source.jalview.org Git - jalview.git/commit

git://source.jalview.org / jalview.git / commit

author	Renia Correya <rcorreya001@dundee.ac.uk>
	Tue, 3 Sep 2024 10:37:49 +0000 (16:07 +0530)
committer	Renia Correya <rcorreya001@dundee.ac.uk>
	Tue, 3 Sep 2024 10:37:49 +0000 (16:07 +0530)
commit	bd2650d414b4687c32f580751fc0de7f65f8d1f3
tree	696b97dadc0171c0f4969350605ff26830d3e8db	tree \| snapshot
parent	391348cbefa931101392b98c60d0494f3f382ef3	commit \| diff

Resolved merge conflicts from develop into JAL-4386

148 files changed:

build.gradle		diff \| blob \| history
getdown/lib/FJVL_VERSION		diff \| blob \| history
getdown/lib/JVL_VERSION		diff \| blob \| history
getdown/lib/getdown-core.jar		diff \| blob \| history
getdown/lib/getdown-launcher-local.jar		diff \| blob \| history
getdown/lib/getdown-launcher.jar		diff \| blob \| history
getdown/src/getdown/ant/pom.xml		diff \| blob \| history
getdown/src/getdown/core/pom.xml		diff \| blob \| history
getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java		diff \| blob \| history
getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java		diff \| blob \| history
getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java		diff \| blob \| history
getdown/src/getdown/core/src/main/java/jalview/bin/GetdownLauncherUpdate.java	[new file with mode: 0644]	blob
getdown/src/getdown/core/src/main/java/jalview/util/ErrorLog.java		diff \| blob \| history
getdown/src/getdown/core/src/main/java/jalview/util/LaunchUtils.java		diff \| blob \| history
getdown/src/getdown/core/src/test/java/com/threerings/getdown/data/EnvConfigTest.java		diff \| blob \| history
getdown/src/getdown/launcher/pom.xml		diff \| blob \| history
getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/Getdown.java		diff \| blob \| history
getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java		diff \| blob \| history
getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/ProxyUtil.java		diff \| blob \| history
getdown/src/getdown/lib/SOURCE_HEADER	[deleted file]	blob \| history
getdown/src/getdown/lib/jRegistryKey.dll	[deleted file]	blob \| history
getdown/src/getdown/lib/jregistrykey/jregistrykey/1.0/jregistrykey-1.0.jar	[deleted file]	blob \| history
getdown/src/getdown/lib/jregistrykey/jregistrykey/1.0/jregistrykey-1.0.pom	[deleted file]	blob \| history
getdown/src/getdown/lib/jregistrykey/jregistrykey/maven-metadata-local.xml	[deleted file]	blob \| history
getdown/src/getdown/lib/manifest.mf	[deleted file]	blob \| history
getdown/src/getdown/mvn_cmd		diff \| blob \| history
getdown/src/getdown/pom.xml		diff \| blob \| history
gradle.properties		diff \| blob \| history
help/markdown/releases/release-2_11_4_0.md		diff \| blob \| history
j11lib/getdown-core.jar		diff \| blob \| history
j8lib/getdown-core.jar		diff \| blob \| history
src/jalview/analysis/AAFrequency.java		diff \| blob \| history
src/jalview/analysis/AlignSeq.java		diff \| blob \| history
src/jalview/analysis/AlignmentUtils.java		diff \| blob \| history
src/jalview/analysis/ConnectivityException.java		diff \| blob \| history
src/jalview/analysis/Finder.java		diff \| blob \| history
src/jalview/analysis/PaSiMap.java		diff \| blob \| history
src/jalview/analysis/ccAnalysis.java		diff \| blob \| history
src/jalview/analysis/scoremodels/DistanceScoreModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/FeatureDistanceModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/ScoreModels.java		diff \| blob \| history
src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java		diff \| blob \| history
src/jalview/analysis/scoremodels/SimilarityParams.java		diff \| blob \| history
src/jalview/api/AlignViewControllerI.java		diff \| blob \| history
