[BioRuby-cvs] bioruby/test/unit/bio/appl/blast test_xmlparser.rb, NONE, 1.1

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/blast
In directory pub.open-bio.org:/tmp/cvs-serv11084/test/unit/bio/appl/blast

Added Files:
	test_xmlparser.rb 
Log Message:
* Initial import unit test for XMLParser based Bio::Blast::Report.


--- NEW FILE: test_xmlparser.rb ---
#
# test/unit/bio/appl/blast/test_xmlparser.rb - Unit test for Bio::Blast::Report
#
#   Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
#
#  This library is free software; you can redistribute it and/or
#  modify it under the terms of the GNU Lesser General Public
#  License as published by the Free Software Foundation; either
#  version 2 of the License, or (at your option) any later version.
#
#  This library is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
#  Lesser General Public License for more details.
#
#  You should have received a copy of the GNU Lesser General Public
#  License along with this library; if not, write to the Free Software
#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
#
#  $Id: test_xmlparser.rb,v 1.1 2005/10/28 02:32:38 nakao Exp $
#

require 'pathname'
libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)

require 'test/unit'
require 'bio/appl/blast'


module Bio
  class TestBlastFormat7XMLParserData
    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
    TestDataBlast = Pathname.new(File.join(bioruby_root, 'test', 'data', 'blast')).cleanpath.to_s

    def self.input
      File.open(File.join(TestDataBlast, 'eco:b0002.faa')).read
    end

    def self.output
      File.open(File.join(TestDataBlast, 'eco:b0002.faa.m7')).read 
    end
  end

    
  class TestBlastReport < Test::Unit::TestCase
    require 'bio/appl/blast/report'

    def setup
      @report = Bio::Blast::Report.new(Bio::TestBlastFormat7XMLParserData.output)
    end
    
    def test_iterations
      @report.iterations
    end

    def test_parameters
      @report.parameters
    end

    def test_program
      @report.program
    end

    def test_version
      @report.version
    end

    def test_reference
      @report.reference
    end

    def test_db
      assert_equal(@report.db, "eco:b0002.faa")
    end

    def test_query_id
      @report.query_id
    end

    def test_query_def
      @report.query_def
    end

    def test_query_len
      @report.query_len
    end

    def test_matrix
      @report.matrix
    end

    def test_expect
      @report.expect
    end

    def test_inclusion
      @report.inclusion
    end

    def test_sc_match
      @report.sc_match
    end

    def test_sc_mismatch
      @report.sc_mismatch
    end

    def test_gap_open
      @report.gap_open
    end

    def test_gap_extend
      @report.gap_extend
    end

    def test_filter
      @report.filter
    end

    def test_pattern
      @report.pattern
    end

    def test_extrez_query
      @report.entrez_query
    end

    def test_each_iteration
    end

    def test_each_hit
    end

    def test_hits
    end

    def test_statistics
    end

    def test_db_num
      @report.db_num
    end

    def test_db_len
      @report.db_len
    end

    def test_hsp_len
      @report.hsp_len
    end

    def test_eff_space
      @report.eff_space
    end

    def test_kappa
      @report.kappa
    end

    def test_lambda
      @report.lambda
    end

    def test_entropy
      @report.entropy
    end
    
    def test_message
      @report.message
    end
  end
  

  class TestBlastReportIteration < Test::Unit::TestCase
    def setup
      data = Bio::TestBlastData.data
      report = Bio::Blast::Report.new(data)
      @itr = report.iterations.first
    end

    def test_hits
      @itr.hits
    end

    def test_statistics
      @itr.statistics
    end

    def test_num
      @itr.num
    end

    def test_message
      @itr.message
    end
  end


  class TestBlastReportHit < Test::Unit::TestCase
    def setup
      data = Bio::TestBlastFormat7XMLParserData.output
      report = Bio::Blast::Report.new(data)
      @hit = report.hits.first
    end

    def test_hsps
      @hit.hsps
    end

    def test_query_id
      @hit.query_id
    end

    def test_query_def
      @hit.query_def
    end

    def test_query_len
      @hit.query_len
    end

    def test_num
      @hit.num
    end

    def test_hit_id
      @hit.hit_id
    end

    def test_len
      @hit.len
    end

    def test_target_len
      @hit.target_len
    end

    def test_definition
      @hit.definition
    end

    def test_taeget_def
      @hit.target_def
    end

    def test_accession
      @hit.accession
    end

    def test_target_id
      @hit.target_id
    end
    
    def test_evalue
      @hit.evalue
    end

    def test_bit_score
      @hit.bit_score
    end

    def test_identity
      @hit.identity
    end

    def test_overlap
      @hit.overlap
    end

    def test_query_seq
      @hit.query_seq
    end

    def test_target_seq
      @hit.target_seq
    end

    def test_midline
      @hit.midline
    end

    def test_query_start
      @hit.query_start
    end

    def test_query_end
      @hit.query_end
    end

    def test_target_start
      @hit.target_start
    end

    def test_target_end
      @hit.target_end
    end

    def test_lap_at
      @hit.lap_at
    end
  end


  class TestBlastReportHsp < Test::Unit::TestCase
    def setup
      data = Bio::TestBlastFormat7XMLParserData.output
      report = Bio::Blast::Report.new(data)
      @hsp = report.hits.first.hsps.first
    end
    
    def test_num
      assert_equal(@hsp.num, 1)
    end

    def test_hit_score
      @hsp.bit_score
    end

    def test_score
      @hsp.score
    end

    def test_evalue
      @hsp.evalue
    end

    def test_identity
      @hsp.identity
    end

    def test_gaps
      @hsp.gaps
    end

    def test_positive
      @hsp.positive
    end

    def test_align_len
      @hsp.align_len
    end

    def test_density
      @hsp.density
    end

    def test_query_frame
      @hsp.query_frame
    end

    def test_query_from
      @hsp.query_from
    end

    def test_query_to
      @hsp.query_to
    end

    def test_hit_frame
      @hsp.hit_frame
    end

    def test_hit_from
      @hsp.hit_from
    end

    def test_hit_to
      @hsp.hit_to
    end

    def test_pattern_from
      @hsp.pattern_from
    end

    def test_pattern_to
      @hsp.pattern_to 
    end

    def test_qseq
      @hsp.qseq
    end

    def test_midline
      @hsp.midline
    end

    def test_hseq
      @hsp.hseq
    end

    def test_percent_identity
      @hsp.percent_identity
    end

    def test_mismatch_count
      @hsp.mismatch_count
    end
  end
end