jalview

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JAL-3853 patch sequence annotation report code and tweak the test. When merging from 2.11.2 develop there will be conflicts that need merging re HTMLXML tags

JAL-3848 ensure annotation from a service gets a calcId so it can be updated and tracked across multiple views - nb - service.getId() probably isn’t the right value to use for this!

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    /src/jalview/io/AnnotationFile.java
JAL-3848 don’t include sequence limits in sequence id as it confuses slivka-0.8’s jalview-feature-file creation script

JAL-3848 - actually test the Slivka and JABAWS disorder services - nb still need asserts to verify the disorder annotation from Slivka looks like Jabaws

JAL-3848 print exception for failed align jobs

JAL-3848 add latest slivka-client fixes.

JAL-3850 fixed full class name

JAL-3850 using reflection for SimpleHttpFileServerFactory

JAL-3848 patched SwingJS runtime rebuilt

JAL-3948 - temporarily add the ojdk8 calendardata file (GPL licensed)

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    /resources/sun/util/resources/CalendarData.properties
Merge branch 'improvement/JAL-3848_slivka_0.8_updated_jslib' of https://source.jalview.org/git/jalview into improvement/JAL-3848_slivka_0.8_updated_jslib

JAL-3848 j2s 3.2.10-v1 slivka-java-client jslib

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    /utils/jalviewjs/libjs/slivka-client-site.zip
JAL-3848 nominal build of slivka 0.8 compatible java client library

    • binary
    /utils/jalviewjs/libjs/slivka-client-site.zip
JAL-3842 fix automatic what's new link for custom version builds

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
JAL-3847 set default behaviour as exclude when dealing with duplicate entries in jars and zips

JAL-3847 set default behaviour as exclude when dealing with duplicate entries in jars and zips

JAL-3842 JAL-3746 (need to cherry pick to develop) - automatically generate link to latest release notes in what's new

JAL-3594 Updated the Jalview Develop getdown splashscreen image with Geoff's license free photo

JAL-3842 2.11.1.5 what’s new, release notes, and version bump

Merge branch 'patch/JAL-3840_2_11_1_4' into releases/Release_2_11_1_Branch

JAL-3840 don’t update the modal residue count for gaps

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    /src/jalview/datamodel/ResidueCount.java
JAL-3840 don’t update the modal residue count for gaps

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    /src/jalview/datamodel/ResidueCount.java