Opened 8 years ago

Closed 8 years ago

Last modified 12 months ago

#609 closed defect (fixed)

'Add marked partial species' fails if no overlap

Reported by: westram Owned by: westram
Priority: major Milestone: arb7.0
Component: ARB_PARSIMONY Version: SVN
Keywords: Cc:

Description (last modified by westram)

if partial and (one) full-length species do not overlap at all, the partial will be added there.

Reason:

  • no mismatches occur, as the dots act like 'N's
  • happens easily if a species has wrong alignment
    (e.g. acc='L39865' in ssurefnr99_119)

Reproduce:

  • load attached db
  • run attached macro which does:
    • insert marked 'CloTyro3' using 'Add marked partial species' into both trees
    • startup editor with the (full) species used as insert position
      • 'BacStear' chosen in 'tree_full'
      • 'CorGluta' chosen in 'tree_part'

The insertion into 'tree_full' reproduces the bug:

  • sequences of 'BacStear' and 'CloTyro3' do not overlap at all
  • 'tree_part' does not contain 'BacStear' - so the bug does not happen here

blocked by #619

Attachments (2)

_logged.amc (1.9 KB) - added by westram 8 years ago.
wrong_partial.arb (80.8 KB) - added by westram 8 years ago.

Download all attachments as: .zip

Change History (10)

comment:1 Changed 8 years ago by westram

  • Owner changed from devel to westram
  • Status changed from new to _started

comment:2 Changed 8 years ago by westram

  • Description modified (diff)

Changed 8 years ago by westram

Changed 8 years ago by westram

comment:3 Changed 8 years ago by westram

added a test demonstrating wrong behavior with [13099]

comment:4 Changed 8 years ago by westram

  • Description modified (diff)

comment:5 follow-up: Changed 8 years ago by westram

  • Resolution set to fixed
  • Status changed from _started to closed

by [13452]

comment:6 in reply to: ↑ 5 Changed 8 years ago by westram

by [13452]

discarded! refixed by [13461]

comment:7 Changed 7 years ago by westram

  • Milestone set to arb6.1

mark changes that got fixed after arb 6.0.x

comment:8 Changed 12 months ago by westram

  • Milestone changed from arb6.1 to arb7.0

Milestone renamed

Note: See TracTickets for help on using tickets.