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# File 'lib/bio/io/flatfile/indexer.rb', line 621
def self.update_index(name, parser, options, *files)
db = DataBank.open(name)
if parser then
raise 'file format mismatch' if db.format != parser.format
else
begin
dbclass_orig =
Bio::FlatFile.autodetect_file(db.fileids[0].filename)
rescue TypeError, Errno::ENOENT
end
begin
dbclass_new =
Bio::FlatFile.autodetect_file(files[0])
rescue TypeError, Errno::ENOENT
end
case db.format
when 'swiss', 'embl'
parser = Parser.new(db.format)
if dbclass_new and dbclass_new != parser.dbclass
raise 'file format mismatch'
end
when 'genbank'
dbclass = dbclass_orig or dbclass_new
if dbclass == Bio::GenBank or dbclass == Bio::GenPept
parser = Parser.new(dbclass_orig)
elsif !dbclass then
raise 'cannnot determine format. please specify manually.'
else
raise 'file format mismatch'
end
if dbclass_new and dbclass_new != parser.dbclass
raise 'file format mismatch'
end
else
raise 'unsupported format'
end
end
parser.set_primary_namespace(db.primary.name)
parser.add_secondary_namespaces(*db.secondary.names)
if options['renew'] then
newfiles = db.fileids.filenames.find_all do |x|
FileTest.exist?(x)
end
newfiles.concat(files)
newfiles2 = newfiles.sort
newfiles2.uniq!
newfiles3 = []
newfiles.each do |x|
newfiles3 << x if newfiles2.delete(x)
end
t = db.index_type
db.close
case t
when MAGIC_BDB
Indexer::makeindexBDB(name, parser, options, *newfiles3)
when MAGIC_FLAT
Indexer::makeindexFlat(name, parser, options, *newfiles3)
else
raise 'Unsupported index type'
end
return true
end
need_update = []
newfiles = files.dup
db.fileids.cache_all
db.fileids.each_with_index do |f, i|
need_update << i unless f.check
newfiles.delete(f.filename)
end
b = db.fileids.size
begin
db.fileids.recalc
rescue Errno::ENOENT => evar
DEBUG.print "Error: #{evar}\n"
DEBUG.print "assumed --renew option\n"
db.close
options = options.dup
options['renew'] = true
update_index(name, parser, options, *files)
return true
end
db.fileids.add(*newfiles)
db.fileids.recalc
need_update.concat((b...(b + newfiles.size)).to_a)
DEBUG.print "writing DabaBank...\n"
db.write('wb', BDBdefault::flag_append)
case db.index_type
when MAGIC_BDB
addindex_bdb(db, BDBdefault::flag_append,
need_update, parser, options)
when MAGIC_FLAT
addindex_flat(db, :add, need_update, parser, options)
else
raise 'Unsupported index type'
end
db.close
true
end
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