jalview

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JAL-2877 disabled Jalview's own viewer for testing

JAL-1953 fixed interface misnaming

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    /src/jalview/ext/archaeopteryx/AptxFrame.java
JAL-1953 renaming of concrete implementation as well

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    /src/jalview/ext/archaeopteryx/Aptx.java
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    /src/jalview/ext/archaeopteryx/AptxFrame.java
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    /src/jalview/ext/treeviewer/ExternalTreeViewerFrameI.java
JAL-2844 reallow clicks to the left of the root (groups whole tree as 1)

JAL-2866 and .jar removed again

JAL-2866 forester .jar added to lib

JAL-2872 Redundant Aptx GUI menu items hidden, sorting item added

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    /src/jalview/ext/archaeopteryx/AptxInit.java
JAL-2794 disabled branch colors on selection for now

JAL-2871 Added check whether configuration has been loaded in

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    /src/jalview/ext/archaeopteryx/AptxInit.java
JAL-2838 Sorting from the alignment view menu now functional

JAL-2847 Rearranging and cleaning up of database query code

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    /src/jalview/ext/archaeopteryx/AptxInit.java
JAL-2794 associate leaves now iterates through ALL nodes (also internal)

JAL-2847 various error popups for db querying now have formatted strings

JAL-2847 Strings for the various tree databases added

JAL-2847 if pfam id is detected in first sequence its shown in db query

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    /src/jalview/ext/archaeopteryx/AptxInit.java
JAL-2847 added pfam to DBRef source name lookup

JAL-2805 JAL-2847 JAL-281 added file path to Aptx frame title

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    /src/jalview/ext/archaeopteryx/AptxInit.java
JAL-2838 tree viewer interface expanded to include sorting

Merge remote-tracking branch 'origin/develop' into kjvdh/features/PhylogenyViewer

JAL-2838 filled in actionPerformed of the tree sort menu items

JAL-2838 Aptx frames now appear in the alignment sorting menu

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    /src/jalview/ext/archaeopteryx/AptxInit.java
JAL-2847 start of cleaning up db loading code

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    /src/jalview/ext/archaeopteryx/AptxInit.java
JAL-2844 rearranging code

JAL-2849 release notes

Merge branch 'bug/JAL-2849' into develop

JAL-2849 JAL-2863 file format preferences TODO

JAL-2844 check added for clicks left of root node

JAL-2844 entirely X coord based partitioning

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    /src/jalview/ext/archaeopteryx/AptxInit.java
JAL-2844 somewhat better repainting