Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
Merge branch 'JAL-3878_web_services_overhaul' into try-to-update-slivka-jar JAL-3066 JAL-3362 Update 2.12 alpha with latest slivka-client.jar Conflicts: src/jalview/bin/Cache.java src/jalview/gui/AlignFrame.java src/jalview/gui/Desktop.java src/jalview/workers/AlignCalcManager.java src/jalview/ws/jws2/JPredThread.java src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java src/jalview/ws/slivkaws/SlivkaWSInstance.java swingjs/ver/3.3.1/SwingJS-site.zip swingjs/ver/3.3.1/timestamp

  1. … 26 more files in changeset.
Merge branch 'develop' into merged_2_11_2_0_to_2_12 updates JAL-3362 2.12 alpha with 2.11.2.5 release changes. Still has failing tests. Conflicts: THIRDPARTYLIBS build.gradle gradle.properties help/help/html/features/preferences.html help/help/html/releases.html src/jalview/bin/Cache.java src/jalview/bin/Jalview.java src/jalview/datamodel/SequenceI.java src/jalview/fts/service/uniprot/UniProtFTSRestClient.java src/jalview/gui/AlignFrame.java src/jalview/gui/AlignViewport.java src/jalview/gui/AlignmentPanel.java src/jalview/gui/AnnotationPanel.java src/jalview/gui/Desktop.java src/jalview/gui/FeatureEditor.java src/jalview/gui/IdCanvas.java src/jalview/gui/JvSwingUtils.java src/jalview/gui/OptsAndParamsPage.java src/jalview/gui/OverviewPanel.java src/jalview/gui/PopupMenu.java src/jalview/gui/Preferences.java src/jalview/gui/SeqCanvas.java src/jalview/gui/SeqPanel.java src/jalview/gui/SequenceFetcher.java src/jalview/gui/SplashScreen.java src/jalview/gui/SplitFrame.java src/jalview/gui/StructureChooser.java src/jalview/gui/UserQuestionnaireCheck.java src/jalview/gui/VamsasApplication.java src/jalview/gui/WsJobParameters.java src/jalview/gui/WsParamSetManager.java src/jalview/io/BackupFiles.java src/jalview/io/ModellerDescription.java src/jalview/io/NewickFile.java src/jalview/io/SequenceAnnotationReport.java src/jalview/io/StockholmFile.java src/jalview/javascript/log4j/Logger.java src/jalview/jbgui/GAlignFrame.java src/jalview/jbgui/GCutAndPasteHtmlTransfer.java src/jalview/jbgui/GCutAndPasteTransfer.java src/jalview/jbgui/GDesktop.java src/jalview/jbgui/GPreferences.java src/jalview/project/Jalview2XML.java src/jalview/structure/StructureSelectionManager.java src/jalview/urls/IdentifiersUrlProvider.java src/jalview/util/HttpUtils.java src/jalview/util/MappingUtils.java src/jalview/util/MessageManager.java src/jalview/util/Platform.java src/jalview/util/StringUtils.java src/jalview/viewmodel/AlignmentViewport.java src/jalview/ws/AWSThread.java src/jalview/ws/dbsources/EmblXmlSource.java src/jalview/ws/gui/MsaWSThread.java src/jalview/ws/jws1/Discoverer.java src/jalview/ws/jws2/AADisorderClient.java src/jalview/ws/jws2/AbstractJabaCalcWorker.java src/jalview/ws/jws2/Jws2Client.java src/jalview/ws/jws2/Jws2Discoverer.java src/jalview/ws/jws2/MsaWSClient.java src/jalview/ws/rest/HttpResultSet.java src/jalview/ws/rest/RestClient.java src/jalview/ws/rest/RestJobThread.java src/jalview/ws/utils/UrlDownloadClient.java src/jalview/xml/binding/jalview/DoubleVector.java src/jalview/xml/binding/jalview/JalviewModel.java test/jalview/bin/CommandLineOperations.java test/jalview/ext/jmol/JmolCommandsTest.java test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java test/jalview/gui/AlignViewportTest.java test/jalview/gui/AlignmentPanelTest.java test/jalview/gui/AnnotationChooserTest.java test/jalview/gui/AnnotationRowFilterTest.java test/jalview/gui/JvSwingUtilsTest.java test/jalview/gui/SeqCanvasTest.java test/jalview/gui/SequenceRendererTest.java test/jalview/gui/StructureChooserTest.java test/jalview/io/SequenceAnnotationReportTest.java test/jalview/project/Jalview2xmlTests.java test/jalview/renderer/OverviewResColourFinderTest.java test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java test/jalview/schemes/ClustalxColourSchemeTest.java test/jalview/structure/StructureSelectionManagerTest.java test/jalview/util/ColorUtilsTest.java test/jalview/workers/AlignCalcManagerTest.java test/jalview/ws/gui/Jws2ParamView.java test/jalview/ws/sifts/SiftsClientTest.java

