jalview/src/jalview

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Tuesday 29 Nov
3:34 pm

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

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

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    ./GPreferences.java
  2. … 26 more files in changeset.
Monday 28 Nov
8:47 pm

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

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

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    ./GAlignFrame.java
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    ./GCutAndPasteTransfer.java
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    ./GDesktop.java
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    ./GPreferences.java
  5. … 242 more files in changeset.
Monday 21 Nov
5:02 pm

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

Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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    ./GPreferences.java
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    ./GStructureViewer.java
  3. … 131 more files in changeset.
Wednesday 02 Nov
2:34 pm

Ben Soares

JAL-1988 JAL-3772 Moving packages to somewhere more obvious (jbgui -> gui)

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    ./APQHandlers.java
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    ./GDesktop.java
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    ./QuitHandler.java
  4. … 4 more files in changeset.
Saturday 29 Oct
7:38 pm

Ben Soares

JAL-1988 JAL-3772 removed a debugging log line

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    ./QuitHandler.java
12:16 am

Ben Soares

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.

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    ./QuitHandler.java
  2. … 4 more files in changeset.
Friday 28 Oct
12:48 pm

Ben Soares

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.

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    ./QuitHandler.java
Thursday 27 Oct
6:51 pm

Ben Soares

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

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    ./QuitHandler.java
  2. … 4 more files in changeset.
Monday 24 Oct
6:08 pm

Ben Soares

JAL-1988 JAL-3772 wait timer working first time but blocking desktop gui updates

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    ./QuitHandler.java
  2. … 2 more files in changeset.
3:41 pm

Ben Soares

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.

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    ./GDesktop.java
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    ./QuitHandler.java
  3. … 23 more files in changeset.
Monday 26 Sep
8:17 pm

Ben Soares

JAL-1988 JAL-3772 linked undostack to saved changes flags. No confirmation if all viewports have been saved individually

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    ./QuitHandler.java
  2. … 3 more files in changeset.
Friday 23 Sep
6:34 pm

Ben Soares

JAL-1988 JAL-3772 Quit confirmation dialog boxes with saving files check and wait

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    ./GDesktop.java
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    ./QuitHandler.java
  3. … 4 more files in changeset.
Thursday 22 Sep
3:48 pm

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

JAL-4071 boring GUI bits - add togglable menu item for show/hide sequence feature counts and viewModel/viewStyleI methods

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    ./GAlignFrame.java
  2. … 6 more files in changeset.
Friday 16 Sep
5:52 pm

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

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.

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    ./GAlignFrame.java
  2. … 10 more files in changeset.
2:23 pm

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

JAL-4062 copy highlighted region docs, new Alignment window Edit menu option and Shift+Ctrl/CMD-C keystroke

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    ./GAlignFrame.java
  2. … 5 more files in changeset.
Wednesday 14 Sep
11:05 am

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

JAL-4061 JAL-4062 button in Find dialog to copy highlighted regions to clipboard

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    ./GFinder.java
  2. … 2 more files in changeset.
11:04 am

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

JAL-4061 JAL-4062 Find can now search features

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    ./GFinder.java
  2. … 6 more files in changeset.
Friday 02 Sep
5:26 pm

Ben Soares

JAL-1988 Added a saves in progress check for quit

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    ./APQHandlers.java
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    ./QuitHandler.java
  3. … 3 more files in changeset.
Wednesday 31 Aug
5:19 pm

Ben Soares

JAL-1988 added a saveInProgress stack to BackupFiles

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    ./QuitHandler.java
  2. … 1 more file in changeset.
Monday 25 Jul
10:57 am

Ben Soares

JAL-4034 button looks better also on other OSes with the 0 vertical insets

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    ./GStructureChooser.java
Sunday 24 Jul
5:37 pm

Ben Soares

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

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    ./GStructureChooser.java
Friday 15 Jul
6:38 pm

Ben Soares

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

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    ./GStructureChooser.java
  2. … 1 more file in changeset.
6:02 pm

Ben Soares

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

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    ./GStructureChooser.java
  2. … 1 more file in changeset.
Monday 04 Jul
5:59 pm

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

JAL-4034 Fix #2 show an icon and a button to press to initiate search

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    ./GStructureChooser.java
  2. … 1 more file in changeset.
Tuesday 28 Jun
1:32 pm

Ben Soares

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

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    ./GDesktop.java
1:31 pm

Ben Soares

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

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    ./GDesktop.java
Thursday 23 Jun
4:02 pm

Ben Soares

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

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    ./APQHandlers.java
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    ./GDesktop.java
3:28 pm

Ben Soares

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

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    ./APQHandlers.java
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    ./GDesktop.java
Friday 17 Jun
5:10 pm

Ben Soares

JAL-3027 Avoid FlatLAF Desktop class is JalviewJS

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    ./APQHandlers.java
Wednesday 15 Jun
3:54 pm

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

JAL-1988 JAL-3416 avoid unnecessary static flag

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    ./APQHandlers.java
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    ./GDesktop.java