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JAL-3259
StockholmFileTest not portable: does not cope with platform specific line endings
FileLoader inappropriately uses System.getProperty("file.separator")
gffheader output with \n instead of System.getProperty("line.separator")JAL-3255
install4j logo should be on the 2.11 downloads page
Review FAQs for 2.11 release
New FAQ for opening the 'System java console'
Run 'Memory' test suite as Bamboo task during release process
fix JNetCONF definition in documentation
Sequence features and crossreferences lost if input linked CDNA/Protein view closed before MSA result shown
Sequences disappear when reducing height of alignment view
text color threshold not preserved across tree subgroup operationsJAL-3137
Support HiDPI scaling for hi-resolution displays
Colour by/Align with view selection menu loses focus on OSX/Java 11
Sort group associated annotation rows in same way as ordering of groups in the alignment
Protein structure derived annotation tracks not available as reference annotation unless 'add to alignment' preference is enabled
Java 10 - Mac OSX - can't select from drop-down menu in linked cDNA/Protein splitview
Extra annotation rows appear when removing and recreating group in example project
Java 10 (OSX) - only see news from 7 Sept 2017 in news reader
Resize corners on bottom right of windows aren't visible on OSX/Java 10
templating for integration of slivka client with Jalview
Migrate from Castor to JAXB to enable Jalview project import/export in Jalview-js
optimise calculations triggered by interactive operations
tooltip does not jump when moved to right of window
Add clustalx colour scheme reference to documentationJAL-3044
Citation report
Fix image HTML5 Canvas scaling for hi-res screens
Groovy help page incorrect decription of variable binding / functions
Different terminology between Preferences and Format menu for show unconserved
Cannot reconstruct CDS alignment for alignment of several subsequences of a single dataset sequence
treat '~' tilde as special gap character
Make 'Input path' text fields easier to complete for novices
Can't view multiple-page results in PDB/Uniprot FTS on Java 10
Overview redraws multiple times for a series of edits
migrate from Quaqua to a more widely supported OSX look and feel
Jmol view not always centred on structures when multiple structures are viewed
dont fetch dbrefs or SIFTS for file-based associations of 3D structures
Resolve correct Ensembl REST API endpoint for Uniprot crossreferences to Ensembl
Retrieve Uniprot entries for imported PDB structures
verify compatibility and migrate jalview / compbio services to https
Panning/zooming mode for alignment view
no binding between derived annotation rows and original structure data file parsed via Jmol
Refactor File format suffix export preferences
Jalview does not import reverse-strand RNA sequences via Stockholm
can't drag and drop URLs with spaces for import
Groovy 2.4.12 console doesn't echo StdOut
Custom taxon lists for ensemblGenomes gene id lookup
Jalview Java Console appears during some functional tests
Offer 'Open Groovy Console' as well as Run Groovy Script from Calculations
Short isoforms from Ensembl are expanded to full length Uniprot sequences
Even smaller sequence ID tooltip !
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