jalview

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JAL-3997 check for tooltip being null before checking equivalence to last tooltip string

Merge branch 'task/JAL-3992_update_docs' into bug/JAL-3365_extendedDSSP_via_stockholm

JAL-3992 fix path

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    /help/help/html/features/cursorMode.html
JAL-3288 Replace all javax.swing.JInternalFrame with extended jalview.jbgui.ClassicJInternalFrame

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    /src/jalview/gui/AnnotationChooser.java
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    /src/jalview/gui/AnnotationColourChooser.java
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    /src/jalview/gui/AnnotationColumnChooser.java
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    /src/jalview/gui/AnnotationExporter.java
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    /src/jalview/gui/AnnotationRowFilter.java
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    /src/jalview/gui/CalculationChooser.java
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    /src/jalview/gui/ChimeraViewFrame.java
  1. … 26 more files in changeset.
JAL-3365 per-sequence secondary structure symbol ‘X’ is not properly exported and reimported

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    /examples/PF001426_full.stk
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    /test/jalview/io/StockholmFileTest.java
JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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    /test/jalview/io/StockholmFileTest.java
WIP

JAL-3992 shift+arrow to jump to next gap/residue in cursor/keyboard editing mode

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    /help/help/html/features/cursorMode.html
JAL-3878 Use slivka client's URL when building web service

JAL-3878 Add conservation service discovery

JAL-3878 Build interactive services menu

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    /src/jalview/ws2/gui/WebServicesMenuManager.java
JAL-3878 Implement prot. seq. an. discovery for slivka.

JAL-3878 Implement gui elements for annotation servicces

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    /src/jalview/ws2/gui/AnnotationServiceGuiHandler.java
JAL-3878 Create SlivkaAnnotationWSClient

JAL-3878 Add full name getter to ActionI

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    /src/jalview/ws2/actions/api/ActionI.java
JAL-3878 Log status changes in annotation task

JAL-3878 Allow null value for action name

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    /src/jalview/ws2/actions/BaseAction.java
JAL-3878 Add action and task for annotation services

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    /src/jalview/util/Pair.java
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    /src/jalview/ws2/actions/annotation/AnnotationAction.java
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    /src/jalview/ws2/actions/annotation/AnnotationJob.java
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    /src/jalview/ws2/actions/annotation/AnnotationResult.java
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    /src/jalview/ws2/actions/annotation/AnnotationTask.java
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    /src/jalview/ws2/client/api/AnnotationWebServiceClientI.java
JAL-3991 Made info displayed only when needed (Java 11+)

JAL-3991 Added information output about the slightly alarming 'WARNING: An illegal reflective access operation has occurred' error that occurs for linux users. It can't be avoided so informing the user should help with alarm levels.

JAL-3991 JAVA_COMPILE_VERSION put into build_properties. Check for possible JVM mismatch in jalview.bin.LaunchUtils. STDERR warning from jalview.bin.Launcher. Console and optional popup warning in jalview.bin.Jalview.

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    /resources/lang/Messages_es.properties
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    /src/jalview/util/LaunchUtils.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3990 release notes and what’s new

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3981 patch tests and remove errant imports

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3990 gradle spotlessApply

JAL-3990 release notes for 2.11.2.1 patch release

Merge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_details' into develop

JAL-3878 Introduce IProgressIndicator#addProgressBar

addProgressBar adds a bar to the panel if it doesn't exist

ensuring that the bar is present after the call contrary

to setProgressBar which toggles the progress bar on and off.

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    /src/jalview/gui/IProgressIndicator.java
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    /src/jalview/gui/ProgressBar.java
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    /src/jalview/gui/StructureChooser.java