j11lib

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-4059 update Jmol and JSmol to 15.2.69 - revised Jalview classes interating with Jmol API to handle double precision structure data

    • binary
    ./Jmol-15.2.69-NOLOG4J.jar
  1. … 13 more files in changeset.
JAL-3059 upgrade Jmol from 14.31.53 to 15.2.69 (double precision) - required patches to structure data related classes and Jmol API implementors for float->double

    • binary
    ./Jmol-15.2.69-NOLOG4J.jar
  1. … 14 more files in changeset.
JAL-3416 updated FlatLAF libraries to 2.3. Added the flatlaf-extras library

    • binary
    ./flatlaf-extras-2.3.jar
  1. … 3 more files in changeset.
JAL-1953 2.11.2 with Archeopteryx! Minimal patches and Merge branch 'kjvdh/features/PhylogenyViewer' into merge/2_11_2/PhylogenyViewer also restored last kjvdh build of forester to j8 and j11lib directories Conflicts: .classpath j8lib/forester.jar resources/lang/Messages.properties src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java src/jalview/fts/core/GFTSPanel.java src/jalview/fts/service/pdb/PDBFTSPanel.java src/jalview/gui/AlignFrame.java src/jalview/gui/DasSourceBrowser.java src/jalview/gui/Desktop.java src/jalview/gui/PopupMenu.java src/jalview/gui/SplashScreen.java src/jalview/gui/StructureViewerBase.java src/jalview/io/BioJsHTMLOutput.java src/jalview/io/FileLoader.java src/jalview/io/HtmlSvgOutput.java src/jalview/project/Jalview2XML.java src/jalview/schemabinding/version2/JalviewModelSequence.java src/jalview/util/DBRefUtils.java src/jalview/viewmodel/AlignmentViewport.java src/jalview/ws/DBRefFetcher.java src/jalview/ws/DasSequenceFeatureFetcher.java src/jalview/ws/jws2/Jws2Discoverer.java utils/jalviewjs/buildxml/build.xml

  1. … 38 more files in changeset.
minimal fixes - probably not valid since forester jar out of sync

  1. … 4 more files in changeset.
JAL-4008 update jabaws client to 2.2.1 - definitely no log4j references !

    • binary
    ./jabaws-min-client-NO_LOG4J-2.2.0.jar
    • binary
    ./jabaws-min-client-NO_LOG4J-2.2.1.jar
  1. … 3 more files in changeset.
JAL-3851 allow multiple instances of Endpoints. Fixes to naming of IGV colour scheme

  1. … 11 more files in changeset.
JAL-3416 Updated FlatLaF to 2.1

JAL-3978 Using getdowninstanceappdir and getdowninstanceappbase to avoid conflict with getAppbaseBuildProperties(). Added an if around fetching build_properties to avoid failing to fetch local file appbase.

  1. … 7 more files in changeset.
JAL-3978 Getdown add getdownappbase property to launched Jalview

  1. … 12 more files in changeset.
JAL-3796 commit jni lib in Jmol library that is signed with Jalview's OSX cert

  1. … 1 more file in changeset.
JAL-3972 replace the VAqua 5 patched library with latest VAqua 10

  1. … 1 more file in changeset.
JAL-3103 Remove BrowserLauncher2 and use Desktop.browse(url) with wrapper methods

  1. … 11 more files in changeset.
JAL-3103 Switched to (a wrapper around) BrowserLauncher2

    • binary
    ./BrowserLauncher2-1_3.jar
  1. … 6 more files in changeset.
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 bumped the version to 1.8.3-1.2.12 in source and libraries

  1. … 11 more files in changeset.
JAL-3691 updated getdown libraries and version bump

  1. … 6 more files in changeset.
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
JAL-3691 rebuilt getdown jars

  1. … 4 more files in changeset.
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.

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.

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 'bug/JAL-3523_cwd_not_preserved' into develop rebuilt getdown jars - did not bump version

  1. … 5 more files in changeset.