Class Bio::Blast::NCBIOptions
In: lib/bio/appl/blast/ncbioptions.rb
Parent: Object

A class to parse and store NCBI-tools style command-line options. It is internally used in Bio::Blast and some other classes.

Methods

==   add_options   delete   get   make_command_line_options   new   normalize!   options   parse   set  

Attributes

option_pairs  [R]  (protected) option pairs. internal use only.

Public Class methods

new(options = [])

creates a new object from an array

[Source]

    # File lib/bio/appl/blast/ncbioptions.rb, line 27
27:     def initialize(options = [])
28:       #@option_pairs = []
29:       @option_pairs = _parse_options(options)
30:     end
parse(str)

parses a string and returns a new object

[Source]

    # File lib/bio/appl/blast/ncbioptions.rb, line 96
96:     def self.parse(str)
97:       options = Shellwords.shellwords(str)
98:       self.new(options)
99:     end

Public Instance methods

==(other)

If self == other, returns true. Otherwise, returns false.

[Source]

     # File lib/bio/appl/blast/ncbioptions.rb, line 195
195:     def ==(other)
196:       return true if super(other)
197:       begin
198:         oopts = other.options
199:       rescue
200:         return false
201:       end
202:       return self.options == oopts 
203:     end
add_options(options)

Adds options from given array. Note that existing options will also be normalized.

Arguments:

Returns:self

[Source]

     # File lib/bio/appl/blast/ncbioptions.rb, line 188
188:     def add_options(options)
189:       @option_pairs.concat _parse_options(options)
190:       self.normalize!
191:       self
192:     end
delete(key)

Delete the given option.

Arguments:

  • key: option name as a string, e.g. ‘m’, ‘p’, or ’-m’, ’-p’.
Returns:String or nil

[Source]

     # File lib/bio/appl/blast/ncbioptions.rb, line 132
132:     def delete(key)
133:       re = _key_to_regexp(key)
134: 
135:       # Note: the last option is used for return value
136:       # when two or more same option exist.
137:       oldvalue = nil
138:       @option_pairs = @option_pairs.delete_if do |pair|
139:         if re =~ pair[0] then
140:           oldvalue = pair[1]
141:           true
142:         else
143:           false
144:         end
145:       end
146:       return oldvalue
147:     end
get(key)

Return the option.

Arguments:

  • key: option name as a string, e.g. ‘m’, ‘p’, or ’-m’, ’-p’.
Returns:String or nil

[Source]

     # File lib/bio/appl/blast/ncbioptions.rb, line 113
113:     def get(key)
114:       re = _key_to_regexp(key)
115: 
116:       # Note: the last option is used when two or more same option exist.
117:       value = nil
118:       @option_pairs.reverse_each do |pair|
119:         if re =~ pair[0] then
120:           value = pair[1]
121:           break
122:         end
123:       end
124:       return value
125:     end
make_command_line_options(prior_options = [])

Returns an array for command-line options. prior_options are preferred to be used.

[Source]

     # File lib/bio/appl/blast/ncbioptions.rb, line 207
207:     def make_command_line_options(prior_options = [])
208:       newopts = self.class.new(self.options)
209:       #newopts.normalize!
210:       prior_pairs = _parse_options(prior_options)
211:       prior_pairs.each do |pair|
212:         newopts.delete(pair[0])
213:       end
214:       newopts.option_pairs[0, 0] = prior_pairs
215:       newopts.options
216:     end
normalize!()

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

[Source]

    # File lib/bio/appl/blast/ncbioptions.rb, line 71
71:     def normalize!
72:       hash = {}
73:       newpairs = []
74:       @option_pairs.reverse_each do |pair|
75:         if pair.size == 2 then
76:           key = pair[0]
77:           unless hash[key] then
78:             newpairs.push pair
79:             hash[key] = pair
80:           end
81:         else
82:           newpairs.push pair
83:         end
84:       end
85:       newpairs.reverse!
86:       @option_pairs = newpairs
87:       self
88:     end
options()

current options as an array of strings

[Source]

    # File lib/bio/appl/blast/ncbioptions.rb, line 91
91:     def options
92:       @option_pairs.flatten
93:     end
set(key, value)

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

[Source]

     # File lib/bio/appl/blast/ncbioptions.rb, line 162
162:     def set(key, value)
163:       re = _key_to_regexp(key)
164:       oldvalue = nil
165:       flag = false
166:       # Note: only the last options is modified for multiple same options.
167:       @option_pairs.reverse_each do |pair|
168:         if re =~ pair[0] then
169:           oldvalue = pair[1]
170:           pair[1] = value
171:           flag = true
172:           break
173:         end
174:       end
175:       unless flag then
176:         key = "-#{key}" unless key[0, 1] == '-'
177:         @option_pairs.push([ key, value ])
178:       end
179:       oldvalue
180:     end

[Validate]