optimize does not restrict on marked visible parts of tree

[westram]

Optimize was designed to operate only on subtrees which are visible (i.e. not inside folded groups) and contain marked.

Previous behavior:

• recursive NNI always operates on whole
• KL optimize operates on whole , but stops recursion when inside a folded group

Current behavior [13589]:

• NNI operates on marked visible edges only
• KL starts recursion on marked visible edges and descends along visible edges

Wanted behavior:

• make both criteria configurable:
  • only consider marked branches (opposed to considering all)
  • do not optimize inside folded groups (opposed to optimizing everywhere)

To check:

• ensure flags used to test for folding/marking are correct after modifications

[westram]

[13519] and [13520] added tests showing what's wrong with EdgeChains

• fixing this problem reduces the number of edges in chains (as many are added by mistake)
• as an unwanted result, this affects the quality produced by NNI, because
  • after the fix only marked edges are used
  • as [13521] documents, these mark-flags are invalidated by several operations

⇒ NNI doesn't optimize marked species when called several times, e.g.

• during add+NNI or
• in recursive-NNI)

[westram]

by [13589]

customizable with [13593]

[westram]

mark changes that got fixed after arb 6.0.x

[westram]

Milestone renamed