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Monday 18 Apr
10:31 am

Ben Soares

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

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    ./ClassicJInternalFrame.java
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    ./GAlignFrame.java
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    ./GCutAndPasteHtmlTransfer.java
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    ./GCutAndPasteTransfer.java
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    ./GPCAPanel.java
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    ./GRnaStructureViewer.java
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    ./GSplitFrame.java
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    ./GStructureChooser.java
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    ./GStructureViewer.java
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    ./GTreePanel.java
  11. … 31 more files in changeset.
Tuesday 08 Mar
9:56 pm

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

JAL-3746 apply copyright to source

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    ./FilterOption.java
  2. … 45 more files in changeset.
9:30 pm

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

JAL-3438 spotless for 2.11.2.0

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    ./GCutAndPasteHtmlTransfer.java
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    ./GCutAndPasteTransfer.java
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    ./GDesktop.java
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    ./GFinder.java
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    ./GRnaStructureViewer.java
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    ./GSliderPanel.java
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    ./GSplitFrame.java
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    ./GStructureChooser.java
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    ./GWebserviceInfo.java
  13. … 650 more files in changeset.
12:14 pm

Ben Soares

JAL-3103 Removed code and unused widgets for defaultBrowser

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    ./GPreferences.java
  2. … 2 more files in changeset.
12:03 pm

Ben Soares

JAL-3103 Remove BrowserLauncher2 and use Desktop.browse(url) with wrapper methods

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    ./GPreferences.java
  2. … 11 more files in changeset.
12:34 am

Ben Soares

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

Options
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    ./GPreferences.java
  2. … 11 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..

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    ./FilterOption.java
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    ./GAlignFrame.java
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    ./GAlignmentPanel.java
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    ./GCutAndPasteHtmlTransfer.java
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    ./GCutAndPasteTransfer.java
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    ./GDesktop.java
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    ./GFinder.java
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    ./GPreferences.java
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    ./GRnaStructureViewer.java
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    ./GSliderPanel.java
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    ./GSplitFrame.java
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    ./GStructureChooser.java
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    ./GWebserviceInfo.java
  14. … 656 more files in changeset.
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.

3:40 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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    ./GPreferences.java
  2. … 98 more files in changeset.
2:15 pm

Jim Procter

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!
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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    ./GAlignFrame.java
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  4. … 117 more files in changeset.
3:32 am

Jim Procter

Thursday 10 Feb
12:12 pm

Jim Procter

Wednesday 09 Feb
6:00 pm

Ben Soares

Put logging through Cache methods. Take 2

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    ./GAlignFrame.java
  2. … 23 more files in changeset.
5:36 pm

Ben Soares

Put logging through Cache methods. Take 1

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    ./GPreferences.java
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    ./GWsPreferences.java
  3. … 85 more files in changeset.
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!

10:10 am

Jim Procter

Does this really need to be a string constant ? (I'm not convinced) needs documenting as the log4j internal name for the log if it really needs to be external.

Does this really need to be a string constant ? (I'm not convinced) needs documenting as the log4j internal name for the log if it really needs to be external.

10:05 am

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!
Monday 07 Feb
12:22 pm

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

JAL-819 update branch 'feature/JAL-819undeleteAutoannotation' from 2.11.2 develop

Conflicts:

src/jalview/api/AlignViewportI.java

src/jalview/gui/AnnotationLabels.java

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  2. … 5 more files in changeset.
12:13 pm

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

JAL-722 updated from 2.11.2 develop branch - needs further work before release

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/datamodel/Alignment.java

src/jalview/gui/AlignFrame.java

src/jalview/io/AlignFile.java

src/jalview/project/Jalview2XML.java

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    ./GUserDefinedColours.java
  2. … 11 more files in changeset.
Thursday 27 Jan
2:21 pm

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

Merge branch 'bug/JAL-3633_read_proxy_settings_from_jalview_properties_in_getdown' into develop

Conflicts:

src/jalview/bin/MemorySetting.java

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    ./GPreferences.java
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Wednesday 03 Nov 2021
11:33 am

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

JAL-3915 remove RNAview opts from preferences. Still present in config file ready for when we have a new RNA structure processing service

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    ./GPreferences.java
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Friday 01 Oct 2021
5:36 pm

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

JAL-3616 show name of structure viewer in ‘new view’ button

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    ./GStructureChooser.java
  2. … 2 more files in changeset.