src/jalview/api/AlignViewportI.java		diff \| blob \| history
src/jalview/api/analysis/ScoreModelI.java		diff \| blob \| history
src/jalview/api/analysis/SimilarityParamsI.java		diff \| blob \| history
src/jalview/appletgui/AlignFrame.java		diff \| blob \| history
src/jalview/bin/Cache.java		diff \| blob \| history
src/jalview/bin/GetdownLauncherUpdate.java	[new file with mode: 0644]	blob
src/jalview/bin/Jalview.java		diff \| blob \| history
src/jalview/bin/JalviewLite.java		diff \| blob \| history
src/jalview/bin/Launcher.java		diff \| blob \| history
src/jalview/commands/JustifyLeftOrRightCommand.java		diff \| blob \| history
src/jalview/controller/AlignViewController.java		diff \| blob \| history
src/jalview/datamodel/ContactMapHolder.java		diff \| blob \| history
src/jalview/datamodel/ContactMapHolderI.java		diff \| blob \| history
src/jalview/datamodel/GroupSetHolder.java		diff \| blob \| history
src/jalview/datamodel/PDBEntry.java		diff \| blob \| history
src/jalview/datamodel/Profile.java		diff \| blob \| history
src/jalview/datamodel/ProfileI.java		diff \| blob \| history
src/jalview/datamodel/SecondaryStructureCount.java		diff \| blob \| history
src/jalview/datamodel/SequenceGroup.java		diff \| blob \| history
src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java		diff \| blob \| history
src/jalview/ext/ensembl/EnsemblRestClient.java		diff \| blob \| history
src/jalview/gui/AlignFrame.java		diff \| blob \| history
src/jalview/gui/AlignViewport.java		diff \| blob \| history
src/jalview/gui/AppJmol.java		diff \| blob \| history
src/jalview/gui/CalculationChooser.java		diff \| blob \| history
src/jalview/gui/CutAndPasteTransfer.java		diff \| blob \| history
src/jalview/gui/Desktop.java		diff \| blob \| history
src/jalview/gui/FontChooser.java		diff \| blob \| history
src/jalview/gui/PaSiMapPanel.java		diff \| blob \| history
src/jalview/gui/PairwiseAlignPanel.java		diff \| blob \| history
src/jalview/gui/PopupMenu.java		diff \| blob \| history
src/jalview/gui/ProgressBar.java		diff \| blob \| history
src/jalview/gui/RotatableCanvas.java		diff \| blob \| history
src/jalview/gui/StructureChooser.java		diff \| blob \| history
src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java		diff \| blob \| history
src/jalview/jbgui/GAlignFrame.java		diff \| blob \| history
src/jalview/jbgui/GCutAndPasteTransfer.java		diff \| blob \| history
src/jalview/jbgui/GDesktop.java		diff \| blob \| history
src/jalview/jbgui/GPCAPanel.java		diff \| blob \| history
src/jalview/jbgui/GPaSiMapPanel.java		diff \| blob \| history
src/jalview/jbgui/GPreferences.java		diff \| blob \| history
src/jalview/math/Matrix.java		diff \| blob \| history
src/jalview/math/MatrixI.java		diff \| blob \| history
src/jalview/math/MiscMath.java		diff \| blob \| history
src/jalview/project/Jalview2XML.java		diff \| blob \| history
src/jalview/renderer/AnnotationRenderer.java		diff \| blob \| history
src/jalview/renderer/ResidueShader.java		diff \| blob \| history
src/jalview/schemes/ClustalxColourScheme.java		diff \| blob \| history
src/jalview/schemes/ResidueProperties.java		diff \| blob \| history
src/jalview/util/ArgParserUtils.java		diff \| blob \| history
src/jalview/util/Constants.java		diff \| blob \| history
src/jalview/util/ErrorLog.java		diff \| blob \| history
src/jalview/util/HttpUtils.java		diff \| blob \| history
src/jalview/util/LaunchUtils.java		diff \| blob \| history
src/jalview/util/UserAgent.java		diff \| blob \| history
src/jalview/viewmodel/AlignmentViewport.java		diff \| blob \| history
src/jalview/viewmodel/PaSiMapModel.java		diff \| blob \| history
