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- JAL-2746
User configurable annotation retrieval systems - JAL-2355
Rationalise passing of url links in Jalview - JAL-2144
provide methods for normalising and reasoning about database references - JAL-2014
BLOSUM62 shouldn't be greyed out if consensus/quality/conservation calcs are disabled - JAL-1818
escape close current dialog and transfer key focus for further keystrokes - JAL-1719
Tree windows remain after alignment windows are closed - JAL-1676
flat-file/local cache for reference sequences - JAL-1657
refactor feature/sequence renderer to an AWT/Swing independent pipeline - JAL-1653
JSON schema validation - JAL-1642
Superpowered load and save dialogs - JAL-1638
refactor jalview2XML to its own package - JAL-1615
Replace Export Image, Alignment and Save as .. submenus with dialogs - JAL-1606
JavaFx proof of concept for Jalview - JAL-1600
sequence fetcher doesn't fetch when retrieving structures - JAL-1597
more efficient resolution of IDs when querying contig databases - JAL-1590
taxonomy of human readable annotation row types for use in UI - JAL-1562
refactor help documentation system - JAL-1546
Upgrade help and documentation processes for core-jalview team - JAL-1501
New items available indicator for jalview.org content - JAL-1500
create test case for import/export/recovery of RNA, DNA and Protein accession data from different datasources - JAL-1490
refactor Find and redundancy removal dialog and introduce new API methods - JAL-1463
efficient encoding of programmatically generated alignment and sequence annotation rows - JAL-1462
support for complex html/interactive tooltips - JAL-1455
Visual indicator of any minor(!) problems with data that may affect validity of PCA analysis - JAL-1453
Smoke test to identify exceptions during interactive alignment/calculation updates - JAL-1441
show feature shading state, number of groups and range of shading currently applied - JAL-1440
Jalview's Heads Up Display - info about the current status of the visualization and interaction mode - JAL-1431
Redesign of the JV desktop GUI - JAL-1421
Java Generics are not commonly used - JAL-1415
bidirectional communication between Jmol and Jalview - JAL-1413
Standard :start-end range specification for ID retrieval from all databases - JAL-1404
Restyling and updating the news system - JAL-1381
scalable and efficient datamodel operations - JAL-1344
Local system default preferences for all Jalview users on a system - JAL-1332
A prototype Jalview plugin for Cytoscape 3 - JAL-1318
simplify programmatic access to analysis routines - JAL-1305
Allow distinct sets of annotation for a sequence to be propagated and visually compared - JAL-1301
"Out of Memory - Please restart Jalview" errors when viewing large sets of alignment annotation - JAL-1295
test for export/reimport of annotation created by web service jobs - JAL-1227
option to search data outside the current selection when performing a find - JAL-1191
support for hierarchical features and feature groups - JAL-1186
information about what to do if saving a jalview project fails - JAL-1173
Improve jalview memory efficiency and robustness to out of memory situations - JAL-1172
disable web service menu entries not appropriate for current view - JAL-1150
Create API for manipulating sequence feature display on AlignPanel - JAL-1143
copy and paste does not transfer sequence associated annotation - JAL-1115
Test and address concurrency issues arising from refactoring Vectors to access by a List interface - JAL-1114
standardised API for annotatable groups, alignments, and individual sequences - JAL-1112
Open, extensible data source model - JAL-1105
Unify interface for annotating an annotatable object from a file source
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