REST::DDBJ
- Bio::DDBJ::REST::Mafft
- Bio::DDBJ::REST::RequestManager
- Bio::DDBJ::REST::WABItemplate
- Bio::DDBJ::XML
- Bio::DDBJ::XML::Blast
- Bio::DDBJ::XML::ClustalW
- Bio::DDBJ::XML::DDBJ
- Bio::DDBJ::XML::Fasta
- Bio::DDBJ::XML::GetEntry
- Bio::DDBJ::XML::Gib
- Bio::DDBJ::XML::Gtop
- Bio::DDBJ::XML::PML
- Bio::DDBJ::XML::RequestManager
- Bio::DDBJ::XML::RequestManager::REST
- Bio::DDBJ::XML::SRS
- Bio::DDBJ::XML::TxSearch
- Bio::EBI
- Bio::EBI::SOAP
- Bio::EBI::SOAP::Citation
- Bio::EBI::SOAP::ClustalW
- Bio::EBI::SOAP::Dbfetch
- Bio::EBI::SOAP::Emboss
- Bio::EBI::SOAP::Fasta
- Bio::EBI::SOAP::InterProScan
- Bio::EBI::SOAP::MPsrch
- Bio::EBI::SOAP::MSD
- Bio::EBI::SOAP::Muscle
- Bio::EBI::SOAP::Ontology
- Bio::EBI::SOAP::ScanPS
- Bio::EBI::SOAP::TCoffee
- Bio::EBI::SOAP::WUBlast
- Bio::EMBL
- Bio::EMBLDB
- Bio::EMBLDB::Common
- Bio::EMBOSS
- Bio::Ensembl
- Bio::Ensembl::Base
- Bio::Ensembl::Human
- Bio::Ensembl::Mouse
- Bio::FANTOM
- Bio::FANTOM::MaXML
- Bio::FANTOM::MaXML::Annotation
- Bio::FANTOM::MaXML::Annotation::DataSrc
- Bio::FANTOM::MaXML::Annotations
- Bio::FANTOM::MaXML::Cluster
- Bio::FANTOM::MaXML::Sequence
- Bio::FANTOM::MaXML::Sequences
- Bio::Fasta
- Bio::Fasta::Report
- Bio::Fasta::Report::FLATFILE_SPLITTER
- Bio::Fasta::Report::FastaFormat10Splitter
- Bio::Fasta::Report::Hit
- Bio::Fasta::Report::Hit::Query
- Bio::Fasta::Report::Hit::Target
- Bio::Fasta::Report::Program
- Bio::FastaDefline
- Bio::FastaFormat
- Bio::FastaNumericFormat
- Bio::Fastq
- Bio::Fastq::Error
- Bio::Fastq::Error::Diff_ids
- Bio::Fastq::Error::Long_qual
- Bio::Fastq::Error::No_atmark
- Bio::Fastq::Error::No_ids
- Bio::Fastq::Error::No_qual
- Bio::Fastq::Error::No_seq
- Bio::Fastq::Error::Qual_char
- Bio::Fastq::Error::Qual_range
- Bio::Fastq::Error::Seq_char
- Bio::Fastq::Error::Short_qual
- Bio::Fastq::Error::Skipped_unformatted_lines
- Bio::Fastq::FormatData
- Bio::Fastq::FormatData::FASTQ_ILLUMINA
- Bio::Fastq::FormatData::FASTQ_SANGER
- Bio::Fastq::FormatData::FASTQ_SOLEXA
- Bio::Feature
- Bio::Feature::Qualifier
- Bio::Features
- Bio::Fetch
- Bio::FlatFile
- Bio::FlatFile::AutoDetect
- Bio::FlatFile::AutoDetect::RuleDebug
- Bio::FlatFile::AutoDetect::RuleProc
- Bio::FlatFile::AutoDetect::RuleRegexp
- Bio::FlatFile::AutoDetect::RuleRegexp2
- Bio::FlatFile::AutoDetect::RuleSpecial
- Bio::FlatFile::AutoDetect::RuleTemplate
- Bio::FlatFile::AutoDetect::RulesArray
- Bio::FlatFile::BufferedInputStream
- Bio::FlatFile::Splitter
- Bio::FlatFile::Splitter::Default
- Bio::FlatFile::Splitter::LineOriented
- Bio::FlatFile::Splitter::Template
- Bio::FlatFile::UnknownDataFormatError
- Bio::FlatFileIndex
- Bio::FlatFileIndex::BDB_1
- Bio::FlatFileIndex::BDB_1::BDBMappingFile
- Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
- Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
- Bio::FlatFileIndex::BDBdefault
- Bio::FlatFileIndex::BDBwrapper
- Bio::FlatFileIndex::DEBUG
- Bio::FlatFileIndex::DataBank
- Bio::FlatFileIndex::FileID
- Bio::FlatFileIndex::FileIDs
- Bio::FlatFileIndex::Flat_1
- Bio::FlatFileIndex::Flat_1::FlatMappingFile
- Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
- Bio::FlatFileIndex::Flat_1::Record
- Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
- Bio::FlatFileIndex::Indexer
- Bio::FlatFileIndex::Indexer::NameSpace
- Bio::FlatFileIndex::Indexer::NameSpaces
- Bio::FlatFileIndex::Indexer::Parser
- Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
- Bio::FlatFileIndex::Indexer::Parser::EMBLParser
- Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
