jalview

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Commits this week: 7
Total Committers: 73
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Commits this week: 7

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Wednesday 30 Mar
4:23 pm

Jim Procter

4:22 pm

Jim Procter

make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
4:20 pm

Jim Procter

JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
Monday 07 Mar
8:03 pm

Jim Procter

Thursday 03 Mar
9:26 am

Ben Soares

9:26 am

Ben Soares

Looks good. I've bumped the version to 1.8.3-1.2.12 and recompiled jars.

Looks good. I've bumped the version to 1.8.3-1.2.12 and recompiled jars.

Wednesday 02 Mar
12:20 pm

Jim Procter

JAL-3691 patch toUpper/toLower to use Locale.ROOT for 2.11.2 src
JAL-3691 patch toUpper/toLower to use Locale.ROOT for 2.11.2 src
Saturday 12 Feb
10:09 am

Ben Soares

JAL-3949 fix testProps path and make line count more accurate

Options
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    /test/jalview/bin/CommandLineOperations.java
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    • +1
    /test/jalview/bin/testProps.jvprops
Friday 11 Feb
4:12 pm

Ben Soares

That looks good. I was almost going to do something similar (I was thinking jalview.log.Log, but jalview.bin.Console is just as good) so happy with this!

That looks good. I was almost going to do something similar (I was thinking jalview.log.Log, but jalview.bin.Console is just as good) so happy with this!

3:49 pm

Ben Soares

Added those in. I'm still converting to String with getCanonicalName in the getLogger(Class ...) method because, e.g. JLogger jlogger1 = JLogger.getLogger(Jalview.class); JLogger jlogger2 = JLogger...

Added those in. I'm still converting to String with getCanonicalName in the getLogger(Class ...) method because, e.g.
JLogger jlogger1 = JLogger.getLogger(Jalview.class);
JLogger jlogger2 = JLogger.getLogger("jalview.bin.Jalview");
should really return an existing logger in the registry if it exists, and the String name is the registry key.

3:43 pm

Ben Soares

Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' of https://source.jalview.org/git/jalview into update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more

Options
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    /src/jalview/io/vamsas/DatastoreItem.java
    • -2
    • +2
    /src/jalview/log/JLogger.java
3:43 pm

Ben Soares

JLogger loglevel check on whether to call the actual logger or not. New factory methods with Class.

Options
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    /src/jalview/io/vamsas/DatastoreItem.java
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    /src/jalview/io/vamsas/DatastoreRegistry.java
    • -4
    • +19
    /src/jalview/log/JLogger.java
    • -3
    • +12
    /src/jalview/log/JLoggerLog4j.java
3:40 pm

Ben Soares

I was thinking that JLogger did this comparison anyway, but I've followed it through and it didn't. So I've added if (loglevel.compareTo(this.level) < 0) { return false; } to JLogger.println so t...

I was thinking that JLogger did this comparison anyway, but I've followed it through and it didn't. So I've added

if (loglevel.compareTo(this.level) < 0) { return false; }

to JLogger.println so that a comparison is made between the (enums) of JLogger.level and the message LogLevel, and if it's not going to be logged then it doesn't call the actual logger at all (in this case Log4j, so the log4j object is never even touched [even with logger.isDebugEnabled() because the answer should be no]).
This now applies to all log calls.
The check whether Cache.log != null is equivalent to Cache.log.loggerExists() which already happens within JLoggerLog4j.
There is admittedly the wrapper of the JLogger getting brought to forefront of memory, but that's presumably smaller than the old Cache.log which was a Log4j.Logger object.

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
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/analysis/GeneticCodes.java
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    • +2
    /src/jalview/analysis/PCA.java
    • -260
    • +31
    /src/jalview/bin/Cache.java
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    /src/jalview/bin/Console.java
    • -28
    • +28
    /src/jalview/bin/Jalview.java
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    /src/jalview/ext/ensembl/EnsemblLookup.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/ext/htsjdk/VCFReader.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    • +11
    /src/jalview/ext/pymol/PymolManager.java
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    /src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
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    • +6
    /src/jalview/ext/so/SequenceOntology.java
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    • +2
    /src/jalview/fts/service/alphafold/AlphafoldRestClient.java
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    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
  16. … 84 more files in changeset.
2:15 pm

Jim Procter

2:15 pm

Ben Soares

JAL-3949 fixed failing commandlinetests due to more output and line count limit

Options
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    • +2
    /test/jalview/bin/CommandLineOperations.java
2:14 pm

Ben Soares

JAL-3949 added Java Console autoscrolling help paragraph

Options
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    • +9
    /help/help/html/logging.html
2:09 pm

Jim Procter

AWESOME JOB !!!! one tiny niggle I had was that Cache.debug/Cache.error doesn't read nicely, so I've abstracted the logging stuff even farther to a new jalview.bin.Console class: see https://source...

