Allow Smith-Waterman worker to take sequences from two "Read Sequence" element

Based on: http://ugene.unipro.ru/forum/YaBB.pl?num=1342466056

Currently Smith-Waterman worker can do pairwise alignment only with input sequence and the patter field of the worker. This is incontinent for large-scale data manipulation. What if there is a file with the patter or user wants to find multiple patterns in the sequence.

Create a workflow sample(add to to samples) with Smith-Waterman worker that can take two "Read sequence" elements as an input - one for a reference and one for a pattern (there can be a number of sequences in the pattern). After filter the result to write only the reference sequence with annotations.