jalview

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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

JAL-2805 TreeParser now interface based

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    /src/jalview/ext/forester/io/TreeParserI.java
JAL-2805 Added tree building interface

JAL-2805 name change

JAL-2805 deleted old Aptx class for loading just Newick files

JAL-2805 more interface work

JAL-2794 removed unused interface

JAL-2805 undid accidental double (buggy) binding, more interface support

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    /src/jalview/ext/archaeopteryx/JalviewToAptxAssociation.java
Merge branch 'features/JAL-2758_shorteruniprot' into develop

JAL-2758 remove configurable behaviour - Uniprot sequences are only assigned IDs derived from Entry name

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    /src/jalview/ws/dbsources/Uniprot.java
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    /src/jalview/ws/dbsources/Uniprot.java
JAL-2738 stubs for filtering VEP and VCF fields of interest

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    /src/jalview/io/vcf/VCFLoader.java
JAl-2811 Working for wrapped panels too

Merge branch 'develop' into features/JAL-1793VCF

Conflicts:

.classpath

build.xml

resources/lang/Messages.properties

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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceI.java
JAL-2662 tweak README, format code

JAL-2698 what's new...

JAL-2811 Add layer for cursor in SeqCanvas

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    /src/jalview/gui/SequenceRenderer.java
JAL-2805 warning messages added if Forester detects file loading issues

JAL-2810 release notes

Merge branch 'imp/JAL-2810_ftsIDtab' into develop

JAL-2698 stub for 2.10.3 new known issues entries

JAL-2702 groovy interpreter update and java 9 jnlp release notes

Merge branch 'bug/JAL-2702_groovyconsoleJava9' into develop