src/jalview/workers/SecondaryStructureConsensusThread.java		diff \| blob \| history
src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java		diff \| blob \| history
src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java		diff \| blob \| history
test/jalview/analysis/AlignSeqTest.java		diff \| blob \| history
test/jalview/analysis/AlignmentUtilsTests.java		diff \| blob \| history
test/jalview/analysis/scoremodels/ScoreModelsTest.java		diff \| blob \| history
test/jalview/analysis/scoremodels/SecondaryStructureDistanceModelTest.java		diff \| blob \| history
test/jalview/commands/EditCommandTest.java		diff \| blob \| history
test/jalview/ext/ensembl/EnsemblGeneTest.java		diff \| blob \| history
test/jalview/gui/AssociatePDBFileTest.java		diff \| blob \| history
test/jalview/gui/CalculationChooserTest.java		diff \| blob \| history
test/jalview/project/Jalview2xmlTests.java		diff \| blob \| history
test/jalview/renderer/ResidueShaderTest.java		diff \| blob \| history
test/jalview/schemes/ClustalxColourSchemeTest.java		diff \| blob \| history
test/jalview/util/FileUtilsTest.java		diff \| blob \| history
utils/channels/default/channel_gradle.properties		diff \| blob \| history
utils/channels/default/images/jalview_logo-64.png	[new file with mode: 0644]	blob
utils/channels/default/images/jalview_logo-64@2x.png	[new file with mode: 0644]	blob
utils/channels/develop-SUFFIX/channel_gradle.properties		diff \| blob \| history
utils/channels/develop-SUFFIX/images/jalview_develop_logo-64.png	[new file with mode: 0644]	blob
utils/channels/develop-SUFFIX/images/jalview_develop_logo-64@2x.png	[new file with mode: 0644]	blob
utils/channels/develop/channel_gradle.properties		diff \| blob \| history
utils/channels/develop/images/jalview_develop_logo-64.png	[new file with mode: 0644]	blob
utils/channels/develop/images/jalview_develop_logo-64@2x.png	[new file with mode: 0644]	blob
utils/channels/jalviewjs/channel_gradle.properties		diff \| blob \| history
utils/channels/jalviewjs/images/jalview_logo-64.png	[new file with mode: 0644]	blob
utils/channels/jalviewjs/images/jalview_logo-64@2x.png	[new file with mode: 0644]	blob
utils/channels/release/channel_gradle.properties		diff \| blob \| history
utils/channels/release/images/jalview_logo-64.png	[new file with mode: 0644]	blob
utils/channels/release/images/jalview_logo-64@2x.png	[new file with mode: 0644]	blob
utils/channels/test-release/channel_gradle.properties		diff \| blob \| history
utils/channels/test-release/images/jalview_test-release_logo-64.png	[new file with mode: 0644]	blob
utils/channels/test-release/images/jalview_test-release_logo-64@2x.png	[new file with mode: 0644]	blob
utils/getdown/bin/jalview.ps1		diff \| blob \| history
utils/getdown/bin/jalview.sh		diff \| blob \| history
utils/getdown/bin/run_other_script.ps1	[new file with mode: 0755]	blob
utils/getdown/bin/run_powershell.bat	[moved from utils/getdown/bin/jalview.bat with 100% similarity]	blob \| history
utils/getdown/bin/update.ps1	[new file with mode: 0755]	blob
utils/getdown/bin/update.sh	[new file with mode: 0755]	blob
utils/install4j/default.vmoptions	[new file with mode: 0644]	blob
utils/install4j/file_associations_auto-install4j10.xml		diff \| blob \| history
utils/install4j/file_associations_template-install4j10.xml		diff \| blob \| history
utils/install4j/install4j10_template.install4j		diff \| blob \| history
utils/install4j/macos-install-jalview.sh	[new file with mode: 0755]	blob
utils/install4j/warning.png	[new file with mode: 0644]	blob
utils/osx_signing/sign_dmg.sh	[new file with mode: 0755]	blob
utils/osx_signing/staple_dmg.sh	[new file with mode: 0755]	blob

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