[BioRuby-cvs] bioruby/test/unit/bio/appl/blast test_report.rb, 1.2, 1.3 test_xmlparser.rb, 1.3, 1.4

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/blast
In directory pub.open-bio.org:/tmp/cvs-serv6123/test/unit/bio/appl/blast

Modified Files:
	test_report.rb test_xmlparser.rb 
Log Message:
* Moved test/data/blast/eco:* to test/data/blast/* to avoid file name problems 
  in the Windows file sysmtem.


Index: test_xmlparser.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/blast/test_xmlparser.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** test_xmlparser.rb	18 Dec 2005 17:06:56 -0000	1.3
--- test_xmlparser.rb	3 Feb 2006 17:21:51 -0000	1.4
***************
*** 35,43 ****
  
      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
--- 35,43 ----
  
      def self.input
!       File.open(File.join(TestDataBlast, 'b0002.faa')).read
      end
  
      def self.output
!       File.open(File.join(TestDataBlast, 'b0002.faa.m7')).read 
      end
    end
***************
*** 72,76 ****
  
      def test_db
!       assert_equal("eco:b0002.faa", @report.db)
      end
  
--- 72,76 ----
  
      def test_db
!       assert_equal("b0002.faa", @report.db)
      end
  

Index: test_report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/blast/test_report.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_report.rb	22 Nov 2005 08:31:47 -0000	1.2
--- test_report.rb	3 Feb 2006 17:21:51 -0000	1.3
***************
*** 35,39 ****
  
      def self.input
!       File.open(File.join(TestDataBlast, 'eco:b0002.faa')).read
      end
  
--- 35,39 ----
  
      def self.input
!       File.open(File.join(TestDataBlast, 'b0002.faa')).read
      end
  
***************
*** 41,49 ****
        case format
        when 0
!         File.open(File.join(TestDataBlast, 'eco:b0002.faa.m0')).read 
        when 7
!         File.open(File.join(TestDataBlast, 'eco:b0002.faa.m7')).read 
        when 8
!         File.open(File.join(TestDataBlast, 'eco:b0002.faa.m8')).read 
        end
      end
--- 41,49 ----
        case format
        when 0
!         File.open(File.join(TestDataBlast, 'b0002.faa.m0')).read 
        when 7
!         File.open(File.join(TestDataBlast, 'b0002.faa.m7')).read 
        when 8
!         File.open(File.join(TestDataBlast, 'b0002.faa.m8')).read 
        end
      end
***************
*** 81,90 ****
        xml_quoted_str = "~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs",  Nucleic Acids Res. 25:3389-3402."
        text_str = '~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs",  Nucleic Acids Res. 25:3389-3402.'
!       assert_equal(xml_quoted_str, @report.reference)
        assert_equal(text_str, @report.reference)
      end
  
      def test_db
!       assert_equal('eco:b0002.faa', @report.db)
      end
  
--- 81,90 ----
        xml_quoted_str = "~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs",  Nucleic Acids Res. 25:3389-3402."
        text_str = '~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs",  Nucleic Acids Res. 25:3389-3402.'
! #      assert_equal(xml_quoted_str, @report.reference)
        assert_equal(text_str, @report.reference)
      end
  
      def test_db
!       assert_equal('b0002.faa', @report.db)
      end
  
***************
*** 134,142 ****
  
      def test_pattern
!       assert(@report.pattern)
      end
  
      def test_extrez_query
!       assert(@report.entrez_query)
      end
  
--- 134,142 ----
  
      def test_pattern
!       assert_equal(nil, @report.pattern)
      end
  
      def test_extrez_query
!       assert_equal(nil, @report.entrez_query)
      end
  
***************
*** 186,190 ****
  
      def test_message
!       assert(@report.message)
      end
    end
--- 186,190 ----
  
      def test_message
!       assert_equal(nil, @report.message)
      end
    end
***************
*** 202,206 ****
  
      def test_statistics
!       assert(@itr.statistics)
      end
  
--- 202,209 ----
  
      def test_statistics
!       stat = {"kappa" => 0.041, "eff-space" => 605284, "db-num" => 1, 
!               "hsp-len" => 42, "db-len" => 820, "lambda" => 0.267, 
!               "entropy" => 0.14}
!       assert_equal(stat, @itr.statistics)
      end
  
***************
*** 210,214 ****
  
      def test_message
!       assert(@itr.message)
      end
    end
--- 213,217 ----
  
      def test_message
!       assert_equal(nil, @itr.message)
      end
    end