- Bio::FlatFileIndex::Indexer::Parser::GenBankParser
- Bio::FlatFileIndex::Indexer::Parser::GenPeptParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLClusterParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLSequenceParser
- Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
- Bio::FlatFileIndex::Indexer::Parser::SPTRParser
- Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- Bio::FlatFileIndex::NameSpaces
- Bio::FlatFileIndex::Results
- Bio::FlatFileIndex::Template
- Bio::FlatFileIndex::Template::NameSpace
- Bio::GCG
- Bio::GCG::Msf
- Bio::GCG::Seq
- Bio::GFF
- Bio::GFF::GFF2
- Bio::GFF::GFF2::Escape
- Bio::GFF::GFF2::MetaData
- Bio::GFF::GFF2::Record
- Bio::GFF::GFF2::Record::Value
- Bio::GFF::GFF3
- Bio::GFF::GFF3::Escape
- Bio::GFF::GFF3::Record
- Bio::GFF::GFF3::Record::Gap
- Bio::GFF::GFF3::Record::Gap::Code
- Bio::GFF::GFF3::Record::Target
- Bio::GFF::GFF3::RecordBoundary
- Bio::GFF::GFF3::SequenceRegion
- Bio::GFF::Record
- Bio::GO
- Bio::GO::External2go
- Bio::GO::GeneAssociation
- Bio::GO::Ontology
- Bio::GenBank
- Bio::GenBank::Locus
- Bio::GenPept
- Bio::GenPept::Locus
- Bio::Genscan
- Bio::Genscan::Report
- Bio::Genscan::Report::Exon
- Bio::Genscan::Report::Gene
- Bio::HGC
- Bio::HGC::HiGet
- Bio::HMMER
- Bio::HMMER::Report
- Bio::HMMER::Report::Hit
- Bio::HMMER::Report::Hsp
- Bio::Hinv
- Bio::Hinv::Acc2hit
- Bio::Hinv::Common
- Bio::Hinv::Hit2acc
- Bio::Hinv::HitCnt
- Bio::Hinv::HitDefinition
- Bio::Hinv::HitPubmedId
- Bio::Hinv::HitXML
- Bio::Hinv::Hix2hit
- Bio::Hinv::HixCnt
- Bio::Hinv::HixRepresent
- Bio::Hinv::HixXML
- Bio::Hinv::IdSearch
- Bio::Hinv::KeywordSearch
- Bio::Iprscan
- Bio::Iprscan::Report
- Bio::Iprscan::Report::Match
- Bio::KEGG
- Bio::KEGG::API
- Bio::KEGG::BRITE
- Bio::KEGG::COMPOUND
- Bio::KEGG::Common
- Bio::KEGG::Common::DblinksAsHash
- Bio::KEGG::Common::GenesAsHash
- Bio::KEGG::Common::ModulesAsHash
- Bio::KEGG::Common::OrthologsAsHash
- Bio::KEGG::Common::PathwaysAsHash
- Bio::KEGG::Common::References
- Bio::KEGG::Common::StringsAsHash
- Bio::KEGG::DRUG
- Bio::KEGG::ENZYME
- Bio::KEGG::EXPRESSION
- Bio::KEGG::GENES
- Bio::KEGG::GENOME
- Bio::KEGG::GLYCAN
- Bio::KEGG::KGML
- Bio::KEGG::KGML::Entry
- Bio::KEGG::KGML::Graphics
- Bio::KEGG::KGML::Product
- Bio::KEGG::KGML::Reaction
- Bio::KEGG::KGML::Relation
- Bio::KEGG::KGML::Substrate
- Bio::KEGG::KGML::SubstrateProduct
- Bio::KEGG::Keggtab
- Bio::KEGG::Keggtab::DB
- Bio::KEGG::MODULE
- Bio::KEGG::ORTHOLOGY
- Bio::KEGG::PATHWAY
- Bio::KEGG::REACTION
- Bio::KEGG::Taxonomy
- Bio::KEGGDB
- Bio::LITDB
- Bio::Lasergene
- Bio::Location
- Bio::Locations
- Bio::MAFFT
- Bio::MAFFT::Report
- Bio::MEDLINE
- Bio::Map
- Bio::Map::ActsLikeMap
- Bio::Map::ActsLikeMarker
- Bio::Map::Mapping
- Bio::Map::Marker
- Bio::Map::SimpleMap
- Bio::Meme
- Bio::Meme::Mast
- Bio::Meme::Mast::Report
- Bio::Meme::Motif
- Bio::Muscle
- Bio::Muscle::DEFAULT_PARSER
- Bio::NBRF
- Bio::NCBI
- Bio::NCBI::REST
- Bio::NCBI::REST::EFetch
- Bio::NCBI::REST::EFetch::Methods
- Bio::NCBI::REST::ESearch
- Bio::NCBI::REST::ESearch::Methods
- Bio::NCBI::SOAP
- Bio::NCBI::SOAP::EFetch
- Bio::NCBI::SOAP::EFetchLite
- Bio::NCBI::SOAP::EUtils
- Bio::NCBI::SOAP::EUtilsLite
- Bio::NCBIDB
- Bio::NCBIDB::Common
- Bio::Newick
- Bio::Newick::ParseError
- Bio::Nexus
- Bio::Nexus::CharactersBlock
- Bio::Nexus::DataBlock
- Bio::Nexus::DistancesBlock
- Bio::Nexus::GenericBlock
- Bio::Nexus::NexusMatrix
- Bio::Nexus::NexusMatrix::NexusMatrixError
- Bio::Nexus::NexusParseError
- Bio::Nexus::TaxaBlock
- Bio::Nexus::TreesBlock
