### Home Classes Methods

### In Files

- lib/bio/db/nexus.rb

### Parent

Bio::Nexus::GenericBlock

### Methods

- ::new
- #get_characters_string
- #get_characters_strings_by_name
- #get_datatype
- #get_gap_character
- #get_match_character
- #get_matrix
- #get_missing
- #get_number_of_characters
- #get_number_of_taxa
- #get_row_name
- #get_sequence
- #get_sequences_by_name
- #set_datatype
- #set_gap_character
- #set_match_character
- #set_matrix
- #set_missing
- #set_number_of_characters
- #set_number_of_taxa
- #to_nexus

### 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
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- Bio::EMBL
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- Bio::EMBOSS
- Bio::Ensembl
- Bio::Ensembl::Base
- Bio::Ensembl::Human
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- 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
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- 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::FLATFILE_SPLITTER
- 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
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- Bio::Hinv::HitPubmedId
- Bio::Hinv::HitXML
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- Bio::Hinv::HixXML
- Bio::Hinv::IdSearch
- Bio::Hinv::KeywordSearch
- Bio::Iprscan
- Bio::Iprscan::Report
- Bio::Iprscan::Report::Match
- Bio::KEGG
- Bio::KEGG::API
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- Bio::KEGG::COMPOUND
- Bio::KEGG::Common
- Bio::KEGG::Common::DblinksAsHash
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- Bio::KEGG::EXPRESSION
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- Bio::KEGG::KGML::Entry
- Bio::KEGG::KGML::Graphics
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- Bio::KEGG::KGML::Reaction
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- Bio::KEGG::Keggtab
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- Bio::Nexus
- Bio::Nexus::CharactersBlock
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- Bio::Nexus::GenericBlock
- Bio::Nexus::NexusMatrix
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- Bio::Nexus::TaxaBlock
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- Bio::PAML
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- Bio::PDB
- Bio::PDB::AtomFinder
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- Bio::PDB::Coordinate
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- Bio::PDB::DataType::Pdb_AChar
- Bio::PDB::DataType::Pdb_Atom
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- Bio::PDB::DataType::Pdb_Date
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- Bio::PDB::DataType::Pdb_String
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- Bio::PDB::Heterogen
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- Bio::PDB::Record
- Bio::PDB::Record::ANISOU
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- Bio::PDB::Residue
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- Bio::PROSITE
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- Bio::PSORT::CGIDriver
- Bio::PSORT::IPSORT
- Bio::PSORT::PSORT1
- Bio::PSORT::PSORT1::Remote
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- Bio::Pathway
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- 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
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- Bio::PhyloXML::DomainArchitecture
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- Bio::PhyloXML::Id
- Bio::PhyloXML::Node
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- 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
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- Bio::Probcons
- Bio::Probcons::DEFAULT_PARSER
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- 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
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- Bio::RestrictionEnzyme::DoubleStranded::EnzymeAction
- Bio::RestrictionEnzyme::Fragments
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- Bio::RestrictionEnzyme::Range::CutRanges
- Bio::RestrictionEnzyme::Range::HorizontalCutRange
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- Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
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- Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::SingleStrandComplement
- Bio::RestrictionEnzyme::SortedNumArray
- Bio::RestrictionEnzyme::StringFormatting
- Bio::SOAPWSDL
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- Bio::SOSUI::Report::TMH
- Bio::SPTR
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- Bio::SQL::Biodatabase
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- Bio::SQL::BioentryDbxref
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- Bio::SQL::BioentryQualifierValue
- Bio::SQL::BioentryReference
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- Bio::SQL::DbxrefQualifierValue
- Bio::SQL::DummyBase
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- Bio::SQL::LocationQualifierValue
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- Bio::SQL::SeqfeatureDbxref
- Bio::SQL::SeqfeaturePath
- Bio::SQL::SeqfeatureQualifierValue
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- Bio::SQL::Sequence
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- Bio::SQL::TaxonName
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- Bio::SQL::TermDbxref
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- Bio::SQL::TermRelationship
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- Bio::SQL::TermSynonym
- Bio::SangerChromatogram
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- Bio::Sequence
- Bio::Sequence::AA
- Bio::Sequence::Adapter
- Bio::Sequence::Adapter::BioSQL
- Bio::Sequence::Adapter::EMBL
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- Bio::Sequence::Adapter::Fastq
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- Bio::Sequence::Common
- Bio::Sequence::DBLink
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- Bio::Sequence::Format::AminoFormatter
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- Bio::TargetP
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- Bio::Tcoffee::DEFAULT_PARSER
- Bio::TogoWS
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- Bio::TogoWS::REST
- Bio::TrEMBL
- Bio::Tree
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- Bio::Tree::NoPathError
- Bio::Tree::Node
- Bio::UniProt
- BiorubyController
- BiorubyGenerator
- BiorubyHelper
- Hash
- Object
- String

No matching classes.

