Opened 5 years ago

Last modified 2 months ago

#451 new defect

'Move groups..' changes root

Reported by: westram Owned by: devel
Priority: major Milestone: wishlist
Component: ARB_NTREE Version: SVN
Keywords: Cc:

Description (last modified by westram)

Status quo:

Method used to set root is very naive (see highlighted code):

  • it is set to those 2 target-subtrees that match son-of-root-subtrees of source-tree. order is random. works ok if trees are similar. doesn't work at all if trees differ significantly.
  • if group insertion could handle keeled groups (resp. keeled target subtrees), it would not be necessary to change root at all. Unwanted effects (by not doing so):
    • if both sons of source-root are a group
      ⇒ results differ depending on target root position: sometimes one group is skipped, sometimes both get inserted
    • if one son of source-root is a group
      ⇒ group is (sometimes) placed at wrong son-of-root in destination tree

Wanted fixes:

  • root should be corrected using method implemented with #449 (only perform optionally)
  • insert keeled group if it fits better (see arb documentation for meaning of keeled groups)
    • if both sons of root are groups, they should match the correct subtrees (keeled or not) since implementation of #780. When function can handle keeled groups correctly
      ⇒ check problem again
      e.g. happens with LTPs132_SSU.arb when root is changed:
      Group 'Bacteria' skipped (got superseded by group 'Archaea'; same best target positions)
      

when corrected update [11432]
related: #512
requires: #449

Change History (11)

comment:1 Changed 5 years ago by westram

  • Description modified (diff)

comment:2 Changed 2 years ago by westram

  • Description modified (diff)

comment:3 Changed 2 years ago by westram

  • Description modified (diff)

comment:4 Changed 2 years ago by westram

  • Description modified (diff)

comment:5 Changed 21 months ago by westram

  • Description modified (diff)
  • Milestone set to wishlist

comment:6 Changed 19 months ago by westram

  • Description modified (diff)

comment:7 Changed 11 months ago by westram

  • Priority changed from normal to major

comment:8 Changed 11 months ago by westram

  • Description modified (diff)

comment:9 Changed 5 months ago by westram

  • Description modified (diff)

comment:10 Changed 3 months ago by westram

  • Description modified (diff)

updated ticket while working on #780

comment:11 Changed 2 months ago by westram

  • Description modified (diff)
  • Summary changed from 'Move node info' (TreeAdmin) changes root to 'Move groups..' changes root
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