- Bio::Nexus::Util
- Bio::NucleicAcid
- Bio::NucleicAcid::Data
- Bio::PAML
- Bio::PAML::Baseml
- Bio::PAML::Baseml::Report
- Bio::PAML::Codeml
- Bio::PAML::Codeml::Model
- Bio::PAML::Codeml::PositiveSite
- Bio::PAML::Codeml::PositiveSites
- Bio::PAML::Codeml::Rates
- Bio::PAML::Codeml::Report
- Bio::PAML::Codeml::ReportError
- Bio::PAML::Codeml::ReportSingle
- Bio::PAML::Common
- Bio::PAML::Common::Report
- Bio::PAML::Yn00
- Bio::PAML::Yn00::Report
- Bio::PDB
- Bio::PDB::AtomFinder
- Bio::PDB::Chain
- Bio::PDB::ChainFinder
- Bio::PDB::ChemicalComponent
- Bio::PDB::ChemicalComponent::Record
- Bio::PDB::Coordinate
- Bio::PDB::DataType
- Bio::PDB::DataType::ConstLikeMethod
- Bio::PDB::DataType::Pdb_AChar
- Bio::PDB::DataType::Pdb_Atom
- Bio::PDB::DataType::Pdb_Character
- Bio::PDB::DataType::Pdb_Date
- Bio::PDB::DataType::Pdb_IDcode
- Bio::PDB::DataType::Pdb_Integer
- Bio::PDB::DataType::Pdb_LString
- Bio::PDB::DataType::Pdb_List
- Bio::PDB::DataType::Pdb_Real
- Bio::PDB::DataType::Pdb_Residue_name
- Bio::PDB::DataType::Pdb_SList
- Bio::PDB::DataType::Pdb_Specification_list
- Bio::PDB::DataType::Pdb_String
- Bio::PDB::DataType::Pdb_StringRJ
- Bio::PDB::DataType::Pdb_SymOP
- Bio::PDB::HetatmFinder
- Bio::PDB::Heterogen
- Bio::PDB::HeterogenFinder
- Bio::PDB::Model
- Bio::PDB::ModelFinder
- Bio::PDB::Record
- Bio::PDB::Record::ANISOU
- Bio::PDB::Record::ATOM
- Bio::PDB::Record::HETATM
- Bio::PDB::Record::Jrnl
- Bio::PDB::Record::Remark1
- Bio::PDB::Record::Remark2
- Bio::PDB::Residue
- Bio::PDB::ResidueFinder
- Bio::PDB::Utils
- Bio::PROSITE
- Bio::PSORT
- Bio::PSORT::CGIDriver
- Bio::PSORT::IPSORT
- Bio::PSORT::PSORT1
- Bio::PSORT::PSORT1::Remote
- Bio::PSORT::PSORT1::Report
- Bio::PSORT::PSORT2
- Bio::PSORT::PSORT2::Remote
- Bio::PSORT::PSORT2::Report
- Bio::PSORT::PSORTB
- Bio::PSORT::WoLF_PSORT
- Bio::PTS1
- Bio::PTS1::Report
- Bio::Pathway
- Bio::Phylip
- Bio::Phylip::DistanceMatrix
- Bio::Phylip::PhylipFormat
- Bio::PhyloXML
- Bio::PhyloXML::Accession
- Bio::PhyloXML::Annotation
- Bio::PhyloXML::BinaryCharacters
- Bio::PhyloXML::BranchColor
- Bio::PhyloXML::CladeRelation
- Bio::PhyloXML::Confidence
- Bio::PhyloXML::Date
- Bio::PhyloXML::Distribution
- Bio::PhyloXML::DomainArchitecture
- Bio::PhyloXML::Events
- Bio::PhyloXML::Id
- Bio::PhyloXML::Node
- Bio::PhyloXML::Other
- Bio::PhyloXML::Parser
- Bio::PhyloXML::Point
- Bio::PhyloXML::Polygon
- Bio::PhyloXML::Property
- Bio::PhyloXML::ProteinDomain
- Bio::PhyloXML::Reference
- Bio::PhyloXML::Sequence
- Bio::PhyloXML::SequenceRelation
- Bio::PhyloXML::Taxonomy
- Bio::PhyloXML::Tree
- Bio::PhyloXML::Uri
- Bio::PhyloXML::Writer
- Bio::Probcons
- Bio::PubMed
- Bio::REBASE
- Bio::RefSeq
- Bio::Reference
- Bio::References
- Bio::Registry
- Bio::Registry::DB
- Bio::RestrictionEnzyme
- Bio::RestrictionEnzyme::Analysis
- Bio::RestrictionEnzyme::CutSymbol
- Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
- Bio::RestrictionEnzyme::DenseIntArray
- Bio::RestrictionEnzyme::DoubleStranded
- Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::CutLocations
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::EnzymeAction
- Bio::RestrictionEnzyme::Fragments
- Bio::RestrictionEnzyme::Range
- Bio::RestrictionEnzyme::Range::CutRange
- Bio::RestrictionEnzyme::Range::CutRanges
- Bio::RestrictionEnzyme::Range::HorizontalCutRange
- Bio::RestrictionEnzyme::Range::SequenceRange
- Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
- Bio::RestrictionEnzyme::Range::VerticalCutRange
- Bio::RestrictionEnzyme::SingleStrand
- Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::SingleStrandComplement
- Bio::RestrictionEnzyme::SortedNumArray
- Bio::RestrictionEnzyme::StringFormatting
- Bio::SOAPWSDL
- Bio::SOFT
- Bio::SOSUI
- Bio::SOSUI::Report
- Bio::SOSUI::Report::TMH
- Bio::SPTR
- Bio::SQL
- Bio::SQL::Biodatabase
- Bio::SQL::Bioentry
- Bio::SQL::BioentryDbxref
- Bio::SQL::BioentryPath
- Bio::SQL::BioentryQualifierValue
- Bio::SQL::BioentryReference
- Bio::SQL::BioentryRelationship
- Bio::SQL::Biosequence
- Bio::SQL::Comment
- Bio::SQL::Dbxref
- Bio::SQL::DbxrefQualifierValue
- Bio::SQL::DummyBase
- Bio::SQL::Location
- Bio::SQL::LocationQualifierValue
- Bio::SQL::Ontology
- Bio::SQL::Reference
- Bio::SQL::Seqfeature
- Bio::SQL::SeqfeatureDbxref
- Bio::SQL::SeqfeaturePath
- Bio::SQL::SeqfeatureQualifierValue
- Bio::SQL::SeqfeatureRelationship
- Bio::SQL::Sequence
- Bio::SQL::Taxon
- Bio::SQL::TaxonName
- Bio::SQL::Term
- Bio::SQL::TermDbxref
- Bio::SQL::TermPath
- Bio::SQL::TermRelationship
- Bio::SQL::TermRelationshipTerm
- Bio::SQL::TermSynonym
- Bio::SangerChromatogram
- Bio::Scf
- Bio::Sequence
- Bio::Sequence::AA
- Bio::Sequence::Adapter
- Bio::Sequence::Adapter::BioSQL
- Bio::Sequence::Adapter::EMBL
- Bio::Sequence::Adapter::FastaFormat
- Bio::Sequence::Adapter::FastaNumericFormat
- Bio::Sequence::Adapter::Fastq
- Bio::Sequence::Adapter::GenBank
- Bio::Sequence::Adapter::SangerChromatogram
- Bio::Sequence::Common
- Bio::Sequence::DBLink
- Bio::Sequence::Format
- Bio::Sequence::Format::AminoFormatter
- Bio::Sequence::Format::Formatter
- Bio::Sequence::Format::Formatter::Fasta
- Bio::Sequence::Format::Formatter::Fasta_ncbi
- Bio::Sequence::Format::Formatter::Fasta_numeric
- Bio::Sequence::Format::Formatter::Fastq
- Bio::Sequence::Format::Formatter::Fastq_illumina
- Bio::Sequence::Format::Formatter::Fastq_sanger
- Bio::Sequence::Format::Formatter::Fastq_solexa
- Bio::Sequence::Format::Formatter::Qual
- Bio::Sequence::Format::Formatter::Raw
- Bio::Sequence::Format::FormatterBase
- Bio::Sequence::Format::INSDFeatureHelper
- Bio::Sequence::Format::NucFormatter
- Bio::Sequence::Format::NucFormatter::Embl
- Bio::Sequence::Format::NucFormatter::Genbank
- Bio::Sequence::NA
- Bio::Sequence::NA::MidiTrack
- Bio::Sequence::QualityScore
- Bio::Sequence::QualityScore::Converter
- Bio::Sequence::QualityScore::Phred
- Bio::Sequence::QualityScore::Solexa
- Bio::Sequence::SequenceMasker
- Bio::Shell
- Bio::Shell::ColoredCodonTable
- Bio::Shell::Core
- Bio::Shell::Demo
- Bio::Shell::Ghost
- Bio::Shell::Irb
- Bio::Shell::Private
- Bio::Shell::Script
- Bio::Shell::Setup
- Bio::Shell::Web
- Bio::Shell::Web::Results
- Bio::SiRNA
- Bio::SiRNA::Pair
- Bio::SiRNA::ShRNA
- Bio::Sim4
- Bio::Sim4::Report
- Bio::Sim4::Report::Hit
- Bio::Sim4::Report::Segment
- Bio::Sim4::Report::SegmentPair
- Bio::Sim4::Report::SeqDesc
- Bio::Spidey
- Bio::Spidey::Report
- Bio::Spidey::Report::Hit
- Bio::Spidey::Report::Segment
- Bio::Spidey::Report::SegmentPair
- Bio::Spidey::Report::SeqDesc
- Bio::SwissProt
- Bio::TMHMM
- Bio::TMHMM::Report
- Bio::TMHMM::TMH
- Bio::TRANSFAC
- Bio::TRANSFAC::CELL
- Bio::TRANSFAC::CLASS
- Bio::TRANSFAC::FACTOR
- Bio::TRANSFAC::GENE
- Bio::TRANSFAC::MATRIX
- Bio::TRANSFAC::SITE
- Bio::TargetP
- Bio::TargetP::Report
- Bio::Taxonomy
- Bio::Tcoffee
- Bio::Tcoffee::DEFAULT_PARSER
- Bio::TogoWS
- Bio::TogoWS::AccessWait
- Bio::TogoWS::REST
- Bio::TrEMBL
- Bio::Tree
- Bio::Tree::Edge
- Bio::Tree::NoPathError
- Bio::Tree::Node
- Bio::UniProt
- BiorubyController
- BiorubyGenerator
- BiorubyHelper
- Hash
- Object
- String

