# File lib/bio/io/flatfile/index.rb 259 def primary_namespace 260 check_closed? 261 @db.primary.name 262 end
class Bio::FlatFileIndex
Bio::FlatFileIndex is a class for OBDA flatfile index.
Constants
- MAGIC_BDB
-
magic string for BerkeleyDB/1 index
- MAGIC_FLAT
-
magic string for flat/1 index
Public Class Methods
Source
# File lib/bio/io/flatfile/indexer.rb 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
Source
# File lib/bio/io/flatfile/indexer.rb 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
Source
# File lib/bio/io/flatfile/index.rb 113 def initialize(name) 114 @db = DataBank.open(name) 115 end
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 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
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/indexer.rb 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
Source
# File lib/bio/io/flatfile/index.rb 297 def always_check_consistency(bool) 298 @db.always_check 299 end
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 288 def always_check_consistency=(bool) 289 @db.always_check=(bool) 290 end
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 278 def check_consistency 279 check_closed? 280 @db.check_consistency 281 end
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 132 def close 133 check_closed? 134 @db.close 135 @db = nil 136 end
Closes the databank. Returns nil.
Source
# File lib/bio/io/flatfile/index.rb 139 def closed? 140 if @db then 141 false 142 else 143 true 144 end 145 end
Returns true if already closed. Otherwise, returns false.
Source
# File lib/bio/io/flatfile/index.rb 172 def default_namespaces 173 @names 174 end
Returns default namespaces. Returns an array of strings or nil. nil means all namespaces.
Source
# File lib/bio/io/flatfile/index.rb 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
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 122 def get_by_id(key) 123 search(key).to_s 124 end
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 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
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 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
Same as include?, but serching only specified namespaces.
Source
# File lib/bio/io/flatfile/index.rb 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
Same as include?, but serching only primary namespace.
Source
# File lib/bio/io/flatfile/index.rb 251 def namespaces 252 check_closed? 253 r = secondary_namespaces 254 r.unshift primary_namespace 255 r 256 end
Returns names of namespaces defined in the databank. (example: [ ‘LOCUS’, ‘ACCESSION’, ‘VERSION’ ] )
Source
Returns name of primary namespace as a string.
Source
# File lib/bio/io/flatfile/index.rb 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
Searching databank and returns a Bio::FlatFileIndex::Results object.
Source
# File lib/bio/io/flatfile/index.rb 189 def search_namespaces(key, *names) 190 check_closed? 191 @db.search_namespaces(key, *names) 192 end
Searching only specified namespeces. Returns a Bio::FlatFileIndex::Results object.
Source
# File lib/bio/io/flatfile/index.rb 197 def search_primary(key) 198 check_closed? 199 @db.search_primary(key) 200 end
Searching only primary namespece. Returns a Bio::FlatFileIndex::Results object.
Source
# File lib/bio/io/flatfile/index.rb 265 def secondary_namespaces 266 check_closed? 267 @db.secondary.names 268 end
Returns names of secondary namespaces as an array of strings.