jalview

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JAL-2831 ported to applet

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    /src/jalview/appletgui/ScalePanel.java
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    /src/jalview/appletgui/SeqCanvas.java
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    /src/jalview/appletgui/SeqPanel.java
JAL-2831 tidies and tests

JAL-2805 viewport is passed along to the tree parser

JAL-2795 added duplication check when calculated nodes are bound to seqs

JAL-2805 added getters for hashmaps filled with associated seqs/nodes

JAL-2805 added static method for logging duplications when using map.put

JAL-2805 more sensible interface method params

JAL-2805 finished up interface comments

JAL-2805 re-enabled one2many checks

JAL-2805 interface comments, progress on associating leaves

Merge branch 'bug/JAL-2811' into bug/JAL-2831

JAL-2811 Changed to overlay on via graphics context, not separate image

JAL-2811 Missed commit

JAL-2811 Made it work for hidden columns/seqs too

JAL-2831 Attempt at cursor fix for wrapped mode

JAL-2758 update uniprot retrieval test

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    /test/jalview/ws/dbsources/UniprotTest.java
Merge branch 'bug/JAL-2811' into bug/JAL-2831

JAL-2831 deal with hidden cols and seqs in new cursor code

JAL-2831 Added move viewport event and set up cursor code to use it

Merge branch 'imp/JAL-2774' into bug/JAL-2831

JAL-2754 corrected merge conflict

JAL-2758 release notes

JAL-2698 formatting

JAL-2805 interface comments

JAL-2805 some more name changes

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    /src/jalview/ext/forester/ForesterDataConversions.java
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    /src/jalview/ext/forester/ForesterMatrix.java
JAL-2805 more name changes for clarity

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    /src/jalview/ext/archaeopteryx/AptxBinding.java
JAL-2805 more interface name changing

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    /src/jalview/ext/forester/io/ExternalTreeParserI.java
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    /src/jalview/ext/forester/io/ForesterTreeParser.java
JAL-2805 name changed of interfaces for consistency

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    /src/jalview/ext/archaeopteryx/ExternalTreeViewerBindingI.java
JAL-2805 Jalview sequence binding interface expanded