Class: Bio::Blast::Report::BlastXmlSplitter

Inherits:
FlatFile::Splitter::Default show all
Defined in:
lib/bio/appl/blast/report.rb

Overview

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

Instance Attribute Summary

Attributes inherited from FlatFile::Splitter::Default

#delimiter, #delimiter_overrun, #header

Attributes inherited from FlatFile::Splitter::Template

#entry_pos_flag, #parsed_entry

Instance Method Summary collapse

Constructor Details

#initialize(klass, bstream) ⇒ BlastXmlSplitter

creates a new splitter object



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# File 'lib/bio/appl/blast/report.rb', line 518

def initialize(klass, bstream)
  super(klass, bstream)
  @parsed_entries = []
  @raw_unsupported = false
end

Instance Method Details

#entry ⇒ Object

current raw entry as a String



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# File 'lib/bio/appl/blast/report.rb', line 563

def entry
  raise 'not supported for new BLAST XML format' if @raw_unsupported
  super
end

#entry_ended_pos ⇒ Object

(end position of the entry) + 1



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# File 'lib/bio/appl/blast/report.rb', line 577

def entry_ended_pos
  if entry_pos_flag then
    raise 'not supported for new BLAST XML format' if @raw_unsupported
  end
  super
end

#entry_start_pos ⇒ Object

start position of the entry



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# File 'lib/bio/appl/blast/report.rb', line 569

def entry_start_pos
  if entry_pos_flag then
    raise 'not supported for new BLAST XML format' if @raw_unsupported
  end
  super
end

#get_entry ⇒ Object

get an entry and return the entry as a string



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# File 'lib/bio/appl/blast/report.rb', line 538

def get_entry
  if @parsed_entries.empty? then
    @raw_unsupported = false
    ent = super
    prepare_parsed_entries(ent)
    self.parsed_entry = @parsed_entries.shift
  else
    raise 'not supported for new BLAST XML format'
  end
  ent
end

#get_parsed_entry ⇒ Object

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



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# File 'lib/bio/appl/blast/report.rb', line 551

def get_parsed_entry
  if @parsed_entries.empty? then
    get_entry
  else
    self.parsed_entry = @parsed_entries.shift
    self.entry = nil
    @raw_unsupported = true
  end
  self.parsed_entry
end

#rewind ⇒ Object

rewinds



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# File 'lib/bio/appl/blast/report.rb', line 525

def rewind
  ret = super
  @parsed_entries.clear
  @raw_unsupported = false
  ret
end

#skip_leader ⇒ Object

do nothing



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# File 'lib/bio/appl/blast/report.rb', line 533

def skip_leader
  nil
end