Class: SequenceServer::BLAST::Report

Inherits:
Object
  • Object
show all
Defined in:
lib/sequenceserver/blast/report.rb

Overview

Captures results of a BLAST search.

A report is constructed from a search id. Search id is simply the basename of the temporary file that holds BLAST results in binary BLAST archive format.

For a given search id, result is obtained in XML format using the Formatter class, parsed into a simple intermediate representation (Array of values and Arrays) and information extracted from the intermediate representation (ir).

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(search_id, databases = nil) ⇒ Report

Expects a BLAST search id and an Array of Database objects that were used to BLAST. The second argument being optional to aid test suite.


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# File 'lib/sequenceserver/blast/report.rb', line 16

def initialize(search_id, databases = nil)
  @search_id = search_id
  @querydb = Array databases
  @queries = []

  generate
end

Instance Attribute Details

#paramsObject (readonly)

Returns the value of attribute params


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# File 'lib/sequenceserver/blast/report.rb', line 29

def params
  @params
end

#programObject (readonly)

:nodoc: Attributes parsed out from XML output.


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# File 'lib/sequenceserver/blast/report.rb', line 28

def program
  @program
end

#program_versionObject (readonly)

:nodoc: Attributes parsed out from XML output.


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# File 'lib/sequenceserver/blast/report.rb', line 28

def program_version
  @program_version
end

#queriesObject (readonly)

Returns the value of attribute queries


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# File 'lib/sequenceserver/blast/report.rb', line 30

def queries
  @queries
end

#querydbObject (readonly)

Returns the value of attribute querydb


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# File 'lib/sequenceserver/blast/report.rb', line 24

def querydb
  @querydb
end

#search_idObject (readonly)

Returns the value of attribute search_id


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# File 'lib/sequenceserver/blast/report.rb', line 24

def search_id
  @search_id
end

#statsObject (readonly)

Returns the value of attribute stats


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# File 'lib/sequenceserver/blast/report.rb', line 29

def stats
  @stats
end