Mateusz Warowny

JAL-3066 Fix NullPointerException thrown when showing HMMER run dialog

Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration

Merge branch 'bug/JAL-3809_ws_params_dialog_fix' into alpha/JAL-3066_Jalview_212_slivka-integration

Merge branch 'bug/JAL-3810_annotation_ws_stopping_abruptly' into bug/JAL-3809_ws_params_dialog_fix

Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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    /src/jalview/ws/api/JPredServiceI.java
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    /src/jalview/ws/jws2/JPredClient.java
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    /src/jalview/ws/jws2/JPredThread.java
JAL-3807 - Add single sequence capabilities to jws2.JPredClient

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    /src/jalview/ws/api/JPredServiceI.java
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    /src/jalview/ws/jws2/JPredClient.java
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    /src/jalview/ws/jws2/JPredThread.java
JAL-3807 - Move new JPred client to the jws2 package.

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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/jws2/JPredClient.java
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    /src/jalview/ws/jws2/JPredThread.java
JAL-3807 - Move new JPred client to the jws2 package.

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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/jws2/JPredClient.java
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    /src/jalview/ws/jws2/JPredThread.java
JAL-3807 - Re-implement results processing.

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    /src/jalview/ws/JPredThread.java
JAL-3807 - Re-implement results processing.

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    /src/jalview/ws/JPredThread.java
Merge branch 'bug/JAL-3810_annotation_ws_stopping_abruptly' into bug/JAL-3809_ws_params_dialog_fix

JAL-3810 - Add trace method to javascript implementation of Logger

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    /src/jalview/javascript/log4j/Logger.java
JAL-3810 - Replace log.trace() calls with log.debug()

JAL-3809 - Change CompletionStage to CompletableFuture.

Seems that swingjs doesn't have completion stages

properly implemented.

JAL-3809 - fixed param edit for msa but default is broken.

Edit settings dialog now works asynchronously. Everything

works properly in java. In javascript, edit settings dialog

works properly for msa services, but running without the

dialog does not work.

Annotation services do not add annotations to the seuqnces.

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/WsJobParameters.java
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    /src/jalview/ws/jws2/MsaWSClient.java
JAL-3809 - Fixed param edit dialog for jalviewjs.

Edit settings dialog now works asynchronously.

Annotation services still do not add annotations to the sequences.

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/WsJobParameters.java
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    /src/jalview/ws/jws2/MsaWSClient.java
JAL-3807 JPred can now successfully submit and track the job.

This one should be compiling

Implementing JPredThread methods and SlivkaJPredServiceInstance

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    /src/jalview/ws/JPredThread.java
Implementing JPredThread methods and SlivkaJPredServiceInstance

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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
JAL-3807 JPred can now successfully submit and track the job.

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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
Some preliminary refactoring

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    /src/jalview/ws/JPredClient.java
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    /src/jalview/ws/JPredThread.java
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    /src/jalview/ws/api/JPredMutlipleAlignmentServiceI.java
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    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
JAL-3690 Introduce AlignCalcManager2 tests.

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    /src/jalview/api/AlignCalcManagerI2.java
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    /test/jalview/workers/AlignCaclManager2Test.java
Merge branch 'Jalview-JS/develop' into feature/JAL-3690_callback-based-web-services

Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3690 AlignCalcManager - add full support for oneshot workers

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    /src/jalview/workers/AlignCalcManager2.java
JAL-3690 AlignCalcManager - add full support for oneshot workers

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    /src/jalview/workers/AlignCalcManager2.java
JAL-3690 AACon ws menu entry fix.

JAL-3690 AACon ws menu entry fix.