Incosistent alphabet deriving for alignments: pasting to MSA

Current problem

Modification of an alignment alphabet after pasting of data into the alignment must be handled similarly to other use cases (see UGENE-4804, UGENE-4833, UGENE-4816).

Required solution

Actions

Apply modification for the following actions:

1. Pasting of raw data with one sequence into an alignment.
2. Pasting of raw data with several sequences into an alignment (divided by Unix/Mac OS X new line "\n").
3. Pasting of raw data with several sequences into an alignment (divided by Windows new line "\r\n").
4. Pasting of formatted data with one sequence into an alignment (e.g. pasting of a GenBank file).
5. Pasting of formatted data with several sequences into an alignment (e.g. pasting of a multi-FASTA).
6. Pasting of URI to a file with one sequence into an alignment.
7. Pasting of URI to a file with several sequences into an alignment.

Note that there are three sources to launch the actions (each of them must be covered in GUI tests):

1. "Actions > Copy/Paste > Paste" item of the main menu is used.
2. "Copy/Paste > Paste" item of the alignment context menu.
3. Using hotkey (Ctrl+V for Windows and Linux, Cmd+V for Mac OS X).

Rules for Switching Alphabets

See the description of rules in UGENE-4804.

Use Cases

For each action, specified above, make sure that the following scenarios work properly in accordance with the alphabets switching rules.

Use case 1:

1. Open an alignment with some alphabet.
2. Do the action for a sequence (or sequences) of the same alphabet.
   Expected state:
   • For actions 1, 4, 6: The sequence was added to the bottom of the alignment.
     For actions 2, 3, 5, 7: The sequences were added to the bottom of the alignment.
   • There are NO notifications.

Use case 2 (for actions 1, 4, 6):

1. Open an alignment with some alphabet.
2. Use a sequence of another alphabet.
   Expected state:
   • For actions 1, 4, 6: The sequence was added to the bottom of the alignment.
     For actions 2, 3, 5, 7 (see UCs below): The sequences were added to the bottom of the alignment.
   • A warning notification appears:

     The alignment has been modified, so that its alphabet has been switched from "%1" to "%2". Use "Undo", if you'd like to restore the original alignment.

     Here "%1" and "%2" are taken from values: "Standard DNA", "Extended DNA", "Standard RNA", "Extended RNA", "Standard amino acid", "Extended amino acid", "Raw".

3. Undo the modifications.
   Expected state:
   • The alignment has been reverted to the previous state.
   • There are NO notifications.

Use case 3 (for actions 2, 3, 5, 7):
Similar to UC2. The alphabet of the first sequence of the several added sequences differs.

Use case 4 (for actions 2, 3, 5, 7):
Similar to UC2. The alphabet of a sequence in the middle of the several added sequences differs.

Use case 5 (for actions 2, 3, 5, 7):
Similar to UC2.

• The alphabet of the alignment is "Standard DNA".
• The alphabet of the first sequence of the several added is "Extended DNA".
• The alphabet of the last sequence of the several added is "Standard amino acid".

Use case 6:

1. Open an alignment with some alphabet.
2. Do the action for a sequence (or sequences) of another alphabet.
   Expected state: The warning notification appears.
3. Click "Undo".
   Expected state: There are NO notifications.
4. Click "Redo".
   Expected state: The warning notification appears again.