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- JAL-3744
Cannot read Gzip file in JalviewJS - JAL-3660
Jalview does not honour file format when exporting file as new format via command line - JAL-3657
LinkedHashMap copy constructor fails in SwingJS - JAL-3648
AnnotationPanel vertical scrollbar does not appear after mouse drag resize - JAL-3647
Jalview code should not call addNotify() - JAL-3646
Tooltips are needlessly truncating;links in tooltips - JAL-3645
Sort By Tree submenu shown as greyed out when no trees available for a view - JAL-3639
IntervalStore-v1.1 fails to find RESNUM 0 in 4IM2 - JAL-3638
Navigate to next gapped or ungapped position in cursor mode - JAL-3614
Find dialog and prompts indicate when a selection was searched rather than whole alignment - JAL-3605
Review way in which URLs for features are reported to user and preserved via GFF & Jalview Features - JAL-3601
JavaScript Problems with server-side redirection and swingjs/j2s - JAL-3600
Save project very slow in Jalview-JS/develop - JAL-3589
Fetch from PDB fails in JalviewJS - JAL-3586
Drag and drop of alignment file fails in JalviewJS - JAL-3585
Focus lost when popup menu closes - JAL-3583
Tidy up alignment panel tooltip code - JAL-3516
JalviewJS runtime path not resolved when when core files are used - JAL-3506
JavaScript libraries known to work/not work with JalviewJS - JAL-3498
enum coding failing to transpile to Javascript - JAL-3490
Find doesn't report matches that span hidden gapped columns - JAL-3478
Class.getProtectionDomain not supported in SwingJS - JAL-3475
Maintain and update beta test links for JalviewJS - JAL-3463
Thread.sleep() is not supported in SwingJS - alerts - JAL-3454
file loading with String filename for PDB structure file can fail - JAL-3445
provide support in Jalview for BSML files - JAL-3444
Feature transparency not working in JalviewJS - JAL-3437
JS not loading JVP files - JAL-3436
JS AlignPanel file...reload does not work if file loaded using AlignFrame File...AddSequences...From File - JAL-3433
Address memory leaks (for Jalview 2.11_js) - JAL-3429
OverviewPanel no longer works when columns hidden - JAL-3423
TestNG tests not running under Windows/Eclipse - JAL-3418
fix unattended test execution for Jalview-JS/JAL-3253-applet - JAL-3401
JVP project opening must hold off repaints until fully loaded - JAL-3397
Alternative to NCList for IntervalStore; improvements for FeatureStore - JAL-3392
adds Calculation workers report to Jalview.getInstance() - JAL-3380
JalviewJS needs to be able to get data from an embedded frame's div tag - JAL-3366
Jmol structure viewer has unspecified, too small default dimensions - JAL-3345
Scroll alignment on drag from ScalePanel out of SeqPanel - JAL-3308
Review excluded tests in Jalview.2.11 for Jalview 2.11.1 - JAL-3298
Sunset the use of JNLP/Webstart for Distributing Jalview - JAL-3276
JalviewJS export for Jalview.app - JAL-3274
Embed build details in JalviewJS builds - JAL-3268
JSmol loading is slow - need additional core packages - JAL-3261
tidy up Cache.get/set/Properties usage to avoid direct manipulation of applicationProperties - JAL-3225
Integrate Gradle building into Eclipse - JAL-3223
Update SwingJS for Java 11 - JAL-3210
Merge develop (2.11) to JalviewJS - JAL-3207
Build a JalviewJS examples page - JAL-3192
Create one or more JalviewJS 'core' downloads
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