Opened 11 years ago

Last modified 11 years ago

#352 new enhancement

Editing alignments extremely slow with large DB/tree

Reported by: epruesse Owned by: devel
Priority: major Milestone:
Component: ARB_EDIT4 Version: SVN
Keywords: Cc: bfuchs@…


When editing alignments, each key-press causes a large delay when using the big SILVA Ref datasets. Possibly due to a cascade of CBs or too much DB activity in general.

Change History (4)

comment:1 Changed 11 years ago by epruesse

  • Cc bfuchs@… added

comment:2 follow-up: Changed 11 years ago by epruesse

possibly fixed/alleviated in gtkport branch

comment:3 in reply to: ↑ 2 Changed 11 years ago by epruesse

Replying to epruesse: in r10749

comment:4 Changed 11 years ago by epruesse

The issue is probably caused by updating the "selected species" database entry.

The first time, "key-down" is pressed in the editor, that database entry is changed. The change is sent to arb_ntree. Even if the refresh is delayed (as per r10749) the redraw and jumping needs to lock the DB for reading for a long time (given a large tree). Therefore, the subsequent editing or changes to the active-sequence are delayed until NTREE releases the DB lock. Until then, the editor blocks.

Making the selected species a global awar would not help, as these are also backed by the main database.

A possible approach would be to make tree jumping/redraw more independent of the DB.

More effort (much more) would be to separate "read" from "write" transactions and/or lock only subtrees of the DB.

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