Class | Bio::FlatFileIndex
In: | lib/bio/io/flatfile/index.rb lib/bio/io/flatfile/indexer.rb lib/bio/io/flatfile/bdb.rb
Parent: | Object

Bio::FlatFileIndex is a class for OBDA flatfile index.

### Methods

always_check_consistency always_check_consistency= check_consistency close closed? default_namespaces default_namespaces= formatstring2class get_by_id include? include_in_namespaces? include_in_primary? makeindex namespaces new open primary_namespace search search_namespaces search_primary secondary_namespaces update_index

### Classes and Modules

Module Bio::FlatFileIndex::BDB_1
Module Bio::FlatFileIndex::BDBdefault
Module Bio::FlatFileIndex::DEBUG
Module Bio::FlatFileIndex::Flat_1
Module Bio::FlatFileIndex::Indexer
Module Bio::FlatFileIndex::Template
Class Bio::FlatFileIndex::BDBwrapper
Class Bio::FlatFileIndex::DataBank
Class Bio::FlatFileIndex::FileID
Class Bio::FlatFileIndex::FileIDs
Class Bio::FlatFileIndex::NameSpaces
Class Bio::FlatFileIndex::Results

### Constants

MAGIC_FLAT | = | 'flat/1' |  | magic string for flat/1 index
MAGIC_BDB | = | 'BerkeleyDB/1' |  | magic string for BerkeleyDB/1 index

### Public Class methods

formatstring2class(format_string)

[Source]

         # File lib/bio/io/flatfile/indexer.rb, line 734
    734:     def self.formatstring2class(format_string)
    735:       case format_string
    736:       when /genbank/i
    737:         dbclass = Bio::GenBank
    738:       when /genpept/i
    739:         dbclass = Bio::GenPept
    740:       when /embl/i
    741:         dbclass = Bio::EMBL
    742:       when /sptr/i
    743:         dbclass = Bio::SPTR
    744:       when /fasta/i
    745:         dbclass = Bio::FastaFormat
    746:       else
    747:         raise "Unsupported format : #{format}"
    748:       end
    749:     end

makeindex(is_bdb, dbname, format, options, *files)

[Source]

         # File lib/bio/io/flatfile/indexer.rb, line 751
    751:     def self.makeindex(is_bdb, dbname, format, options, *files)
    752:       if format then
    753:         dbclass = formatstring2class(format)
    754:       else
    755:         dbclass = Bio::FlatFile.autodetect_file(files[0])
    756:         raise "Cannot determine format" unless dbclass
    757:         DEBUG.print "file format is #{dbclass}\n"
    758:       end
    759:
    760:       options = {} unless options
    761:       pns = options['primary_namespace']
    762:       sns = options['secondary_namespaces']
    763:
    764:       parser = Indexer::Parser.new(dbclass, pns, sns)
    765:
    766:       #if /(EMBL|SPTR)/ =~ dbclass.to_s then
    767:         #a = [ 'DR' ]
    768:         #parser.add_secondary_namespaces(*a)
    769:       #end
    770:       if sns = options['additional_secondary_namespaces'] then
    771:         parser.add_secondary_namespaces(*sns)
    772:       end
    773:
    774:       if is_bdb then
    775:         Indexer::makeindexBDB(dbname, parser, options, *files)
    776:       else
    777:         Indexer::makeindexFlat(dbname, parser, options, *files)
    778:       end
    779:     end

new(name)

Opens existing databank. Databank is a directory which contains indexed files and configuration files. The type of the databank (flat or BerkeleyDB) are determined automatically.

Unlike +FlatFileIndex.open+, block is not allowed.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 113
    113:     def initialize(name)
    114:       @db = DataBank.open(name)
    115:     end

open(name) {|i| ...}

Opens existing databank. Databank is a directory which contains indexed files and configuration files. The type of the databank (flat or BerkeleyDB) are determined automatically.

If block is given, the databank object is passed to the block. The databank will be automatically closed when the block terminates.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 88
     88:     def self.open(name)
     89:       if block_given? then
     90:         begin
     91:           i = self.new(name)
     92:           r = yield i
     93:         ensure
     94:           if i then
     95:             begin
     96:               i.close
     97:             rescue IOError
     98:             end
     99:           end
    100:         end
    101:       else
    102:         r = self.new(name)
    103:       end
    104:       r
    105:     end

update_index(dbname, format, options, *files)

[Source]

         # File lib/bio/io/flatfile/indexer.rb, line 781
    781:     def self.update_index(dbname, format, options, *files)
    782:       if format then
    783:         parser = Indexer::Parser.new(dbclass)
    784:       else
    785:         parser = nil
    786:       end
    787:       Indexer::update_index(dbname, parser, options, *files)
    788:     end

### Public Instance methods

always_check_consistency(bool)

If true, consistency checks will be performed every time accessing flatfiles. If nil/false, no checks are performed.

