jalview/src/jalview

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Wednesday 13 Apr
11:46 pm

Mateusz Warowny

WIP

Options
    • -25
    • +13
    ./AlignCalcManager2.java
  2. … 2 more files in changeset.
Wednesday 23 Feb
2:26 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3417 propagate description from AnnotationProvider to the worker

Options
    • -0
    • +3
    ./AnnotationWorker.java
Tuesday 23 Nov 2021
3:31 pm

Mateusz Warowny

JAL-3878 Handle nulls when filtering annotation workers by name.

Options
    • -2
    • +2
    ./AlignCalcManager2.java
1:50 pm

Mateusz Warowny

JAL-3878 Add methods to get and remove workers by their calc name.

Options
    • -0
    • +29
    ./AlignCalcManager2.java
  2. … 1 more file in changeset.
Thursday 21 Oct 2021
3:52 pm

Mateusz Warowny

JAL-3878 Add methods to get and remove workers by their calc name.

Options
    • -0
    • +29
    ./AlignCalcManager2.java
  2. … 1 more file in changeset.
Wednesday 13 Oct 2021
2:30 pm

Mateusz Warowny <warownia1@gmail.com>

JAL-3878 Add getCalcName to AlignCalcWorkerI.

getCalcName() can be used to identify services that run the calculator.

when an alternative calculator (different host or parameters) is created

the old ones sharing the name can be stopped.

Options
    • -0
    • +6
    ./ColumnCounterSetWorker.java
    • -0
    • +6
    ./ComplementConsensusThread.java
    • -0
    • +6
    ./ConsensusThread.java
    • -0
    • +6
    ./ConservationThread.java
    • -0
    • +6
    ./InformationThread.java
    • -0
    • +6
    ./StrucConsensusThread.java
  7. … 3 more files in changeset.
2:30 pm

Mateusz Warowny <warownia1@gmail.com>

JAL-3878 Add getCalcName to AlignCalcWorkerI.

getCalcName() can be used to identify services that run the calculator.

when an alternative calculator (different host or parameters) is created

the old ones sharing the name can be stopped.

Options
    • -0
    • +6
    ./ColumnCounterSetWorker.java
    • -0
    • +6
    ./ComplementConsensusThread.java
    • -0
    • +6
    ./ConsensusThread.java
    • -0
    • +6
    ./ConservationThread.java
    • -0
    • +6
    ./InformationThread.java
    • -0
    • +6
    ./StrucConsensusThread.java
  7. … 3 more files in changeset.
Friday 09 Jul 2021
11:38 am

Mateusz Warowny

JAL-3690 Remove references to old AlignCalcManager.

Options
    • -410
    • +0
    ./AlignCalcManager.java
    • -1
    • +0
    ./AlignCalcWorker.java
  3. … 4 more files in changeset.
Tuesday 06 Jul 2021
5:42 pm

Jim Procter

5:42 pm

Jim Procter

WIP
WIP
Wednesday 27 Jan 2021
2:36 pm

Mateusz Warowny

JAL-3690 Introduce AlignCalcManager2 tests.

Options
    • -7
    • +10
    ./AlignCalcManager2.java
  2. … 2 more files in changeset.
Tuesday 19 Jan 2021
5:29 pm

Mateusz Warowny

JAL-3690 AlignCalcManager - add full support for oneshot workers

Options
    • -87
    • +124
    ./AlignCalcManager2.java
5:29 pm

Mateusz Warowny

JAL-3690 AlignCalcManager - add full support for oneshot workers

Options
    • -87
    • +124
    ./AlignCalcManager2.java
Monday 18 Jan 2021
4:50 pm

Mateusz Warowny

JAL-3690 Allow unregistered workers to be run with CalcManager.

Options
    • -5
    • +10
    ./AlignCalcManager2.java
4:50 pm

Mateusz Warowny

JAL-3690 Allow unregistered workers to be run with CalcManager.

Options
    • -5
    • +10
    ./AlignCalcManager2.java
Monday 14 Dec 2020
7:58 pm

Jim Procter

Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

Options
    • -0
    • +4
    ./AlignCalcManager.java
  2. … 56 more files in changeset.
Friday 27 Nov 2020
4:01 pm

Mateusz Warowny

JAL-3690 List.copyOf() workaround

Options
    • -1
    • +3
    ./AlignCalcManager2.java
Friday 13 Nov 2020
3:51 pm

Mateusz Warowny

JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker

Options
    • -1
    • +1
    ./AlignCalcManager.java
    • -8
    • +11
    ./AlignCalcManager2.java
  3. … 9 more files in changeset.
Thursday 12 Nov 2020
3:13 pm