AWESOME JOB !!!! one tiny niggle I had was that Cache.debug/Cache.error doesn't read nicely, so I've abstracted the logging stuff even farther to a new jalview.bin.Console class: see https://source.jalview.org/crucible/changelog/~br=update%402fJAL-3949_jalview_bin_Console_to_cure_sanity_even_more/jalview/

1:49 pm

Jim Procter

the reason for conditionals is that Java won't perform the string append operation if logLevel>debug. It saves a minor amount of processing time which is important for code that is executed lots.

the reason for conditionals is that Java won't perform the string append operation if logLevel>debug. It saves a minor amount of processing time which is important for code that is executed lots.

1:46 pm

Jim Procter

You could have .getLogger(Class ..) rather than having to call getCanonicalName ?

You could have .getLogger(Class ..) rather than having to call getCanonicalName ?

1:36 pm

Jim Procter

JAL-3949 An attempt at converting to Log4j 2 -- no output achieved!
JAL-3949 An attempt at converting to Log4j 2 -- no output achieved!
12:39 pm

Ben Soares

JAL-3949 read ~/.jalview_properties before initialising the logging

Options
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    /src/jalview/bin/Jalview.java
3:35 am

Ben Soares

Merge branch 'develop' into update/JAL-3949_abstracted_logging_for_jalviewjs_and_sanity

Options
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    /src/jalview/io/EMBLLikeFlatFile.java
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    /src/jalview/util/MappingUtils.java
3:34 am

Ben Soares

JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls for this. Removal of jalview.javascript.log4j. Improvements to the Java Console (controllable autoscrolling).

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    /gradle.properties
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/analysis/GeneticCodes.java
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    /src/jalview/analysis/PCA.java
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    /src/jalview/analysis/TreeModel.java
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    /src/jalview/bin/Cache.java
    • -46
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    /src/jalview/bin/Jalview.java
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    /src/jalview/ext/ensembl/EnsemblLookup.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/ext/htsjdk/VCFReader.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/pymol/PymolManager.java
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    • +6
    /src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
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    • +5
    /src/jalview/ext/so/SequenceOntology.java
    • -1
    • +1
    /src/jalview/fts/core/GFTSPanel.java
  16. … 105 more files in changeset.
3:32 am

Jim Procter

Thursday 10 Feb
3:08 pm

Jim Procter

3:07 pm

Jim Procter

JAL-3553: Create working getdown appbase and jvl file(s) for each old version of Jalview
JAL-3553: Create working getdown appbase and jvl file(s) for each old version of Jalview
12:12 pm

Jim Procter

Tuesday 08 Feb
11:42 am

Jim Procter

I'm abandoning this review for now (see my comments on the issue). For what its worth since this is a string literal you should at least follow convention JALVIEW_LOGGER rather than a generic 'LOGG...

I'm abandoning this review for now (see my comments on the issue). For what its worth since this is a string literal you should at least follow convention JALVIEW_LOGGER rather than a generic 'LOGGER_NAME'. The code for routing logged content from other loggers should probably be a method on Cache... or even better, separate all this out into the jalview.util.Log4j class so Cache doesn't get polluted with log configuration cruft.

11:24 am

Ben Soares

At the moment it is only used in jalview.bin.Cache, but it is used in separate places where appenders are added. Previous to this it was relying on the String name of the appender being correctly u...

At the moment it is only used in jalview.bin.Cache, but it is used in separate places where appenders are added. Previous to this it was relying on the String name of the appender being correctly used. However the Strings that were being used were not the same so it was broken (I don't know how that manifested itself, but it definitely would not have worked the way it used to!).
Feasibly a separate logger made in the future (e.g. API logger?) will want to add this Appender and will likely not be made in jalview.bin.Cache, so putting a constant String somewhere generically connected with Log4j seemed sensible. Correct it needs documenting!