class Bio::Blast::NCBIOptions
A class to parse and store NCBI-tools style command-line options. It is internally used in Bio::Blast and some other classes.
Attributes
(protected) option pairs. internal use only.
Public Class Methods
creates a new object from an array
# File lib/bio/appl/blast/ncbioptions.rb 30 def initialize(options = []) 31 #@option_pairs = [] 32 @option_pairs = _parse_options(options) 33 end
parses a string and returns a new object
# File lib/bio/appl/blast/ncbioptions.rb 99 def self.parse(str) 100 options = Shellwords.shellwords(str) 101 self.new(options) 102 end
Public Instance Methods
If self == other, returns true. Otherwise, returns false.
# File lib/bio/appl/blast/ncbioptions.rb 198 def ==(other) 199 return true if super(other) 200 begin 201 oopts = other.options 202 rescue 203 return false 204 end 205 return self.options == oopts 206 end
Adds options from given array. Note that existing options will also be normalized.
Arguments:
-
options: options as an Array of String objects.
- Returns
-
self
# File lib/bio/appl/blast/ncbioptions.rb 191 def add_options(options) 192 @option_pairs.concat _parse_options(options) 193 self.normalize! 194 self 195 end
Delete the given option.
Arguments:
-
key: option name as a string, e.g. ‘m’, ‘p’, or ‘-m’, ‘-p’.
- Returns
-
String or nil
# File lib/bio/appl/blast/ncbioptions.rb 135 def delete(key) 136 re = _key_to_regexp(key) 137 138 # Note: the last option is used for return value 139 # when two or more same option exist. 140 oldvalue = nil 141 @option_pairs = @option_pairs.delete_if do |pair| 142 if re =~ pair[0] then 143 oldvalue = pair[1] 144 true 145 else 146 false 147 end 148 end 149 return oldvalue 150 end
Return the option.
Arguments:
-
key: option name as a string, e.g. ‘m’, ‘p’, or ‘-m’, ‘-p’.
- Returns
-
String or nil
# File lib/bio/appl/blast/ncbioptions.rb 116 def get(key) 117 re = _key_to_regexp(key) 118 119 # Note: the last option is used when two or more same option exist. 120 value = nil 121 @option_pairs.reverse_each do |pair| 122 if re =~ pair[0] then 123 value = pair[1] 124 break 125 end 126 end 127 return value 128 end
Returns an array for command-line options. prior_options are preferred to be used.
# File lib/bio/appl/blast/ncbioptions.rb 210 def make_command_line_options(prior_options = []) 211 newopts = self.class.new(self.options) 212 #newopts.normalize! 213 prior_pairs = _parse_options(prior_options) 214 prior_pairs.each do |pair| 215 newopts.delete(pair[0]) 216 end 217 newopts.option_pairs[0, 0] = prior_pairs 218 newopts.options 219 end
Normalize options. For two or more same options (e.g. ‘-p blastn -p blastp’), only the last option is used. (e.g. ‘-p blastp’ for above example).
Note that completely illegal options are left untouched.
- Returns
-
self
# File lib/bio/appl/blast/ncbioptions.rb 74 def normalize! 75 hash = {} 76 newpairs = [] 77 @option_pairs.reverse_each do |pair| 78 if pair.size == 2 then 79 key = pair[0] 80 unless hash[key] then 81 newpairs.push pair 82 hash[key] = pair 83 end 84 else 85 newpairs.push pair 86 end 87 end 88 newpairs.reverse! 89 @option_pairs = newpairs 90 self 91 end
current options as an array of strings
# File lib/bio/appl/blast/ncbioptions.rb 94 def options 95 @option_pairs.flatten 96 end
Sets the option to given value.
For example, if you want to set ‘-p blastall’ option,
obj.set('p', 'blastall')
or
obj.set('-p', 'blastall')
(above two are equivalent).
Arguments:
-
key: option name as a string, e.g. ‘m’, ‘p’.
-
value: value as a string, e.g. ‘7’, ‘blastp’.
- Returns
-
previous value; String or nil
# File lib/bio/appl/blast/ncbioptions.rb 165 def set(key, value) 166 re = _key_to_regexp(key) 167 oldvalue = nil 168 flag = false 169 # Note: only the last options is modified for multiple same options. 170 @option_pairs.reverse_each do |pair| 171 if re =~ pair[0] then 172 oldvalue = pair[1] 173 pair[1] = value 174 flag = true 175 break 176 end 177 end 178 unless flag then 179 key = "-#{key}" unless key[0, 1] == '-' 180 @option_pairs.push([ key, value ]) 181 end 182 oldvalue 183 end