[BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.9,1.10

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv9484/lib/bio/appl/blat

Modified Files:
	report.rb 
Log Message:
changed documents


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** report.rb	20 Jun 2006 14:34:38 -0000	1.9
--- report.rb	27 Jun 2006 15:17:07 -0000	1.10
***************
*** 34,38 ****
      # On the other hand, in many other homology search programs,
      # the start position of a sequence is numbered as 1.
!     # To keep compatibility, the BLAT parser adds 1 to every position number.
      #
      # Note that Bio::Blat::Report#query_def, #query_id, #query_len  methods
--- 34,39 ----
      # On the other hand, in many other homology search programs,
      # the start position of a sequence is numbered as 1.
!     # To keep compatibility, the BLAT parser adds 1 to every position number
!     # except Bio::Blat::Report::Seqdesc and some Bio::Blat specific methods.
      #
      # Note that Bio::Blat::Report#query_def, #query_id, #query_len  methods
***************
*** 335,346 ****
          #--
          # methods described in the BLAT FAQ at the UCSC genome browser.
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5)
          #++
  
          # Calculates the pslCalcMilliBad value defined in the
!         # BLAT FAQ (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          def milli_bad
            w = (self.protein? ? 3 : 1)
--- 336,347 ----
          #--
          # methods described in the BLAT FAQ at the UCSC genome browser.
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4)
          #++
  
          # Calculates the pslCalcMilliBad value defined in the
!         # BLAT FAQ (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def milli_bad
            w = (self.protein? ? 3 : 1)
***************
*** 359,366 ****
          # Calculates the percent identity compatible with the BLAT web server
          # as described in the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          def percent_identity
            100.0 - self.milli_bad * 0.1
--- 360,367 ----
          # Calculates the percent identity compatible with the BLAT web server
          # as described in the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def percent_identity
            100.0 - self.milli_bad * 0.1
***************
*** 372,376 ****
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          def protein?
            return nil if self.block_sizes.empty?
--- 373,377 ----
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def protein?
            return nil if self.block_sizes.empty?
***************
*** 397,404 ****
          # Calculates the score compatible with the BLAT web server
          # as described in the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat5).
          def score
            w = (self.protein? ? 3 : 1)
--- 398,405 ----
          # Calculates the score compatible with the BLAT web server
          # as described in the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          #
          # The algorithm is taken from the BLAT FAQ
!         # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
          def score
            w = (self.protein? ? 3 : 1)