jalview/test/jalview/ws

jabaws

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Tuesday 08 Mar
9:30 pm

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

JAL-3438 spotless for 2.11.2.0

Options
    • -20
    • +15
    ./DisorderAnnotExportImport.java
    • -2
    • +2
    ./JalviewJabawsTestUtils.java
    • -3
    • +4
    ./MinJabawsClientTests.java
    • -31
    • +26
    ./RNAStructExportImport.java
  5. … 658 more files in changeset.
Wednesday 02 Mar
6:25 pm

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

JAL-3438 - all src and test run through spotless..

Options
    • -20
    • +15
    ./DisorderAnnotExportImport.java
    • -2
    • +2
    ./JalviewJabawsTestUtils.java
    • -3
    • +4
    ./MinJabawsClientTests.java
    • -31
    • +26
    ./RNAStructExportImport.java
  5. … 665 more files in changeset.
Friday 11 Feb
3:27 pm

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

JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

Conflicts:

src/jalview/bin/Jalview.java

Options
    • -1
    • +2
    ./DisorderAnnotExportImport.java
    • -1
    • +2
    ./RNAStructExportImport.java
  3. … 97 more files in changeset.
Wednesday 22 Sep 2021
12:08 am

Ben Soares

JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

Options
    • -1
    • +3
    ./DisorderAnnotExportImport.java
    • -1
    • +3
    ./RNAStructExportImport.java
  3. … 101 more files in changeset.
Thursday 22 Jul 2021
6:00 pm

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

JAL-3848 - actually test the Slivka and JABAWS disorder services - nb still need asserts to verify the disorder annotation from Slivka looks like Jabaws

Options
    • -3
    • +18
    ./DisorderAnnotExportImport.java
Tuesday 06 Jul 2021
5:42 pm

Jim Procter

5:42 pm

Jim Procter

WIP
WIP
Wednesday 15 Jul 2020
5:39 pm

Mateusz Warowny

JAL-3690 refactoring web-services discovery

Options
    • -1
    • +1
    ./DisorderAnnotExportImport.java
  2. … 9 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.

1:52 pm

Mungo Carstairs

Unclear what notifySequence() adds. As placed here, it is hardly ever reached.

Unclear what notifySequence() adds. As placed here, it is hardly ever reached.

12:36 pm

Mungo Carstairs

Not sure how to review this (and the appletgui/js classes) without pointers to documentation and/or examples of how it is used.

Not sure how to review this (and the appletgui/js classes) without pointers to documentation and/or examples of how it is used.

12:18 pm

Mungo Carstairs

Needs proper Javadoc

Needs proper Javadoc

11:37 am

Mungo Carstairs

Files added to doc folder: are this intended as working documents, or publishable documentation? Bearing in mind that that are findable on the web and a user might reasonably expect them to provide...

Files added to doc folder: are this intended as working documents, or publishable documentation? Bearing in mind that that are findable on the web and a user might reasonably expect them to provide documentation.
e.g. http://source.jalview.org/gitweb/?p=jalview.git;a=blob;f=doc/JalviewJS-startupParams.md;h=9ff33529b2dbc2da34d2a573ccf5d042194fbb0d;hb=refs/heads/Jalview-JS/develop

Thursday 25 Jun 2020
2:16 pm

Mungo Carstairs

Due to the number of changes this is likely to be a 'best efforts' review.

Due to the number of changes this is likely to be a 'best efforts' review.

2:14 pm

Mungo Carstairs

Commits to JS-develop from 2nd to 25th June 2020
Commits to JS-develop from 2nd to 25th June 2020
2:01 pm

Mungo Carstairs

Wednesday 03 Jun 2020
4:41 am

Bob Hanson

I suggest we close this. It's all ancient history now.

I suggest we close this. It's all ancient history now.

12:23 am

Bob Hanson

JAL-3446 JAL-3401 from JAL-3253 HoldRepaint and SeqCanvas sizing issues.

- integrated changes from 0b573ed (gmungoc)

Options
    • -2
    • +2
    ./JalviewJabawsTestUtils.java
  2. … 7 more files in changeset.
Tuesday 04 Feb 2020
11:49 am

Mateusz Warowny

startDiscoverer should not return Thread because Discoverer's internal implementation may spawn more threads or use a thread pool. Returned thread is not a reliable indicator whether the discoverer...

startDiscoverer should not return Thread because Discoverer's internal implementation may spawn more threads or use a thread pool. Returned thread is not a reliable indicator whether the discoverer is still running. isRunning() should be used instead. The return type was kept for compatibility with Jws2Discoverer and other classes relying on it.

11:47 am

Mateusz Warowny

Adding the same change listener over and over by the Desktop class may cause events to be received multiple times. PropertyChangeListener uses an array internally and doesn't check for repeated lis...

Adding the same change listener over and over by the Desktop class may cause events to be received multiple times. PropertyChangeListener uses an array internally and doesn't check for repeated listeners.

11:33 am

Mateusz Warowny

How about adding WSDiscoverer.isEnabled()

How about adding WSDiscoverer.isEnabled()

11:31 am

Mateusz Warowny

JAL-3515 Extract core WSDiscoverer methods to a separate interface
JAL-3515 Extract core WSDiscoverer methods to a separate interface
11:26 am

Mateusz Warowny

JAL-3515 Extract core WSDiscoverer methods to a separate interface

Creating WSDiscovererI interface helps to separating exposed methods from internal implementation details of Jws2Discoverer and implements the same functionality in SlivkaWSDiscoverer

Options
    • -1
    • +2
    ./AAConAnnotAndSettingsIO.java
    • -1
    • +5
    ./DisorderAnnotExportImport.java
  3. … 6 more files in changeset.
Monday 14 Oct 2019
3:33 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3453 test changes needed to allow tests to proceed unheeded by dialogs.

Options
    • -1
    • +3
    ./RNAStructExportImport.java
  2. … 3 more files in changeset.
Monday 07 Oct 2019
9:03 am

Jim Procter

JAL-3070 jaba/slivka independent tests for disorder and AACon services

Options
    • -3
    • +7
    ./AAConAnnotAndSettingsIO.java
    • -3
    • +5
    ./DisorderAnnotExportImport.java
Thursday 03 Oct 2019
5:53 pm

Jim Procter

JAL-3070 test jabaws and slivka AACon service functionality

Options
    • -60
    • +58
    ./AAConAnnotAndSettingsIO.java
4:25 pm

Jim Procter

JAL-3070 basic AACon service functionality test

Options
    • -0
    • +198
    ./AAConAnnotAndSettingsIO.java