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

Inherits:

FlatFile::Splitter::Default

• Object
• FlatFile::Splitter::Template
• FlatFile::Splitter::Default
• Bio::Blast::Report::BlastXmlSplitter

show all

Defined in:

lib/bio/appl/blast/report.rb

Overview

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)

• - (Object) entry

  current raw entry as a String.

• - (Object) entry_ended_pos

  (end position of the entry) + 1.

• - (Object) entry_start_pos

  start position of the entry.

• - (Object) get_entry

  get an entry and return the entry as a string.

• - (Object) get_parsed_entry

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

• - (BlastXmlSplitter) initialize(klass, bstream) constructor

  creates a new splitter object.

• - (Object) rewind

  rewinds.

• - (Object) skip_leader

  do nothing.

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# File 'lib/bio/appl/blast/report.rb', line 482

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

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# File 'lib/bio/appl/blast/report.rb', line 527

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

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# File 'lib/bio/appl/blast/report.rb', line 541

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

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

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

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# File 'lib/bio/appl/blast/report.rb', line 502

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

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# File 'lib/bio/appl/blast/report.rb', line 515

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

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# File 'lib/bio/appl/blast/report.rb', line 489

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

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# File 'lib/bio/appl/blast/report.rb', line 497

def skip_leader
  nil
end