# Bio::Nexus::CharactersBlock

## DESCRIPTION

Bio::Nexus::CharactersBlock represents a characters nexus block.

# Example of Characters block:

Begin Characters;

    Dimensions NChar=20
               NTax=4;
    Format DataType=DNA
    Missing=x
    Gap=- MatchChar=.;
    Matrix
     fish  ACATA GAGGG TACCT CTAAG
     frog  ACTTA GAGGC TACCT CTAGC
     snake ACTCA CTGGG TACCT TTGCG
     mouse ACTCA GACGG TACCT TTGCG;

End;

## USAGE

    require 'bio/db/nexus'

    # Create a new parser:
    nexus = Bio::Nexus.new( nexus_data_as_string )

    # Get first characters block (same methods as Nexus::DataBlock except
    # it lacks get_taxa method):
    characters_block = nexus.get_characters_blocks[ 0 ]

### Constants

GAP
MATCHCHAR
MISSING

### Public Class Methods

new( name ) click to toggle source

Creates a new CharactersBlock object named 'name'.

Arguments:

- (required) name: String

    # File lib/bio/db/nexus.rb, line 951
    def initialize( name )
      super( name )
      @number_of_taxa = 0
      @number_of_characters = 0
      @data_type = String.new
      @gap_character = String.new
      @missing = String.new
      @match_character = String.new
      @matrix = NexusMatrix.new
    end

### Public Instance Methods

get_characters_string( row ) click to toggle source

Returns character data as String for matrix row 'row'.

Arguments:

- (required) row: Integer

Returns | String

    # File lib/bio/db/nexus.rb, line 1106
    def get_characters_string( row )
      get_matrix.get_row_string( row, "" )
    end

get_characters_strings_by_name( name ) click to toggle source

Returns character data as String Array for matrix rows named 'name'.

Arguments:

- (required) name: String

Returns | Array of Strings

    # File lib/bio/db/nexus.rb, line 1095
    def get_characters_strings_by_name( name )
      get_matrix.get_row_strings_by_name( name, "" )
    end

get_datatype() click to toggle source

Gets the "datatype" property.

Returns | String

    # File lib/bio/db/nexus.rb, line 1018
    def get_datatype
      @data_type
    end

get_gap_character() click to toggle source

Gets the "gap character" property.

Returns | String

    # File lib/bio/db/nexus.rb, line 1025
    def get_gap_character
      @gap_character
    end

get_match_character() click to toggle source

Gets the "match character" property.

Returns | String

    # File lib/bio/db/nexus.rb, line 1039
    def get_match_character
      @match_character
    end

get_matrix() click to toggle source

Gets the matrix.

Returns | Bio::Nexus::NexusMatrix

    # File lib/bio/db/nexus.rb, line 1046
    def get_matrix
      @matrix
    end

get_missing() click to toggle source

Gets the "missing" property.

Returns | String

    # File lib/bio/db/nexus.rb, line 1032
    def get_missing
      @missing
    end

get_number_of_characters() click to toggle source

Gets the "number of characters" property.

Returns | Integer

    # File lib/bio/db/nexus.rb, line 1011
    def get_number_of_characters
      @number_of_characters
    end

get_number_of_taxa() click to toggle source

Gets the "number of taxa" property.

Returns | Integer

    # File lib/bio/db/nexus.rb, line 1003
    def get_number_of_taxa
      @number_of_taxa
    end

get_row_name( row ) click to toggle source

Returns the String in the matrix at row 'row' and column 0, which usually is interpreted as a sequence name (if the matrix contains molecular sequence characters).

