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Friday 02 Sep
5:26 pm

Ben Soares

JAL-1988 Added a saves in progress check for quit

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    ./BackupFiles.java
  2. … 4 more files in changeset.
Wednesday 31 Aug
5:19 pm

Ben Soares

JAL-1988 added a saveInProgress stack to BackupFiles

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    ./BackupFiles.java
  2. … 1 more file in changeset.
Friday 10 Jun
12:13 pm

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

Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into develop

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    ./AppletFormatAdapter.java
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Monday 06 Jun
12:22 pm

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

JAL-4023 store distances as doubles

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    ./NewickFile.java
  2. … 1 more file in changeset.
Friday 03 Jun
2:15 pm

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

JAL-1953 JAL-2889 don’t read additional lines when looking for phyloxml header

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    ./IdentifyFile.java
2:13 pm

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

JAL-4021 todo & fix FileFormat tests

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    ./FileFormat.java
  2. … 2 more files in changeset.
11:37 am

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

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

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    ./FileFormat.java
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    ./FileLoader.java
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    ./IdentifyFile.java
  4. … 36 more files in changeset.
Thursday 02 Jun
5:23 pm

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

minimal fixes - probably not valid since forester jar out of sync

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    ./NewickFile.java
  2. … 4 more files in changeset.
4:05 pm

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

Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh/features/PhylogenyViewer_tabbedsupport Update from Release 2.11.2 develop branch JAL-1953 Conflicts: .classpath .project resources/lang/Messages.properties src/jalview/bin/Jalview.java 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/CalculationChooser.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/gui/TreePanel.java src/jalview/gui/WebserviceInfo.java src/jalview/io/BioJsHTMLOutput.java src/jalview/io/FileLoader.java src/jalview/io/HtmlSvgOutput.java src/jalview/io/NewickFile.java src/jalview/math/Matrix.java src/jalview/math/MatrixI.java src/jalview/util/MappingUtils.java src/jalview/ws/DBRefFetcher.java src/jalview/ws/DasSequenceFeatureFetcher.java src/jalview/ws/jws2/Jws2Discoverer.java utils/eclipse/org.eclipse.jdt.core.jalview.prefs utils/eclipse/org.eclipse.jdt.ui.prefs

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    ./BioJsHTMLOutput.java
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    ./FileLoader.java
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    ./NewickFile.java
  4. … 36 more files in changeset.
Monday 18 Apr
10:31 am

Ben Soares

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

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    ./VamsasAppDatastore.java
  2. … 40 more files in changeset.
Saturday 16 Apr
1:38 pm

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

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

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    ./StockholmFile.java
  2. … 2 more files in changeset.
1:36 pm

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

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

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    ./StockholmFile.java
  2. … 2 more files in changeset.
Tuesday 05 Apr
6:37 pm

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

JAL-3981 patch tests and remove errant imports

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    ./SequenceAnnotationReport.java
  2. … 1 more file in changeset.
6:14 pm

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

JAL-3990 gradle spotlessApply

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    ./SequenceAnnotationReport.java
  2. … 3 more files in changeset.
Tuesday 29 Mar
11:20 pm

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

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

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    ./vcf/VCFLoader.java
  2. … 1 more file in changeset.
8:06 pm

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

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

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    ./vcf/VCFLoader.java
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Friday 25 Mar
2:30 pm

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

JAL-3980 defensive copy - inefficient but fixes bug

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    ./SequenceAnnotationReport.java
2:16 pm

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

JAL-3981 Additional line breaks - sort of helps

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    ./SequenceAnnotationReport.java
Thursday 24 Mar
5:02 pm

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

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

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    ./SequenceAnnotationReport.java
  2. … 1 more file 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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    ./EMBLLikeFlatFile.java
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    ./EmblFlatFile.java
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    ./GenBankFile.java
  4. … 43 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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    ./AnnotationFile.java
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    ./AppletFormatAdapter.java
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    ./BackupFilenameParts.java
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    ./BackupFiles.java
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    ./BioJsHTMLOutput.java
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    ./EMBLLikeFlatFile.java
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    ./FeaturesFile.java
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    ./FileFormat.java
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    ./FileFormats.java
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    ./FileLoader.java
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    ./FormatAdapter.java
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    ./HtmlSvgOutput.java
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    ./IdentifyFile.java
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    ./JSONFile.java
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    ./JalviewFileChooser.java
  16. … 647 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

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    ./HTMLOutput.java
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Monday 07 Mar
8:03 pm

Jim Procter

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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    ./AnnotationFile.java
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    ./AppletFormatAdapter.java
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    ./BackupFiles.java
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    ./BioJsHTMLOutput.java
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    ./EMBLLikeFlatFile.java
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    ./FeaturesFile.java
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    ./FileFormat.java
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    ./FileFormats.java
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    ./FileLoader.java
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    ./FormatAdapter.java
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    ./HTMLOutput.java
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    ./HtmlSvgOutput.java
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    ./IdentifyFile.java
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    ./JSONFile.java
  16. … 654 more files in changeset.
Wednesday 16 Feb
1:27 pm

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

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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    ./AppletFormatAdapter.java
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12:17 pm

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

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

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    ./gff/ExonerateHelper.java
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

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    ./vamsas/DatastoreItem.java
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3:43 pm

Ben Soares

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

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    ./vamsas/DatastoreItem.java
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    ./vamsas/DatastoreRegistry.java
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