No matching classes.

# Bio::Shell::Ghost

### Attributes

cache[RW]

A hash to store temporal (per session) configurations

config[RW]

A hash to store persistent configurations

### Public Instance Methods

check_marshal() click to toggle source

object

    # File lib/bio/shell/core.rb, line 299
    def check_marshal
      if @config[:marshal] and @config[:marshal] != MARSHAL
        raise "Marshal version mismatch"
      end
    end

close_history() click to toggle source

    # File lib/bio/shell/core.rb, line 382
    def close_history
      if @cache[:histfile]
        STDERR.print "Saving history (#{history_file}) ... "
        @cache[:histfile].close
        STDERR.puts "done"
      end
    end

closing_splash() click to toggle source

    # File lib/bio/shell/core.rb, line 566
    def closing_splash
      STDERR.puts
      STDERR.puts
      if @config[:color]
        STDERR.print splash_message_color
      else
        STDERR.print splash_message
      end
      STDERR.puts
      STDERR.puts
    end

config_color() click to toggle source

    # File lib/bio/shell/core.rb, line 251
    def config_color
      bind = Bio::Shell.cache[:binding]
      flag = ! @config[:color]
      @config[:color] = flag
      if flag
        IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR
        eval("conf.prompt_mode = :BIORUBY_COLOR", bind)
      else
        IRB.conf[:PROMPT_MODE] = :BIORUBY
        eval("conf.prompt_mode = :BIORUBY", bind)
      end
    end

