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  1. Jalview
  2. JAL-4107

update 2.12 alpha branch from 2.11.2.6 / 2.11.x

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    Details

    • Type: Task
    • Status: In Progress
    • Priority: Blocker
    • Resolution: Unresolved
    • Affects Version/s: 2.12.0
    • Fix Version/s: 2.12.0
    • Component/s: Dev and Dep
    • Labels:
      None

      Description

      getting Jalview 2.12 alpha build synced with 2.11 series releases, and making JalviewJS work too.

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          GitLab Commit - JAL-4107 bring in more of the 2.11.5 version calcs

          GitLab Commit - JAL-4107 catch case when args parser not actually constructed

          GitLab Commit - JAL-4107 check CDS/Protein MSA tracking is still consistent in 2.12

          GitLab Commit - JAL-4107 Copy in badly merged...

          GitLab Commit - JAL-4107 fix bad merge bits. still quite there

          GitLab Commit - JAL-4107 fix bad merge of jalview.bin.Commands - noticed due to regression of JAL-4563

          GitLab Commit - JAL-4107 fix CommandsTest failures where af was null after all CLI args were parsed

          GitLab Commit - JAL-4107 fix overviewTitle setting - set title after displaying alignment in desktop

          GitLab Commit - JAL-4107 fix progressBarTest - some duplicated lines in merge

          GitLab Commit - JAL-4107 fix sense of assert for annotation calcId tests

          GitLab Commit - JAL-4107 fixing some broken @j2s code

          GitLab Commit - JAL-4107 JAL-1551 formatting and various patches - more tests are running

          GitLab Commit - JAL-4107 JAL-3357 <br> works in browser better than <br/>

          GitLab Commit - JAL-4107 JAL-3848 fix failing annotationFileIO calcId/props tests: only set...

          GitLab Commit - JAL-4107 JAL-3878 TODO/FIXME - tidy up stale callbacks after windows are closed

          GitLab Commit - JAL-4107 JAL-4153 noticed a deadlock with AnnotationColumnChooserTest in...

          GitLab Commit - JAL-4107 JAL-4397 -Ptest_output=1 to view additional geometry info for...

          GitLab Commit - JAL-4107 JAL-4609 TODO/FIXME for saveSesssion

          GitLab Commit - JAL-4107 JAL-4610 more 2.11.5 syncing - no effect still

          GitLab Commit - JAL-4107 JAL-15551 formatting

          GitLab Commit - JAL-4107 make url lists local to preferences instance and rejig the...

          GitLab Commit - JAL-4107 merge from 2.11.5.0 to 2.12

          GitLab Commit - JAL-4107 more patching to address NPEs and exceptions when tests run concurrently

          GitLab Commit - JAL-4107 reinstate invokeLaters and 2.11.5/Native logic to avoid race conditions in tests

          GitLab Commit - JAL-4107 reinstate overview having a reference to an internal frame and fix...

          GitLab Commit - JAL-4107 reinstate overview window naming & tracking from 2.11.5

          GitLab Commit - JAL-4107 singleThread a failing test on bamboo

          GitLab Commit - JAL-4107 sync with 2.11.5.0 Commands parser rather than previous (bad) merge

          GitLab Commit - JAL-4107 testng Assert.assertEquals doesn't compare arrays of arrays

          GitLab Commit - JAL-4107 update 2.12 from 2.11.3 - continuing MMW merge

          GitLab Commit - JAL-4107 update 2.12 from 2.11.3 - continuing MMW merge

          GitLab Commit - JAL-4107 update fileglob src/jalview/b*/*.java to 19 files

          GitLab Commit - JAL-4107 wait for occupancy calculations to finish before checking

          GitLab Commit - JAL-4107 wrong conditional for checking if there was a file argument given

          GitLab Commit - JAL-4610 JAL-4107 2.11.5 ordering of layout/fontChanged calls

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              Assignee:
              soares Ben Soares
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated: