generalize ACI to work with groups

[epruesse]

Currently, ACI et al always operate on single sequences. The only exception that I know of is taxonomy which also works on groups.

It would be very helpful for a number of tasks to be able to work with groups more flexibly.

Examples:

• counting the number of species in a group (all or marked)
• computing the fraction that is marked

Also allow to configure group-number shown at groups in -display using an ACI (see discussion in #209)

related: #652

[westram]

Quite difficult because

• the ACI always operates on one -item (e.g. species, organism, gene or SAI)
• groups are no -items, they are just a property of the (currently selected) .

Possible implementation:

• add ACI commands to generate selections of -Items:
  • selections could be stored as string
    • e.g. "SELECTION!SPECIESELEMCOUNT:id1,id2,id3,...,idN"
  • possible commands:
    • select(ITEMTYPE[,attribute,value])
      where
      • ITEMTYPE=['SPECIES','GENE','ORGANISM','SAI']
      • attribute=ACI
      • value=string Returns selection of items for which 'attribute' evaluates to 'value'.
    • select_marked(ITEMTYPE)
    • tree_members(ITEMTYPE[,treename]) — only for SPECIES and ORGANISM
• add ACI commands modifying selection(s) of -Items:
  • union(selection1,selection2,…)
  • intersection(selection1,selection2,…)
  • difference(selection1,selection2)
  • keep_elements(selection,attribute,value) — keep all elements where 'attribute' evaluates to 'value'
  • remove_elements(selection,attribute,value) — remove all elements where 'attribute' evaluates to 'value'
  • genes_of(ORGANISM-selection)
  • organisms_of(GENE-selection)
  • …
• add ACI commands retrieving information from selections:
  • elements(selection) — retrieves number of elements
  • …

Your example

E.g. counting the number of species in a group that are marked. Or computing the fraction that is marked.

could be done with the above commands using

tree_members(SPECIES)|keep_elements("taxonomy","your/wanted/group")|dd;intersection(select_marked(SPECIES))|elements|swap|per_cent

[westram]

Decided against implementing ACI commands for groups (at least atm/in the way sketched above).

Reasons:

• I fear commands sketched above would be far too slow for use in display
• beside counting marked/all of groups I got no ideas for useful commands
• group-ACIs would only apply to
  • displayed and
  • planned group-search (#652)

For now, I'll implement some predefined ways to display group/marked counters together with #118.

For later, a better way to implement group-specific commands would be to implement a possibility to inject commands into ACI by caller (e.g. group-search or -display).