config_echo() click to toggle source

    # File lib/bio/shell/core.rb, line 243
    def config_echo
      bind = Bio::Shell.cache[:binding]
      flag = ! @config[:echo]
      @config[:echo] = IRB.conf[:ECHO] = flag
      eval("conf.echo = #{flag}", bind)
      STDERR.puts "Echo #{flag ? 'on' : 'off'}"
    end

config_message(str = nil) click to toggle source

    # File lib/bio/shell/core.rb, line 275
    def config_message(str = nil)
      str ||= MESSAGE
      @config[:message] = str
      opening_splash
    end

config_pager(cmd = nil) click to toggle source

    # File lib/bio/shell/core.rb, line 264
    def config_pager(cmd = nil)
      @config[:pager] = cmd
    end

config_show() click to toggle source

    # File lib/bio/shell/core.rb, line 237
    def config_show
      @config.each do |k, v|
        STDERR.puts "#{k}\t= #{v.inspect}"
      end
    end

config_splash() click to toggle source

    # File lib/bio/shell/core.rb, line 268
    def config_splash
      flag = ! @config[:splash]
      @config[:splash] = flag
      STDERR.puts "Splash #{flag ? 'on' : 'off'}"
      opening_splash
    end

configure(savedir) click to toggle source

save/restore the environment

    # File lib/bio/shell/core.rb, line 115
    def configure(savedir)
      @config = {}
      @cache  = {
        :savedir => savedir,
        :workdir => Dir.pwd,
      }
      create_save_dir
      load_config
      load_plugin
    end

create_flat_dir(dbname) click to toggle source

bioflat

    # File lib/bio/shell/core.rb, line 188
    def create_flat_dir(dbname)
      dir = File.join(bioflat_dir, dbname.to_s.strip)
      unless File.directory?(dir)
        FileUtils.makedirs(dir)
      end
      return dir
    end

create_real_dir(dir) click to toggle source

    # File lib/bio/shell/core.rb, line 174
    def create_real_dir(dir)
      unless File.directory?(dir)
        begin
          STDERR.print "Creating directory (#{dir}) ... "
          FileUtils.makedirs(dir)
          STDERR.puts "done"
        rescue
          warn "Error: Failed to create directory (#{dir}) : #{$!}"
        end
      end
    end

create_save_dir() click to toggle source

directories

    # File lib/bio/shell/core.rb, line 150
    def create_save_dir
      create_real_dir(session_dir)
      create_real_dir(plugin_dir)
      create_real_dir(data_dir)
    end

create_save_dir_ask() click to toggle source

    # File lib/bio/shell/core.rb, line 156
    def create_save_dir_ask
      if File.directory?(session_dir)
        @cache[:save] = true
      end
      unless @cache[:save]
        if ask_yes_or_no("Save session in '#{@cache[:workdir]}' directory? [y/n] ")
          create_real_dir(session_dir)
          create_real_dir(plugin_dir)
          create_real_dir(data_dir)
          create_real_dir(bioflat_dir)
          @cache[:save] = true
        else
          @cache[:save] = false
        end
      end
      return @cache[:save]
    end

find_flat_dir(dbname) click to toggle source

    # File lib/bio/shell/core.rb, line 196
    def find_flat_dir(dbname)
      dir = File.join(bioflat_dir, dbname.to_s.strip)
      if File.exists?(dir)
        return dir
      else
        return nil
      end
    end

load_config() click to toggle source

config

    # File lib/bio/shell/core.rb, line 207
    def load_config
      load_config_file(config_file)
    end

load_config_file(file) click to toggle source

    # File lib/bio/shell/core.rb, line 211
    def load_config_file(file)
      if File.exists?(file)
        STDERR.print "Loading config (#{file}) ... "
        if hash = YAML.load(File.read(file))
          @config.update(hash)
        end
        STDERR.puts "done"
      end
    end

load_history() click to toggle source

    # File lib/bio/shell/core.rb, line 390
    def load_history
      if @cache[:readline]
        load_history_file(history_file)
      end
    end

load_history_file(file) click to toggle source

    # File lib/bio/shell/core.rb, line 396
    def load_history_file(file)
      if File.exists?(file)
        STDERR.print "Loading history (#{file}) ... "
        File.open(file).each do |line|
          unless line[/^# /]
            Readline::HISTORY.push line.chomp
          end
        end
        STDERR.puts "done"
      end
    end

load_object() click to toggle source

    # File lib/bio/shell/core.rb, line 305
    def load_object
      begin
        check_marshal
        load_object_file(object_file)
      rescue
        warn "Error: Load aborted : #{$!}"
      end
    end

