jalview

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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...
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
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.

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
Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

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    /src/jalview/io/gff/ExonerateHelper.java
JAL-1761 backbone type parameter for configuring which atoms are used for superposition of structures

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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/pymol/PymolCommands.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    /test/jalview/ext/jmol/JmolCommandsTest.java
JAL-1761 need to pass molecule type when generating superposition commands

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    /test/jalview/ext/jmol/JmolCommandsTest.java
JAL-3551 patch test for altloc handling atom spec in superposition code

JAL-1761 need to pass molecule type when generating superposition commands

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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/pymol/PymolCommands.java
JAL-3906 use indicate to highlight current mousedOver residue in Jalview in a Pymol view

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    /src/jalview/gui/PymolBindingModel.java
JAL-3746 update release date to later in Feb 2022

JAL-3551 pymol documentation

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    /help/help/html/features/pymol.html
Merge branch 'task/r_2_11_2/JAL-3956_alphaFill_authoritative_IDs' into develop

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    /src/jalview/ext/pymol/PymolCommands.java
JAL-3956 - PDBEntry objects constructed from 3D-Beacons have authoritative IDs overriding any embedded IDs

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    /src/jalview/datamodel/PDBEntry.java
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    /test/jalview/datamodel/PDBEntryTest.java
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' into develop

Conflicts:

test/jalview/bin/CommandLineOperations.java

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    /test/jalview/bin/CommandLineOperations.java
JAL-3949 fix testProps path and make line count more accurate

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    /test/jalview/bin/CommandLineOperations.java
JAL-3949 increase command line ops test timeout

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    /test/jalview/bin/CommandLineOperations.java
JAL-3949 ensure Jalview command line ops setup actually quits after SETUP_TIME milliseconds - seems there’s less stderr noise than before !

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    /test/jalview/bin/CommandLineOperations.java
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' into develop

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    /src/jalview/gui/StructureViewerBase.java
JAL-3931 fix - escape % symbols after urlencoding

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    /src/jalview/gui/StructureViewerBase.java
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!

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.

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

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    /src/jalview/io/vamsas/DatastoreItem.java
JLogger loglevel check on whether to call the actual logger or not. New factory methods with Class.

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    /src/jalview/io/vamsas/DatastoreItem.java
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.

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

Conflicts:

src/jalview/bin/Jalview.java

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/analysis/GeneticCodes.java
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    /src/jalview/bin/Console.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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    /src/jalview/ext/so/SequenceOntology.java
  1. … 84 more files in changeset.