(PSI-BLAST) Returns iterations. It returns an array of Bio::Blast::Default::Report::Iteration class. Note that normal blastall result usually contains one iteration.

matrix [R]

name of the matrix

num_hits [R]

number of hits. Note that this may differ from hits.size.

posted_date [R]

posted date of the database

sc_match [R]

match score of the matrix

sc_mismatch [R]

mismatch score of the matrix

Public Class Methods

new (str)

Source

   # File lib/bio/appl/blast/format0.rb
48 def initialize(str)
49   str = str.sub(/\A\s+/, '')
50   str.sub!(/\n(T?BLAST.*)/m, "\n") # remove trailing entries for sure
51   @entry_overrun = $1
52   @entry = str
53   data = str.split(/(?:^[ \t]*\n)+/)
54 
55   format0_split_headers(data)
56   @iterations = format0_split_search(data)
57   format0_split_stat_params(data)
58 end

Creates a new Report object from BLAST result text.

open (filename, *mode)

Source

   # File lib/bio/appl/blast/format0.rb
43 def self.open(filename, *mode)
44   Bio::FlatFile.open(self, filename, *mode)
45 end

Opens file by using Bio::FlatFile.open.

Public Instance Methods

converged? ()

Source

    # File lib/bio/appl/blast/format0.rb
203 def converged?
204   @iterations.last.converged?
205 end

(PSI-BLAST) Same as iterations.last.converged?. Returns true if the last iteration is converged, otherwise, returns false.

db ()

Source

    # File lib/bio/appl/blast/format0.rb
227 def db
228   unless defined?(@db)
229     if /Database *\: *(.*)/m =~ @f0database then
230       a = $1.split(/^/)
231       a.pop if a.size > 1
232       @db = a.collect { |x| x.sub(/\s+\z/, '') }.join(' ')
233     end
234   end #unless
235   @db
236 end

Returns the name (filename or title) of the database.

each ()

Alias for: each_hit

each_hit () { |x| ... }

Source

    # File lib/bio/appl/blast/format0.rb
178 def each_hit
179   @iterations.last.each do |x|
180     yield x
181   end
182 end

Iterates over each hit of the last iteration. Same as iterations.last.each_hit. Yields a Bio::Blast::Default::Report::Hit object. This is very useful in most cases, e.g. for blastall results.

Also aliased as: each

each_iteration () { |x| ... }

Source

    # File lib/bio/appl/blast/format0.rb
168 def each_iteration
169   @iterations.each do |x|
170     yield x
171   end
172 end

(PSI-BLAST) Iterates over each iteration. Same as iterations.each. Yields a Bio::Blast::Default::Report::Iteration object.

entropy ()

Source

    # File lib/bio/appl/blast/format0.rb
128 def entropy;        @iterations.last.entropy;        end

Same as iterations.last.entropy.

gapped_entropy ()

Source

    # File lib/bio/appl/blast/format0.rb
135 def gapped_entropy; @iterations.last.gapped_entropy; end

Same as iterations.last.gapped_entropy.

gapped_kappa ()

Source

    # File lib/bio/appl/blast/format0.rb
131 def gapped_kappa;   @iterations.last.gapped_kappa;   end

Same as iterations.last.gapped_kappa.

gapped_lambda ()

Source

    # File lib/bio/appl/blast/format0.rb
133 def gapped_lambda;  @iterations.last.gapped_lambda;  end

Same as iterations.last.gapped_lambda.

hits ()

Source

    # File lib/bio/appl/blast/format0.rb
189 def hits
190   @iterations.last.hits
191 end

Same as iterations.last.hits. Returns the last iteration’s hits. Returns an array of Bio::Blast::Default::Report::Hit object. This is very useful in most cases, e.g. for blastall results.

kappa ()

Source

    # File lib/bio/appl/blast/format0.rb
124 def kappa;          @iterations.last.kappa;          end

Same as iterations.last.kappa.

lambda ()

Source

    # File lib/bio/appl/blast/format0.rb
126 def lambda;         @iterations.last.lambda;         end

Same as iterations.last.lambda.

message ()

Source

    # File lib/bio/appl/blast/format0.rb
195 def message
196   @iterations.last.message
197 end

(PSI-BLAST) Same as iterations.last.message.

pattern ()

Source

    # File lib/bio/appl/blast/format0.rb
155 def pattern; @iterations.first.pattern; end

(PHI-BLAST) Same as iterations.first.pattern. Note that it returns the FIRST iteration’s value.

pattern_positions ()

Source

    # File lib/bio/appl/blast/format0.rb
160 def pattern_positions
161   @iterations.first.pattern_positions
162 end

(PHI-BLAST) Same as iterations.first.pattern_positions. Note that it returns the FIRST iteration’s value.

program ()

Source

    # File lib/bio/appl/blast/format0.rb
138 def program;        format0_parse_header; @program;        end

Returns program name.

query_def ()

Source

    # File lib/bio/appl/blast/format0.rb
150 def query_def; format0_parse_query; @query_def; end

Returns definition of the query.

query_len ()

Source

    # File lib/bio/appl/blast/format0.rb
147 def query_len; format0_parse_query; @query_len; end

Returns length of the query.

reference ()

Source

    # File lib/bio/appl/blast/format0.rb
211 def reference
212   references[0]
213 end

Returns the bibliography reference of the BLAST software. Note that this method shows only the first reference. When you want to get additional references, you can use references method.

references ()

Source

    # File lib/bio/appl/blast/format0.rb
217 def references
218   unless defined?(@references)
219     @references = @f0references.collect do |x|
220       x.to_s.gsub(/\s+/, ' ').strip
221     end
222   end #unless
223   @references
224 end

Returns the bibliography references of the BLAST software. Returns an array of strings.

to_s ()

Source

   # File lib/bio/appl/blast/format0.rb
69 def to_s; @entry; end

Returns whole entry as a string.

version ()

Source

    # File lib/bio/appl/blast/format0.rb
140 def version;        format0_parse_header; @version;        end

Returns version of the program.

version_date ()

Source

    # File lib/bio/appl/blast/format0.rb
144 def version_date;   format0_parse_header; @version_date;   end

Returns released date of the program.

version_number ()

Source

    # File lib/bio/appl/blast/format0.rb
142 def version_number; format0_parse_header; @version_number; end

Returns version number string of the program.