Mateusz Warowny

Merge branch 'improvement/JAL-3848_slivka_0.8' into alpha/JAL-3066_Jalview_212_slivka-integration

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

Merge commit '0b438477b16470202bddfecb54e0587036b37202' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3848 Update slivka client javajs library.

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    /utils/jalviewjs/libjs/slivka-client-site.zip
JAL-3848 print exception for failed align jobs

JAL-3848 add latest slivka-client fixes.

Merge branch 'jpred-fix' into bug/JAL-3807_jpred-with-slivka

JAL-3807 Fix SlivkaWSInstance not fetching alignments.

Merge branch 'bug/JAL-3849_aacon-parameters' into improvement/JAL-3848_slivka_0.8

JAL-3690 Remove references to old AlignCalcManager.

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    /src/jalview/api/AlignCalcManagerI.java
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    /src/jalview/workers/AlignCalcWorker.java
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    /test/jalview/gui/AlignViewportTest.java
JAL-3849 Remove join() which blocked the ui.

JAL-3848 SlivkaParamSet: reformat code and add service description.

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    /src/jalview/ws/slivkaws/SlivkaParamSet.java
JAL-3848 Update slivka client library.

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    /src/jalview/ws/slivkaws/SlivkaParamSet.java
WIP

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    /src/jalview/ws/slivkaws/SlivkaParamSet.java
Revert "Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration"

This reverts commit 95f4ae66fbaecbbdc1c3ab3c6c9c611a3a9a3e46, reversing

changes made to bc7c2cf5500c5a4124a69ef8e7b1374d8997558f.

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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
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    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
JAL-3066 Fix NullPointerException thrown when showing HMMER run dialog

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()