--- /dev/null
+---
+channel: release
+version: 2.11.1.0
+date: 2020-04-22
+---
+
+## New Features
+
+- <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 --> Map 'virtual' codon features shown on protein (or vice versa) for display in alignments, on structure views (including transfer to UCSF chimera), in feature reports and for export.
+- <!-- JAL-3121 --> Feature attributes from VCF files can be exported and re-imported as GFF3 files
+- <!-- JAL-3376 --> Capture VCF "fixed column" values POS, ID, QUAL, FILTER as Feature Attributes
+- <!-- JAL-3375 --> More robust VCF numeric data field validation while parsing
+- <!-- JAL-3533 --> Feature Settings dialog keeps same screen position if reopened
+- <!-- JAL-3535 --> Feature Settings dialog title includes name of associated view
+- <!-- JAL-3538 --> Font anti-aliasing in alignment views enabled by default
+- <!-- JAL-3468 --> Very long feature descriptions truncated in tooltips and menus
+- <!-- JAL-3549 --> Warn if Sort by Score or Density attempted with no feature types visible
+- <!-- JAL-3574 --> Improved support for filtering feature attributes with large integer values
+
+
+### Jalview Installer
+- <!-- JAL-3449 --> Versions for install4j and getdown and installer template version reported in console (may be null when Jalview launched as executable jar or via conda)
+- <!-- JAL-3393 --> Layout improvements for OSX .dmg Finder and higher quality background images
+- <!-- JAL-3394 --> New installer/application launcher generated with install4j 8.0.4
+- <!-- JAL-3420 --> Jalview File Associations shown for Unix Platforms
+- <!-- JAL-3477 --> Improved defaults for maximum memory setting when running on large memory machines
+
+
+### Release processes
+- <!-- JAL-3508 --> New point release version scheme - 2.11.1.0
+- <!-- JAL-3577 --> 'Jalview Test' installers/apps for easier access to test-release channel builds
+
+
+### Build System
+- <!-- JAL-3510 --> Clover updated to 4.4.1
+- <!-- JAL-3513 --> Test code included in Clover coverage report
+
+
+### Groovy Scripts
+- <!-- JAL-3547 --> exportconsensus.groovy prints a FASTA file to stdout containing the consensus sequence for each alignment in a Jalview session
+- <!-- JAL-3578 --> ComputePeptideVariants.groovy to translate genomic sequence_variant annotation from CDS as missense_variant or synonymous_variant on protein products.
+
+
+## Issues Resolved
+
+- <!-- JAL-3581 --> Hidden sequence markers still visible when 'Show hidden markers' option is not ticked
+- <!-- JAL-247 --> Hidden sequence markers not shown in EPS and PNG output when 'Automatically set ID width' is set in jalview preferences or properties file
+- <!-- JAL-3571 --> Feature Editor dialog can be opened when 'Show Sequence Features' option is not ticked
+- <!-- JAL-3549 --> Undo 'Null' operation shown after sort by buttons in Feature Settings dialog are clicked when no features are visible
+- <!-- JAL-3412 --> ID margins for CDS and Protein views not equal when split frame is first opened
+- <!-- JAL-3296 --> Sequence position numbers in status bar not correct after editing a sequence's start position
+- <!-- JAL-3377 --> Alignment is misaligned in wrapped mode with annotation and exceptions thrown when only a few columns shown in wrapped mode
+- <!-- JAL-3386 --> Sequence IDs missing in headless export of wrapped alignment figure with annotations
+- <!-- JAL-3388--> Sorting Structure Chooser table by Sequence ID fails with ClassCastException
+- <!-- JAL-3389 --> Chimera session not restored from Jalview Project
+- <!-- JAL-3441 --> Double-click on 'Show feature' checkbox in feature settings dialog also selects columns
+- <!-- JAL-3473 --> SpinnerNumberModel causes IllegalArgumentException in some circumstances
+- <!-- JAL-3534 --> Multiple feature settings dialogs can be opened for a view
+- <!-- JAL-2764 --> Feature Settings dialog is orphaned if alignment window is closed
+- <!-- JAL-3406 --> Credits missing some authors in Jalview help documentation for 2.11.0 release
+- <!-- JAL-3529 --> Export of Pfam alignment as Stockholm includes Pfam ID as sequence's accession rather than its Uniprot Accession
+
+
+### Java 11 Compatibility issues
+- <!-- JAL-2987 --> OSX - Can't view some search results in PDB/Uniprot search panel
+
+
+### Installer
+- <!-- JAL-3447 --> Jalview should not create file associations for 3D structure files (.pdb, .mmcif. .cif)
+
+
+### Repository and Source Release
+- <!-- JAL-3474 --> removed obsolete .cvsignore files from repository
+- <!-- JAL-3541 --> Clover report generation running out of memory
+
+
+### New Known Issues
+- <!-- JAL-3523 --> OSX - Current working directory not preserved when Jalview.app launched with parameters from command line
+- <!-- JAL-3525 --> Sequence IDs aligned to wrong margin and clipped in headless figure export when Right Align option enabled
+- <!-- JAL-3542 --> Jalview Installation type always reports 'Source' in console output
+- <!-- JAL-3562 --> Test Suite: Certain Functional tests fail on jalview's bamboo server but run fine locally.
git://source.jalview.org / jalview.git / blobdiff