By default, always_check_consistency is true.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 297
    297:     def always_check_consistency(bool)
    298:       @db.always_check
    299:     end

always_check_consistency=(bool)

If true is given, consistency checks will be performed every time accessing flatfiles. If nil/false, no checks are performed.

By default, always_check_consistency is true.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 288
    288:     def always_check_consistency=(bool)
    289:       @db.always_check=(bool)
    290:     end

check_consistency()

Check consistency between the databank(index) and original flat files.

If the original flat files are changed after creating the databank, raises RuntimeError.

Note that this check only compares file sizes as described in the OBDA specification.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 278
    278:     def check_consistency
    279:       check_closed?
    280:       @db.check_consistency
    281:     end

close()

Closes the databank. Returns nil.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 132
    132:     def close
    133:       check_closed?
    134:       @db.close
    135:       @db = nil
    136:     end

closed?()

Returns true if already closed. Otherwise, returns false.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 139
    139:     def closed?
    140:       if @db then
    141:         false
    142:       else
    143:         true
    144:       end
    145:     end

default_namespaces()

Returns default namespaces. Returns an array of strings or nil. nil means all namespaces.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 172
    172:     def default_namespaces
    173:       @names
    174:     end

default_namespaces=(names)

Set default namespaces. `default_namespaces = nil` means all namespaces in the databank.

`default_namespaces= [ str1, str2, … ]` means set default namespeces to str1, str2, …

Default namespaces specified in this method only affect get_by_id, search, and include? methods.

Default of default namespaces is nil (that is, all namespaces are search destinations by default).

[Source]

         # File lib/bio/io/flatfile/index.rb, line 160
    160:     def default_namespaces=(names)
    161:       if names then
    162:         @names = []
    163:         names.each { |x| @names.push(x.dup) }
    164:       else
    165:         @names = nil
    166:       end
    167:     end

get_by_id(key)

common interface defined in registry.rb Searching databank and returns entry (or entries) as a string. Multiple entries (contatinated to one string) may be returned. Returns empty string if not found.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 122
    122:     def get_by_id(key)
    123:       search(key).to_s
    124:     end

include?(key)

Searching databank. If some entries are found, returns an array of unique IDs (primary identifiers). If not found anything, returns nil.

This method is useful when search result is very large and search method is very slow.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 210
    210:     def include?(key)
    211:       check_closed?
    212:       if @names then
    213:         r = @db.search_namespaces_get_unique_id(key, *@names)
    214:       else
    215:         r = @db.search_all_get_unique_id(key)
    216:       end
    217:       if r.empty? then
    218:         nil
    219:       else
    220:         r
    221:       end
    222:     end

include_in_namespaces?(key, *names)

Same as include?, but serching only specified namespaces.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 226
    226:     def include_in_namespaces?(key, *names)
    227:       check_closed?
    228:       r = @db.search_namespaces_get_unique_id(key, *names)
    229:       if r.empty? then
    230:         nil
    231:       else
    232:         r
    233:       end
    234:     end

include_in_primary?(key)

Same as include?, but serching only primary namespace.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 238
    238:     def include_in_primary?(key)
    239:       check_closed?
    240:       r = @db.search_primary_get_unique_id(key)
    241:       if r.empty? then
    242:         nil
    243:       else
    244:         r
    245:       end
    246:     end

namespaces()

Returns names of namespaces defined in the databank. (example: [ ‘LOCUS’, ‘ACCESSION’, ‘VERSION’ ] )

[Source]

         # File lib/bio/io/flatfile/index.rb, line 251
    251:     def namespaces
    252:       check_closed?
    253:       r = secondary_namespaces
    254:       r.unshift primary_namespace
    255:       r
    256:     end

primary_namespace()

Returns name of primary namespace as a string.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 259
    259:     def primary_namespace
    260:       check_closed?
    261:       @db.primary.name
    262:     end

search(key)

Searching databank and returns a Bio::FlatFileIndex::Results object.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 177
    177:     def search(key)
    178:       check_closed?
    179:       if @names then
    180:         @db.search_namespaces(key, *@names)
    181:       else
    182:         @db.search_all(key)
    183:       end
    184:     end

search_namespaces(key, *names)

Searching only specified namespeces. Returns a Bio::FlatFileIndex::Results object.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 189
    189:     def search_namespaces(key, *names)
    190:       check_closed?
    191:       @db.search_namespaces(key, *names)
    192:     end

search_primary(key)

Searching only primary namespece. Returns a Bio::FlatFileIndex::Results object.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 197
    197:     def search_primary(key)
    198:       check_closed?
    199:       @db.search_primary(key)
    200:     end

secondary_namespaces()

Returns names of secondary namespaces as an array of strings.

[Source]

         # File lib/bio/io/flatfile/index.rb, line 265
    265:     def secondary_namespaces
    266:       check_closed?
    267:       @db.secondary.names
    268:     end

[Validate]