Mateusz Warowny

JAL-3690 - fixed state inconsistency when restarting the calcworker

Options
    • -54
    • +22
    ./AlignCalcManager2.java
Wednesday 11 Nov 2020
6:42 pm

Mateusz Warowny

JAL-3690 partially reworked AlignCalcManager

todo:

- modify SeqAnnotationServiceCalcWorker to implement PollableAlignCalcWorkerI

- fix race condition where worker state gets overriden by the old job (QUEUED to IDLE)

Options
    • -183
    • +304
    ./AlignCalcManager2.java
  2. … 2 more files in changeset.
Monday 26 Oct 2020
12:20 pm

Mateusz Warowny

JAL-3690 - introduce shutdown method that cleans up manager's resources.

Options
    • -42
    • +108
    ./AlignCalcManager2.java
  2. … 3 more files in changeset.
Wednesday 21 Oct 2020
2:54 pm

Mateusz Warowny

JAL-3690 Catch and notify about worker cancellation separately.

Options
    • -0
    • +17
    ./AlignCalcManager2.java
  2. … 1 more file in changeset.
2:51 pm

Mateusz Warowny

JAL-3690 Fix concurrent modification exception when workers are cancelled

Options
    • -26
    • +32
    ./AlignCalcManager2.java
Sunday 02 Aug 2020
6:12 pm

Mateusz Warowny

JAL - 3690 AlignCalc rebuilt - WIP

Options
    • -37
    • +14
    ./AlignCalcManager.java
    • -0
    • +321
    ./AlignCalcManager2.java
    • -2
    • +4
    ./AlignCalcWorker.java
    • -1
    • +1
    ./AnnotationWorker.java
    • -1
    • +1
    ./ColumnCounterSetWorker.java
    • -1
    • +1
    ./ConsensusThread.java
    • -1
    • +1
    ./ConservationThread.java
    • -1
    • +1
    ./InformationThread.java
    • -1
    • +1
    ./StrucConsensusThread.java
  10. … 8 more files in changeset.
6:12 pm

Mateusz Warowny

JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

Options
    • -38
    • +23
    ./AlignCalcManager.java
    • -0
    • +319
    ./AlignCalcManager2.java
    • -2
    • +4
    ./AlignCalcWorker.java
    • -48
    • +26
    ./AnnotationWorker.java
    • -32
    • +10
    ./ColumnCounterSetWorker.java
    • -56
    • +18
    ./ConsensusThread.java
    • -59
    • +29
    ./ConservationThread.java
    • -58
    • +19
    ./InformationThread.java
    • -40
    • +0
    ./StrucConsensusThread.java
  10. … 11 more files in changeset.
6:12 pm

Mateusz Warowny

JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

Options
    • -38
    • +23
    ./AlignCalcManager.java
    • -0
    • +319
    ./AlignCalcManager2.java
    • -2
    • +4
    ./AlignCalcWorker.java
    • -48
    • +26
    ./AnnotationWorker.java
    • -32
    • +10
    ./ColumnCounterSetWorker.java
    • -56
    • +18
    ./ConsensusThread.java
    • -59
    • +29
    ./ConservationThread.java
    • -58
    • +19
    ./InformationThread.java
    • -40
    • +0
    ./StrucConsensusThread.java
  10. … 11 more files in changeset.
Tuesday 30 Jun 2020
4:50 pm

Mungo Carstairs

Ah it does run when a column selection is made in a split frame (and propagated to the other panel). Which seems to work! Maybe just needs a less clumsy AlignmentViewport.isColSelChanged() - this m...

Ah it does run when a column selection is made in a split frame (and propagated to the other panel). Which seems to work!
Maybe just needs a less clumsy AlignmentViewport.isColSelChanged() - this method seems to be trying to do two different things.

2:24 pm

Mungo Carstairs

Suggesting renaming to PROPERTY_COLUMNS = "columns" as this is used to notify changes to column selection or visibility, not sequences

Suggesting renaming to PROPERTY_COLUMNS = "columns" as this is used to notify changes to column selection or visibility, not sequences

2:12 pm

Mungo Carstairs

I think this code path rarely gets run (AlignmentViewport.notifySequence() rarely gets called). So what is it there for?

I think this code path rarely gets run (AlignmentViewport.notifySequence() rarely gets called).
So what is it there for?

1:54 pm

Mungo Carstairs

Suggest renaming notifyAlignment() to notifyAlignmentChanged(), and notifySequence() to notifyColumnChange() as it it fired for changes to column (not sequence) selection or visibility.

Suggest renaming notifyAlignment() to notifyAlignmentChanged(), and notifySequence() to notifyColumnChange() as it it fired for changes to column (not sequence) selection or visibility.