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JAL-3288 Replace all javax.swing.JInternalFrame with extended jalview.jbgui.ClassicJInternalFrame

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JAL-3365 per-sequence secondary structure symbol ‘X’ is not properly exported and reimported

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JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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JAL-3981 patch tests and remove errant imports

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JAL-3990 gradle spotlessApply

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JAL-3982 JAL-3860 encapsulate genomic coordinates mapping/liftover logic

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JAL-3860 JAL-3892 extract genomic assembly mapping logic to static store

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JAL-3980 defensive copy - inefficient but fixes bug

JAL-3981 Additional line breaks - sort of helps

JAL-3981 strategic newlines to help speed up Java's html parser

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JAL-3746 apply copyright to source

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JAL-3438 spotless for 2.11.2.0

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JAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-needed exception handling from jalview code for openURL. Change Default browser input to JComboBox populated by BrowserLauncher2

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

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Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855 combined new logic for 2.11.2 3d-beacons with original hack to resolve PAE and CIF Conflicts: src/jalview/ws/dbsources/EBIAlfaFold.java

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

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

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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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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/

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.

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

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

JAL-3949 An attempt at converting to Log4j 2 -- no output achieved!
JAL-3949 An attempt at converting to Log4j 2 -- no output achieved!
Merge branch 'develop' into update/JAL-3949_abstracted_logging_for_jalviewjs_and_sanity

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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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