jalview

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JAL-3829 report when 3d-beacons doesn’t provide any models

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    /src/jalview/gui/StructureChooser.java
JAL-3878 Add getName() to Operation interface.

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    /src/jalview/ws2/operations/Operation.java
JAL-3783 Updated groovy-all-2.4. Currently newer stable releases cause a problem with shadowJar.

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    /j11lib/groovy-all-2.4.21-indy.jar
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    /j8lib/groovy-all-2.4.21-indy.jar
JAL-3878 Wire web services logic to UI elements.

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3746 update the example corefile for jalviewjs

JAL-3829 open web page for 3d beacons structure by right-clicking and selecting pop up menu item

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
JAL-3878 Fire service changed event after discovery task is done.

JAL-3878 Fix incorrect value of isRunning in SlivkaWSDiscoverer

JAL-3878 Move operation type from WebService to Operation.

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    /src/jalview/ws2/operations/Operation.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Code reformatting.

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    /src/jalview/ws2/WebServiceDiscoverer.java
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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/WebServiceI.java
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    /src/jalview/ws2/WebServiceInfoUpdater.java
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    /src/jalview/ws2/WebServiceWorkerI.java
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    /src/jalview/ws2/operations/Operation.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Display results of completed alignment job

JAL-3878 Change SERVER_ERROR.isSubmitted to false.

Some server errors may occur before the job is submitted.

It's safer to associate the error with the job not being

submitted.

Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3821 data file for failing test

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    /test/jalview/io/J03321_rna.embl.txt
JAL-3829 right click to view popup menu to show link - maybe better to have a link button in the table instead ?

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
JAL-3829 abstract essential TDB metadata from the user configurable data array displayed in the JTable

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    /src/jalview/fts/service/threedbeacons/TDB_FTSData.java
JAL-3878 Move WSJob instantiation out of WebService classes.

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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3594 added BG and UoD logo and banner to splashscreens, and adjusted status text box

Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'features/r2_11_2/JAL-3821_reinstate_patch' into develop

JAL-3821 less ambiguous base class name for EMBL and GenBank flat file parsers

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    /src/jalview/io/EMBLLikeFlatFile.java
JAL-3821 ported to refactored FlatFile parser

JAL-3821 failing test

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    /test/jalview/io/EmblFlatFileTest.java
JAL-3692 JAL-3861 remove extra call to .parse() so we don’t process the file again

Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'patch/JAL-3874_newJmolAndGradleDedup' into develop

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3851 api_specification.md in progress

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    /doc/api_specification.md
JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/analysis/Conservation.java
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    /src/jalview/analysis/GeneticCodes.java
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    /src/jalview/commands/EditCommand.java
  1. … 88 more files in changeset.