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jim procter <jprocter@dundee.ac.uk> in jalview

not related to JAL-3765 ! Actually related to JAL-3675!

not related to JAL-3765 ! Actually related to JAL-3675!

relevant issue is JAL-3626

relevant issue is JAL-3626

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with. This seemed like a quick way to achieve almost the same, but longer term a ...

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with.
This seemed like a quick way to achieve almost the same, but longer term a getdown created visibile indicator would be ideal. I'll create an issue.

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Ben Soares reported JAL-3514 about this build

Ben Soares reported JAL-3514 about this build

why are loops in removeAlreadyRetrievedSeqs now backwards?

why are loops in removeAlreadyRetrievedSeqs now backwards?

JAL-1617 hack to add a fake xref if the uniprot xref isn't present on the embl entry

JAL-1617 formatting and generics

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    /src/jalview/util/DBRefUtils.java
JAL-1617 fake xref database for when Uniprot xrefs aren't added

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    /src/jalview/datamodel/DBRefSource.java
JAL-1617 toString for DBRefEntry

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    /src/jalview/datamodel/DBRefEntry.java
Merge branch 'features/JAL-1565_jpred4' into develop

Merge branch 'features/JAL-1565_jpred4' into Release_2_8_3_Branch

JAL-1565 loading a concise file causes insertions to be automatically hidden in desktop

Merge branch 'features/JAL-845splitPaneMergeDevelop' into develop

Merge branch 'develop' into features/JAL-845splitPaneMergeDevelop JAL-1645 bring JAL-845 feature branch up to date ready for develop merge

Conflicts:

src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java

test/jalview/analysis/DnaTranslation.java

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    /help/html/features/multipleViews.html
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    /src/jalview/analysis/AAFrequency.java
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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/api/AlignmentViewPanel.java
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    /src/jalview/appletgui/APopupMenu.java
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    /src/jalview/appletgui/AlignFrame.java
  1. … 111 more files in changeset.
JAL-1683 bump version for r2.8.3 branch

JAL-1683 replace year/version strings with tokens in source

  1. … 820 more files in changeset.
reassign features already created/documented for 2.9 to 2.8.3 JAL-1682

Merge branch 'Release_2_8_2b1_Branch'

Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

  1. … 116 more files in changeset.
Merge commit '6797d65989b01c8fa5bdeaf6a66e35279b66a7f7' into develop

JAL-1678 fix replace token for launchApp in a buildwq

JAL-1678 fix replace token for launchApp in a buildwq

JAL-1213 JAL-1395 add Jmol to JalviewLite classpath - need to find a way around this in the future

JAL-1678 add version parameter to example files in publish phase

JAL-1678 add version parameter to example files in publish phase

Merge branch 'bug/JAL-1643_File-chooser-improvement' into develop

JAL-1643 add quaqua libs as OSX specific resources

Merge branch 'bug/addcustomlaunchdesktopparams' into develop

JAL-1678 - patch to make sure we only compare positions of the last / or ?

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    /src/jalview/appletgui/AlignFrame.java