Class Bio::Blast::Report::BlastXmlSplitter
In: lib/bio/appl/blast/report.rb
Parent: Bio::FlatFile::Splitter::Default

Flatfile splitter for NCBI BLAST XML format. It is internally used when reading BLAST XML. Normally, users do not need to use it directly.

Methods

Public Class methods

creates a new splitter object

[Source]

     # File lib/bio/appl/blast/report.rb, line 486
486:     def initialize(klass, bstream)
487:       super(klass, bstream)
488:       @parsed_entries = []
489:       @raw_unsupported = false
490:     end

Public Instance methods

current raw entry as a String

[Source]

     # File lib/bio/appl/blast/report.rb, line 531
531:     def entry
532:       raise 'not supported for new BLAST XML format' if @raw_unsupported
533:       super
534:     end

(end position of the entry) + 1

[Source]

     # File lib/bio/appl/blast/report.rb, line 545
545:     def entry_ended_pos
546:       if entry_pos_flag then
547:         raise 'not supported for new BLAST XML format' if @raw_unsupported
548:       end
549:       super
550:     end

start position of the entry

[Source]

     # File lib/bio/appl/blast/report.rb, line 537
537:     def entry_start_pos
538:       if entry_pos_flag then
539:         raise 'not supported for new BLAST XML format' if @raw_unsupported
540:       end
541:       super
542:     end

get an entry and return the entry as a string

[Source]

     # File lib/bio/appl/blast/report.rb, line 506
506:     def get_entry
507:       if @parsed_entries.empty? then
508:         @raw_unsupported = false
509:         ent = super
510:         prepare_parsed_entries(ent)
511:         self.parsed_entry = @parsed_entries.shift
512:       else
513:         raise 'not supported for new BLAST XML format'
514:       end
515:       ent
516:     end

get an entry as a Bio::Blast::Report object

[Source]

     # File lib/bio/appl/blast/report.rb, line 519
519:     def get_parsed_entry
520:       if @parsed_entries.empty? then
521:         ent = get_entry
522:       else
523:         self.parsed_entry = @parsed_entries.shift
524:         self.entry = nil
525:         @raw_unsupported = true
526:       end
527:       self.parsed_entry
528:     end

rewinds

[Source]

     # File lib/bio/appl/blast/report.rb, line 493
493:     def rewind
494:       ret = super
495:       @parsed_entries.clear
496:       @raw_unsupported = false
497:       ret
498:     end

do nothing

[Source]

     # File lib/bio/appl/blast/report.rb, line 501
501:     def skip_leader
502:       nil
503:     end

[Validate]