Jim Procter

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

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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
fix for JAL-1678

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    /src/jalview/appletgui/AlignFrame.java
JAL-653 refactor sequence interface to separate concrete sequence data methods from sequence metadata methods & containers

JAL-845 jim @mungo: should this be in a package local to jalview.analysis.Dna ?

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    /src/jalview/datamodel/AlignedCodon.java
JAL-1551 formatting

JAL-653 set the warningMessage for the file source to allow the GUI to report problems if necessary.

JAL-653 GFF attributes parsing mechanism, with first attempt at processing exonerate's 'similarity' features as cDNA/protein mappings

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    /src/jalview/io/FeaturesFile.java