bio 1.2.1 → 1.3.0

data/test/unit/bio/appl/blast/test_xmlparser.rb

@@ -1,388 +0,0 @@
-#
-# test/unit/bio/appl/blast/test_xmlparser.rb - Unit test for Bio::Blast::Report
-#
-# Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
-# License::    The Ruby License
-#
-#  $Id: test_xmlparser.rb,v 1.7 2007/04/05 23:35:43 trevor 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, 'b0002.faa')).read
-    end
-
-    def self.output
-      File.open(File.join(TestDataBlast, 'b0002.faa.m7')).read 
-#      File.open(File.join(TestDataBlast, '2.2.15.blastp.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("b0002.faa", @report.db)
-    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 = TestBlastFormat7XMLParserData.output
-      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(1, @hsp.num)
-    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