Class: Contig

Inherits:
Object
  • Object
show all
Defined in:
lib/scbi_ace/contig.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(name, length, reads_num, bs_num, orientation) ⇒ Contig

Returns a new instance of Contig.



11
12
13
14
15
16
17
18
19
20
21
22
23
24
 
# File 'lib/scbi_ace/contig.rb', line 11

def initialize(name,length,reads_num,bs_num,orientation)
	
	@name = name
	@length = length
	@reads_num = reads_num
	@bs_num = bs_num
	@orientation = orientation
	
	@reads = {}
	@reads_names = []
	
	@fasta = ''
	@qual = ''
end

Instance Attribute Details

#bs_num ⇒ Object

Returns the value of attribute bs_num.



9
10
11
 
# File 'lib/scbi_ace/contig.rb', line 9

def bs_num
  @bs_num
end

#fasta ⇒ Object

Returns the value of attribute fasta.



9
10
11
 
# File 'lib/scbi_ace/contig.rb', line 9

def fasta
  @fasta
end

#length ⇒ Object

Returns the value of attribute length.



9
10
11
 
# File 'lib/scbi_ace/contig.rb', line 9

def length
  @length
end

#name ⇒ Object

Returns the value of attribute name.



9
10
11
 
# File 'lib/scbi_ace/contig.rb', line 9

def name
  @name
end

#orientation ⇒ Object

Returns the value of attribute orientation.



9
10
11
 
# File 'lib/scbi_ace/contig.rb', line 9

def orientation
  @orientation
end

#qual ⇒ Object

Returns the value of attribute qual.



9
10
11
 
# File 'lib/scbi_ace/contig.rb', line 9

def qual
  @qual
end

#reads ⇒ Object

Returns the value of attribute reads.



9
10
11
 
# File 'lib/scbi_ace/contig.rb', line 9

def reads
  @reads
end

#reads_names ⇒ Object

Returns the value of attribute reads_names.



9
10
11
 
# File 'lib/scbi_ace/contig.rb', line 9

def reads_names
  @reads_names
end

#reads_num ⇒ Object

Returns the value of attribute reads_num.



9
10
11
 
# File 'lib/scbi_ace/contig.rb', line 9

def reads_num
  @reads_num
end

Instance Method Details

#add_fasta(fasta) ⇒ Object 



33
34
35
 
# File 'lib/scbi_ace/contig.rb', line 33

def add_fasta(fasta)
	@fasta = fasta
end

#add_qual(qual) ⇒ Object 



37
38
39
 
# File 'lib/scbi_ace/contig.rb', line 37

def add_qual(qual)
	@qual = qual
end

#add_read(read_name, orientation, start_consensus) ⇒ Object 



26
27
28
29
30
31
 
# File 'lib/scbi_ace/contig.rb', line 26

def add_read(read_name,orientation,start_consensus)
	read= Read.new(read_name,orientation,start_consensus)
	@reads_names << read_name
	@reads[read_name] = read
	return read
end

#get_read(read_name) ⇒ Object 



41
42
43
 
# File 'lib/scbi_ace/contig.rb', line 41

def get_read(read_name)
	return @reads[read_name]
end

#get_read_names ⇒ Object 



45
46
47
 
# File 'lib/scbi_ace/contig.rb', line 45

def get_read_names
	return @reads_names
end