+ s = range.split("-")
+ from = s[ 0 ].to_i
+ to = s[ 1 ].to_i
+ new_msa_domains.add_sequence( Sequence.new( orig_name +
+ " [" + from.to_s +
+ "-" + to.to_s +
+ "] [" + basename + "] [" +
+ current_species + "]",
+ seq.get_sequence_as_string[from..to] ) )
+ if extension > 0
+ from_e = from - extension
+ if from_e < 0
+ from_e = 0
+ end
+ to_e = to + extension
+ if to_e > seq.get_sequence_as_string.length - 1
+ to_e = seq.get_sequence_as_string.length - 1
+ end
+ new_msa_domains_extended.add_sequence( Sequence.new( orig_name +
+ " [" + from.to_s +
+ "-" + to.to_s +
+ "] [extended by " +
+ extension.to_s +
+ "] [" + basename + "] [" +
+ current_species + "]",
+ seq.get_sequence_as_string[ from_e..to_e ] ) )
+ end # extension > 0
+ if extract_linkers
+ if first
+ first = false
+ f = 0
+ t = from - 1
+ if extension > 0
+ f = from - extension
+ end
+ mod_line = line + "\t[" + get_linker_sequence( f, t, seq ) + "|"
+ else
+ mod_line += get_linker_sequence( prev_to + 1, from - 1, seq ) + "|"
+ end
+ prev_to = to
+ end
+ end # range != nil && range.length > 0