'apply to whole alignment' type alternatives for 'invalid input data' error dialogs

In a few cases, Jalview will warn the user that the input data for an analysis is invalid - usually because there aren't enough sequences, they aren't aligned, or there aren't enough sequence groups defined for the analysis to work on.

This can be particularly confusing for analyses such as Multi Harmony, where the user may often create groups manually prior to submitting the alignment to the service. In this case, when the user has just created a group, then any subsequent analysis will be performed on sequences in the new group only rather than the whole view, when actually, the user should have cleared the current selection before submitting to the service.

For warning dialogs like the 'service needs at least two groups on the alignment' message, an option could be provided that submits all the alignment, rather than the selected region. Similarly, for tree calculations, the user could be provided with a button that will first enable 'Pad Gaps' and then perform the calculation.