Major Local pairwise alignment should look in following way:
- in SW dialog at tab "Input and output" should be combobox (with label "Save result as") letting user to choose the way of algorithm result view. The set of those ways consists of two items - "Annotations" and "Multiple alignment". The second variant should be chosen by default.
- Content of tab "Input and output" should vary depending on chosen item in combobox. If "Annotations" chosen, then content should remain as it's now. Else if "Multiple alignment" chosen, then content should consist of line edit with the alignment files directory, which will contain search results, and some advanced options - names of [m]objects (and files at the same time), names of aligned subsequences. Button "Search" should change its label to "Align".
- Advanced options in dialog should be hide by default and should be shown after pressing on corresponding label. Names of [m]objects and names of aligned subsequences should be indicated by specific tags (some kind of regexps), which user can choose. The similar way is used in total cmd in "Rename file" dialog. Those tags are: reference sequence name, count of symbols, start position, end position, counter of results. Also some custom strings may be input from keyboard.
- After terminating SW algorithm new *.aln documents (with specified names) should be created and contain founded subsequences for one pair in each [m]object. Few documents may be loaded to current project, others will stay unloaded.