load_object_file(file) click to toggle source

    # File lib/bio/shell/core.rb, line 314
    def load_object_file(file)
      if File.exists?(file)
        STDERR.print "Loading object (#{file}) ... "
        begin
          bind = Bio::Shell.cache[:binding]
          hash = Marshal.load(File.read(file))
          hash.each do |k, v|
            begin
              Thread.current[:restore_value] = v
              eval("#{k} = Thread.current[:restore_value]", bind)
            rescue
              STDERR.puts "Warning: object '#{k}' couldn't be loaded : #{$!}"
            end
          end
        rescue
          warn "Error: Failed to load (#{file}) : #{$!}"
        end
        STDERR.puts "done"
      end
    end

load_plugin() click to toggle source

plugin

    # File lib/bio/shell/core.rb, line 283
    def load_plugin
      load_plugin_dir(plugin_dir)
    end

load_plugin_dir(dir) click to toggle source

    # File lib/bio/shell/core.rb, line 287
    def load_plugin_dir(dir)
      if File.directory?(dir)
        Dir.glob("#{dir}/*.rb").sort.each do |file|
          STDERR.print "Loading plugin (#{file}) ... "
          load file
          STDERR.puts "done"
        end
      end
    end

load_session() click to toggle source

    # File lib/bio/shell/core.rb, line 126
    def load_session
      load_object
      unless @cache[:mode] == :script
        load_history
        opening_splash
        open_history
      end
    end

open_history() click to toggle source

history

    # File lib/bio/shell/core.rb, line 372
    def open_history
      @cache[:histfile] = File.open(history_file, "a")
      @cache[:histfile].sync = true
    end

opening_splash() click to toggle source

    # File lib/bio/shell/core.rb, line 544
    def opening_splash
      STDERR.puts
      if @config[:splash]
        if @config[:color]
          splash_message_action_color
        else
          splash_message_action
        end
      end
      if @config[:color]
        STDERR.print splash_message_color
      else
        STDERR.print splash_message
      end
      STDERR.puts
      STDERR.puts
      STDERR.print "  Version : BioRuby #{Bio::BIORUBY_VERSION_ID}"
      STDERR.print " / Ruby #{RUBY_VERSION}"
      STDERR.puts
      STDERR.puts
    end

save_config() click to toggle source

    # File lib/bio/shell/core.rb, line 221
    def save_config
      save_config_file(config_file)
    end

save_config_file(file) click to toggle source

    # File lib/bio/shell/core.rb, line 225
    def save_config_file(file)
      begin
        STDERR.print "Saving config (#{file}) ... "
        File.open(file, "w") do |f|
          f.puts @config.to_yaml
        end
        STDERR.puts "done"
      rescue
        warn "Error: Failed to save (#{file}) : #{$!}"
      end
    end

save_history() click to toggle source

not used (use open_history/close_history instead)

    # File lib/bio/shell/core.rb, line 409
    def save_history
      if @cache[:readline]
        save_history_file(history_file)
      end
    end

save_history_file(file) click to toggle source

    # File lib/bio/shell/core.rb, line 415
    def save_history_file(file)
      begin
        STDERR.print "Saving history (#{file}) ... "
        File.open(file, "w") do |f|
          f.puts Readline::HISTORY.to_a
        end
        STDERR.puts "done"
      rescue
        warn "Error: Failed to save (#{file}) : #{$!}"
      end
    end

save_object() click to toggle source

    # File lib/bio/shell/core.rb, line 335
    def save_object
      save_object_file(object_file)
    end

save_object_file(file) click to toggle source

    # File lib/bio/shell/core.rb, line 339
    def save_object_file(file)
      begin
        STDERR.print "Saving object (#{file}) ... "
        File.rename(file, "#{file}.old") if File.exist?(file)
        File.open(file, "w") do |f|
          bind = Bio::Shell.cache[:binding]
          list = eval("local_variables", bind)
          list.collect! { |x| x.to_s }
          list -= ["_"]
          hash = {}
          list.each do |elem|
            value = eval(elem, bind)
            if value
              begin
                Marshal.dump(value)
                hash[elem] = value
              rescue
                # value could not be dumped.
              end
            end
          end
          Marshal.dump(hash, f)
          @config[:marshal] = MARSHAL
        end
        STDERR.puts "done"
      rescue
        File.rename("#{file}.old", file) if File.exist?("#{file}.old")
        warn "Error: Failed to save (#{file}) : #{$!}"
      end
    end

save_script() click to toggle source

    # File lib/bio/shell/core.rb, line 460
    def save_script
      if @script_begin and @script_end and @script_begin <= @script_end
        if File.exists?(script_file)
          message = "Overwrite script file (#{script_file})? [y/n] "
        else
          message = "Save script file (#{script_file})? [y/n] "
        end
        if ask_yes_or_no(message)
          save_script_file(script_file)
        else
          STDERR.puts " ... save aborted."
        end
      elsif @script_begin and @script_end and @script_begin - @script_end == 1
        STDERR.puts " ... script aborted."
      else
        STDERR.puts "Error: Script range #{@script_begin}..#{@script_end} is invalid"
      end
    end

