[BioRuby-cvs] bioruby/lib/bio/appl/targetp report.rb,1.5,1.6

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/targetp
In directory pub.open-bio.org:/tmp/cvs-serv4161/lib/bio/appl/targetp

Modified Files:
	report.rb 
Log Message:
* Updated RDoc.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/targetp/report.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** report.rb	26 Sep 2005 13:00:05 -0000	1.5
--- report.rb	31 Oct 2005 18:00:16 -0000	1.6
***************
*** 1,6 ****
  #
! # bio/appl/targetp/report.rb - TargetP report class
  # 
! #   Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
  #
  #  This library is free software; you can redistribute it and/or
--- 1,17 ----
  #
! # = bio/appl/targetp/report.rb - TargetP report class
  # 
! # Copyright::  Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! # Licence::    LGPL
! #
! #  $Id$
! #
! # == Description
! #
! # TargetP class for http://www.cbs.dtu.dk/services/TargetP/
! #
! # == Example
! # == References
! #--
  #
  #  This library is free software; you can redistribute it and/or
***************
*** 18,32 ****
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #  $Id$
  #
  
  module Bio
  
    class TargetP
  
      class Report
  
        DELIMITER = "\n \n"
  
        def initialize(str)
          @version                  = nil
--- 29,80 ----
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #++
  #
  
  module Bio
  
+ 
    class TargetP
  
+     # = A parser and container class for TargetP report.
      class Report
  
+       # Delimiter
        DELIMITER = "\n \n"
  
+       # Delimiter      
+       RS = DELIMITER
+ 
+       # Returns the program version.
+       attr_reader :version
+       
+       # Returns the query sequences.
+       attr_reader :query_sequences
+ 
+       # Returns 'included' or 'not included'.
+       # If the value is 'included', Bio::TargetP::Report#prediction['TPlen']
+       # contains a valid value.
+       attr_reader :cleavage_site_prediction
+       
+       # Returns ``PLANT'' or ``NON-PLANT'' networks.
+       attr_reader :networks
+ 
+       # Returns a Hash of the prediction results.
+       #
+       # {"Name"=>"MGI_2141503", "Loc."=>"_", "RC"=>3, "SP"=>0.271,
+       #  "other"=>0.844, "mTP"=>0.161, "cTP"=>0.031, "Length"=>640}
+       # 
+       # Keys: Name, Len, SP, mTP, other, Loc, RC
+       # Optional key for PLANT networks: cTP
+       # Optional key in Cleavage site: TPlen
+       #
+       # Use 'Length' and 'Loc.' instead of 'Len' and 'Loc' respectively
+       # for the version 1.0 report.
+       attr_reader :prediction
+ 
+       # Returns a Hash of cutoff values.
+       attr_reader :cutoff
+ 
+       # Sets output report.
        def initialize(str)
          @version                  = nil
***************
*** 39,48 ****
        end
  
-       attr_reader :version, :query_sequences, 
-         :cleavage_site_prediction, :networks,
-         :prediction, :cutoff
- 
        alias pred prediction
  
        def name
          @prediction['Name']
--- 87,93 ----
        end
  
        alias pred prediction
  
+       # Returns the name of query sequence.
        def name
          @prediction['Name']
***************
*** 50,53 ****
--- 95,99 ----
        alias entry_id name 
  
+       # Returns length of query sequence.
        def query_len
          if @prediction['Len']
***************
*** 59,62 ****
--- 105,114 ----
        alias length query_len
  
+       # Returns the predicted localization signal: 
+       # 1. S (Signal peptide)
+       # 2. M (mTP)
+       # 3. C (cTP)
+       # 4. * 
+       # 5. _
        def loc
          if @prediction['Loc'] 
***************
*** 67,70 ****
--- 119,123 ----
        end
  
+       # Returns RC.
        def rc
          @prediction['RC']
***************
*** 73,76 ****
--- 126,130 ----
        private
  
+       # 
        def parse_entry(str)
          labels = []
***************
*** 227,288 ****
  
  
- =begin
- 
- = Bio::TargetP
- 
-     TargetP class for ((<URL:http://www.cbs.dtu.dk/services/TargetP/>))
- 
- = Bio::TargetP::Report
- 
-     A parser and container class for TargetP report.
- 
- --- Bio::TargetP::Report.new(str)
- 
- --- Bio::TargetP::Report#version
- 
-       This class is tested by version 1.0 and 1.1 reports.
- 
- --- Bio::TargetP::Report#query_sequences
- --- Bio::TargetP::Report#cleavage_site_prediction
- 
-       Returns 'included' or 'not included'.
-       If the value is 'included', Bio::TargetP::Report#prediction['TPlen']
-       contains a valid value.
- 
- --- Bio::TargetP::Report#networks
-  
-       There are PLANT and NON-PLANT networks.
- 
- --- Bio::TargetP::Report#entry_id
- --- Bio::TargetP::Report#name
- 
-       Returns the qeury entry_id.
- 
- --- Bio::TargetP::Report#query_len
- 
-       Returns query length.
- 
- --- Bio::TargetP::Report#prediction
- 
-       Returns a Hash of the prediction results.
- 
-       Valid keys: Name, Len, SP, mTP, other, Loc, RC
-       Additional key in PLANT networks: cTP
-       Additional key in Cleavage site: TPlen
- 
-       Use 'Length' and 'Loc.' instead of 'Len' and 'Loc' respectively
-       for the version 1.0 report.
- 
- --- Bio::TargetP::Report#cutoff
-       
-       Returns a Hash of cutoff values.
- 
- --- Bio::TargetP::Report#loc
- 
-       Returns the predicted localization S, M, C, * or _.
- 
- --- Bio::TargetP::Report#rc
- 
- 
- =end
  
--- 281,283 ----