  1. … 242 more files in changeset.
Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

  1. … 131 more files in changeset.
JAL-1988 JAL-3772 Moving packages to somewhere more obvious (jbgui -> gui)

  1. … 4 more files in changeset.
JAL-1988 JAL-3772 removed a debugging log line

JAL-1988 JAL-3772 Removed 'Wait' button from waitDialog, no iterations for GUI. Added bulletpoint to files saving list. Added use of passed in button objects to modal JvOptionPane, so buttons can be controlled (e.g. setEnabled, setVisible) outside of JvOptionPane.

  1. … 4 more files in changeset.
JAL-1988 JAL-3772 Fixed wait between waitDialog appearances, ensuring all files saving will quit straight away. Goodbye message to user if waitDialog still visible.

JAL-1988 Allow generic Container object in JvOptionPane showDialog. Fix dynamically saving files in the wait for save dialog

  1. … 4 more files in changeset.
JAL-1988 JAL-3772 wait timer working first time but blocking desktop gui updates

  1. … 2 more files in changeset.
JAL-1988 JAL-3772 Non-blocking modal dialogs for unsaved changes and saving files. Wait timer not working. Wait dialog update/close on files saved not working.

  1. … 23 more files in changeset.
JAL-1988 JAL-3772 linked undostack to saved changes flags. No confirmation if all viewports have been saved individually

  1. … 3 more files in changeset.
JAL-1988 JAL-3772 Quit confirmation dialog boxes with saving files check and wait

  1. … 4 more files in changeset.
JAL-4071 boring GUI bits - add togglable menu item for show/hide sequence feature counts and viewModel/viewStyleI methods

  1. … 6 more files in changeset.
JAL-518 refactored groovy script into main codebase as an Edit Command and alignment view controller method. Left and Right Justify operations now in Edit menu on alignment window and selection popup.

  1. … 10 more files in changeset.
JAL-4062 copy highlighted region docs, new Alignment window Edit menu option and Shift+Ctrl/CMD-C keystroke

  1. … 5 more files in changeset.
JAL-4061 JAL-4062 button in Find dialog to copy highlighted regions to clipboard

  1. … 2 more files in changeset.
JAL-4061 JAL-4062 Find can now search features

  1. … 6 more files in changeset.
JAL-1988 Added a saves in progress check for quit

  1. … 3 more files in changeset.
JAL-1988 added a saveInProgress stack to BackupFiles

  1. … 1 more file in changeset.
JAL-4034 button looks better also on other OSes with the 0 vertical insets

JAL-4034 add round corners to 3DB confirmation button with icon on a mac

JAL-4034 Use the new non-modal JDialog for 3DBeacons uniprot lookup confirmation. Link dialog to GStructureChooser's frame so it can moveToFront. Minor improvement to Search 3DB button appearance

  1. … 1 more file in changeset.
JAL-4041 Use the new non-modal JDialog for 3DBeacons uniprot lookup confirmation. Link dialog to GStructureChooser's frame so it can be raised.

  1. … 1 more file in changeset.
JAL-4034 Fix #2 show an icon and a button to press to initiate search

  1. … 1 more file in changeset.
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop

JAL-1988 Don't put Quit in the File menu if there's a handler for it

Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop

JAL-1988 Check for setHandler capability to avoid About and Preferences menu options disappearing into a void

JAL-3027 Avoid FlatLAF Desktop class is JalviewJS

JAL-1988 JAL-3416 avoid unnecessary static flag