Class: SequenceGroup

Inherits:
Object
  • Object
show all
Defined in:
lib/seqtrimnext/classes/sequence_group.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(seqs) ⇒ SequenceGroup

Returns a new instance of SequenceGroup.



8
9
10
11
12
13
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 8

def initialize(seqs)
  @stats={}
  @seqs=seqs
  @output_text={}
  @output_files={}
end

Instance Attribute Details

#output_files ⇒ Object

Returns the value of attribute output_files.



5
6
7
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 5

def output_files
  @output_files
end

#output_text ⇒ Object

Returns the value of attribute output_text.



5
6
7
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 5

def output_text
  @output_text
end

#stats ⇒ Object

Returns the value of attribute stats.



5
6
7
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 5

def stats
  @stats
end

Instance Method Details

#add(array) ⇒ Object 



48
49
50
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 48

def add(array)
  @seqs += array
end

#count ⇒ Object 



52
53
54
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 52

def count
  return @seqs.count
end

#delete(seq) ⇒ Object 



20
21
22
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 20

def delete(seq)
  @seqs.delete(seq)
end

#each ⇒ Object 



29
30
31
32
33
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 29

def each
    @seqs.each do |seq|
      yield seq
    end
end

#each_with_index ⇒ Object 



35
36
37
38
39
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 35

def each_with_index
    @seqs.each_with_index do |seq,i|
      yield seq,i
    end
end

#empty? ⇒ Boolean

Returns:

  • (Boolean) 


24
25
26
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 24

def empty?
  return @seqs.empty?
end

#include?(s) ⇒ Boolean

Returns:

  • (Boolean) 


56
57
58
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 56

def include?(s)
  return @seqs.include?(s)
end

#inspect ⇒ Object

def job_identifier

return @seqs[0].seq_name

end



68
69
70
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 68

def inspect
  return "Group with #{@seqs.count} sequences"
end

#push(seq) ⇒ Object 



16
17
18
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 16

def push(seq)
  @seqs.push seq
end

#remove_all_seqs ⇒ Object 



60
61
62
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 60

def remove_all_seqs
  @seqs=[]
end

#reverse_each ⇒ Object 



42
43
44
45
46
 
# File 'lib/seqtrimnext/classes/sequence_group.rb', line 42

def reverse_each
    @seqs.reverse_each do |seq|
      yield seq
    end
end