save_script_file(file) click to toggle source

    # File lib/bio/shell/core.rb, line 479
    def save_script_file(file)
      begin
        STDERR.print "Saving script (#{file}) ... "
        File.open(file, "w") do |f|
          f.puts "#!/usr/bin/env bioruby"
          f.puts
          f.puts Readline::HISTORY.to_a[@script_begin..@script_end]
          f.puts
        end
        STDERR.puts "done"
      rescue
        @script_begin = nil
        warn "Error: Failed to save (#{file}) : #{$!}"
      end
    end

save_session() click to toggle source

    # File lib/bio/shell/core.rb, line 135
    def save_session
      unless @cache[:mode] == :script
        closing_splash
      end
      if create_save_dir_ask
        #save_history     # changed to use our own...
        close_history
        save_object
        save_config
      end
      #STDERR.puts "Leaving directory '#{@cache[:workdir]}'"
    end

script(mode = nil) click to toggle source

script

    # File lib/bio/shell/core.rb, line 429
    def script(mode = nil)
      case mode
      when :begin, "begin", :start, "start"
        @cache[:script] = true
        script_begin
      when :end, "end", :stop, "stop"
        @cache[:script] = false
        script_end
        save_script
      else
        if @cache[:script]
          @cache[:script] = false
          script_end
          save_script
        else
          @cache[:script] = true
          script_begin
        end
      end
    end

script_begin() click to toggle source

    # File lib/bio/shell/core.rb, line 450
    def script_begin
      STDERR.puts "-- 8< -- 8< -- 8< --  Script  -- 8< -- 8< -- 8< --"
      @script_begin = Readline::HISTORY.size
    end

script_end() click to toggle source

    # File lib/bio/shell/core.rb, line 455
    def script_end
      STDERR.puts "-- >8 -- >8 -- >8 --  Script  -- >8 -- >8 -- >8 --"
      @script_end = Readline::HISTORY.size - 2
    end

splash_message() click to toggle source

splash

    # File lib/bio/shell/core.rb, line 497
    def splash_message
      @config[:message] ||= MESSAGE
      @config[:message].to_s.split(//).join(" ")
    end

splash_message_action(message = nil) click to toggle source

    # File lib/bio/shell/core.rb, line 509
    def splash_message_action(message = nil)
      s = message || splash_message
      l = s.length
      x = " "
      0.step(l,2) do |i|
        l1 = l-i;  l2 = l1/2;  l4 = l2/2
        STDERR.print "#{s[0,i]}#{x*l1}#{s[i,1]}\r"
        sleep(0.001)
        STDERR.print "#{s[0,i]}#{x*l2}#{s[i,1]}#{x*(l1-l2)}\r"
        sleep(0.002)
        STDERR.print "#{s[0,i]}#{x*l4}#{s[i,1]}#{x*(l2-l4)}\r"
        sleep(0.004)
        STDERR.print "#{s[0,i+1]}#{x*l4}\r"
        sleep(0.008)
      end
    end

splash_message_action_color(message = nil) click to toggle source

    # File lib/bio/shell/core.rb, line 526
    def splash_message_action_color(message = nil)
      s = message || splash_message
      l = s.length
      c = colors
      x = " "
      0.step(l,2) do |i|
        l1 = l-i;  l2 = l1/2;  l4 = l2/2
        STDERR.print "#{c[:n]}#{s[0,i]}#{x*l1}#{c[:y]}#{s[i,1]}\r"
        sleep(0.001)
        STDERR.print "#{c[:n]}#{s[0,i]}#{x*l2}#{c[:g]}#{s[i,1]}#{x*(l1-l2)}\r"
        sleep(0.002)
        STDERR.print "#{c[:n]}#{s[0,i]}#{x*l4}#{c[:r]}#{s[i,1]}#{x*(l2-l4)}\r"
        sleep(0.004)
        STDERR.print "#{c[:n]}#{s[0,i+1]}#{x*l4}\r"
        sleep(0.008)
      end
    end

splash_message_color() click to toggle source

    # File lib/bio/shell/core.rb, line 502
    def splash_message_color
      str = splash_message
      ruby = colors[:ruby]
      none = colors[:none]
      return str.sub(/R u b y/) { "#{ruby}R u b y#{none}" }
    end

store_history(line) click to toggle source

    # File lib/bio/shell/core.rb, line 377
    def store_history(line)
      Bio::Shell.cache[:histfile].puts "# #{Time.now}"
      Bio::Shell.cache[:histfile].puts line
    end

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