Incosistent alphabet deriving for alignments: remained use cases

Current problem

Adding of a sequence into an alignment is not consistent in the current UGENE version. For example:

1. When an amino acid sequence is added to an alignment with "Extended DNA" alphabet, the result alignment alphabet is amino acid.
2. When an amino acid sequence is added to an alignment with "Standard DNA" alphabet, the result alphabet is "Raw".

So, it must be done more consistent and user-friendly as described below.

Required solution

Actions

Apply modification for the following actions:

1. "Sequence from current project" item in the context menu is used.
2. "Actions > Add > Sequence from current project" item of the main menu is used.
3. "Align sequences to profile with MUSCLE" item is used:
   • In the "Align" sub-menu of the alignment context menu.
   • In the "Actions > Align" sub-menu of the main menu.
   • In the menu of the "Align" toolbar button.
4. "Align profile to profile" item is used:
   In the same three location as above.

Rules for Switching Alphabets

UGENE supports seven alphabets for sequences and multiple alignments ("Standard DNA", "Extended DNA", etc.). The rules for switching between the alphabets on sequence adding to an alignment are described on the figure in the attachment. Each cell of the table on the figure is the intersection of the alignment alphabet (rows) and alphabet of the added sequence (columns). The value of a cell specifies the alphabet of the result alignment.

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 of the same alphabet.
   Expected state:
   • The sequence was added according to the action.
   • There is NO notifications.

Use case 2:

1. Open an alignment with some alphabet.
2. Do the action for a sequence of another alphabet.
   Expected state:
   • The sequence was added according to the action.
   • 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 is NO notifications.

Use case 3:

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