Arguments:

- (required) row: Integer

Returns | String

    # File lib/bio/db/nexus.rb, line 1084
    def get_row_name( row )
      get_matrix.get_name( row )
    end

get_sequence( row ) click to toggle source

Returns the characters in the matrix at row 'row' as Bio::Sequence object. Column 0 of the matrix is set as the definition of the Bio::Sequence object.

Arguments:

- (required) row: Integer

Returns | Bio::Sequence

    # File lib/bio/db/nexus.rb, line 1072
    def get_sequence( row )
      create_sequence( get_characters_string( row ), get_row_name( row )  )
    end

get_sequences_by_name( name ) click to toggle source

Returns character data as Bio::Sequence object Array for matrix rows named 'name'.

Arguments:

- (required) name: String

Returns | Bio::Sequence

    # File lib/bio/db/nexus.rb, line 1056
    def get_sequences_by_name( name )
      seq_strs = get_characters_strings_by_name( name )
      seqs = Array.new
      seq_strs.each do | seq_str |
        seqs.push( create_sequence( seq_str, name ) )
      end
      seqs
    end

set_datatype( data_type ) click to toggle source

Sets the "data type" property.

Arguments:

- (required) data_type: String

    # File lib/bio/db/nexus.rb, line 1130
    def set_datatype( data_type )
      @data_type = data_type
    end

set_gap_character( gap_character ) click to toggle source

Sets the "gap character" property.

Arguments:

- (required) gap_character: String

    # File lib/bio/db/nexus.rb, line 1138
    def set_gap_character( gap_character )
      @gap_character = gap_character
    end

set_match_character( match_character ) click to toggle source

Sets the "match character" property.

Arguments:

- (required) match_character: String

    # File lib/bio/db/nexus.rb, line 1154
    def set_match_character( match_character )
      @match_character = match_character
    end

set_matrix( matrix ) click to toggle source

Sets the matrix.

Arguments:

- (required) matrix: Bio::Nexus::NexusMatrix

    # File lib/bio/db/nexus.rb, line 1162
    def set_matrix( matrix )
      @matrix = matrix
    end

set_missing( missing ) click to toggle source

Sets the "missing" property.

Arguments:

- (required) missing: String

    # File lib/bio/db/nexus.rb, line 1146
    def set_missing( missing )
      @missing = missing
    end

set_number_of_characters( number_of_characters ) click to toggle source

Sets the "number of characters" property.

Arguments:

- (required) number_of_characters: Integer

    # File lib/bio/db/nexus.rb, line 1122
    def set_number_of_characters( number_of_characters )
      @number_of_characters = number_of_characters
    end

set_number_of_taxa( number_of_taxa ) click to toggle source

Sets the "number of taxa" property.

Arguments:

- (required) number_of_taxa: Integer

    # File lib/bio/db/nexus.rb, line 1114
    def set_number_of_taxa( number_of_taxa )
      @number_of_taxa = number_of_taxa
    end

to_nexus() click to toggle source

Returns a String describing this block as nexus formatted data.

Returns | String

    # File lib/bio/db/nexus.rb, line 966
    def to_nexus
      line_1 = String.new
      line_1 << DIMENSIONS
      if ( Nexus::Util::larger_than_zero( get_number_of_taxa ) )
        line_1 << " " <<  NTAX << "=" << get_number_of_taxa
      end
      if ( Nexus::Util::larger_than_zero( get_number_of_characters ) )
        line_1 << " " <<  NCHAR << "=" << get_number_of_characters
      end
      line_1 << DELIMITER

      line_2 = String.new
      line_2 << FORMAT
      if ( Nexus::Util::longer_than_zero( get_datatype ) )
        line_2 << " " <<  DATATYPE << "=" << get_datatype
      end
      if ( Nexus::Util::longer_than_zero( get_missing ) )
        line_2 << " " <<  MISSING << "=" << get_missing
      end
      if ( Nexus::Util::longer_than_zero( get_gap_character ) )
        line_2 << " " <<  GAP << "=" << get_gap_character
      end
      if ( Nexus::Util::longer_than_zero( get_match_character ) )
        line_2 << " " <<  MATCHCHAR << "=" << get_match_character
      end
      line_2 << DELIMITER

      line_3 = String.new
      line_3 << MATRIX
      Nexus::Util::to_nexus_helper( CHARACTERS_BLOCK, [ line_1, line_2, line_3 ] +
                                    get_matrix.to_nexus_row_array  )
    end

[Validate]

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