X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_11_2_0.md;fp=help%2Fmarkdown%2Freleases%2Frelease-2_11_2_0.md;h=3984535ff561fad8c78c53ec821d437bfda0d50b;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=0000000000000000000000000000000000000000;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git diff --git a/help/markdown/releases/release-2_11_2_0.md b/help/markdown/releases/release-2_11_2_0.md new file mode 100644 index 0000000..3984535 --- /dev/null +++ b/help/markdown/releases/release-2_11_2_0.md @@ -0,0 +1,96 @@ +--- +channel: release +version: 2.11.2.0 +date: 2022-03-10 +--- + +## New Features + +- Support for viewing 3D structures with ChimeraX and Pymol in addition to Jmol and Chimera. +- Discover 3D structure data for sequences with Uniprot references via 3D-Beacons +- Rank and select available structures for Uniprot sequences according to number of residues in structure mapped to positions involved in the alignment +- Structure annotation rows for all mapped chains in 3D structures are included in the 'Reference Annotation' for a sequence +- Import Genbank and EMBL format flatfiles +- ENA record's mol_type honoured so RNA molecules imported from ENA records are shown as RNA +- Support for Canonical Uniprot IDs +- New Preferences tab for adjusting Jalview's memory settings at launch +- Sequence IDs split on '_' as well as other non-alphanumerics when discovering database references with 'Fetch DB Refs' +- Suppressed harmless exceptions output to Console whilst discovering database references for a sequence +- Updated Jalview bindings for Uniprot XML schema +- Uniprot and PDBe autosearch option is disabled by default +- Reverted to Jalview 'classic' drop-down menu for selecting which database to fetch from in sequence fetcher dialog. +- Updated Ensembl REST Client compatibility to 15.2 and revised model organism names (rat, xenopus, dmelanogaster now rattus_norvegicus, xenopus_tropicalis, drosophila_melanogaster) +- -nowebservicediscovery command line argument to prevent automatic discovery of analysis webservices on launch +- Allow 'App' directories to be opened when locating Chimera, ChimeraX or Pymol binaries via filechooser opened by double clicking the Structure Preferences' path textbox +- support for HTTP/S access via proxies that require authentication +- New mechanism for opening URLs with system default browser (works on OSX and Linux as well as Windows) +- Upgraded bundled version of Jmol to 14.31.53 +- GPL license info on splash screen and About text + + +### Jalview Native App +- New command line launcher scripts (.sh, .ps1, .bat) usable on macOS, Linux/Unix, Windows and documentation in Help. Installer wizard has option to add this to PATH, or link to it in your PATH.
+ *This is the recommended workaround for known issue about working directory preservation when running native application from command line.* +- Notarized MacOS installer for compliance with latest OSX releases (Monterey) +- Uninstaller application for old (InstallAnywhere based) Jalview installations removed from the OSX disk image +- Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview +- Metal LaF used to improved operation on Linux Ubuntu with HiDPI display in Java 11 (still known issues with HiDPI screens in java 8 and 11. see [JAL-3137](https://issues.jalview.org/browse/JAL-3137)) +- Getdown launcher inherits HTTP/S proxy configuration from jalview_properties +- New Jalview Develop app - making it even easier to get at Jalview's development builds +- New splashscreens for Jalview, Jalview Test and Jalview Develop applications. +- Jalview logos shown for Jalview Java Console and other window widgets in taskbar and dock rather than anonymous 'Java' icons + + +### JalviewJS +- PDB structures mapped to Uniprot Sequences with SIFTS +- setprop commandline argument reinstated for JalviewJS only +- Missing message bundle keys are only reported once per key (avoids excessive log output in js console) +- Feature type is included in the title of the Feature Settings' Colour Chooser dialog +- Build details reported in About window +- Numerous minor GUI additions and improvements in sync with Java application. + + +### Development +- First integrated JalviewJS and Jalview release +- Updated README and doc/building.md +- Improved JalviewJS/Jalview build process, added support for system package provided eclipse installs on linux +- Install4j 9.0.x used for installer packaging +- Improved use of installers for unattended installation with a customizedId of "JALVIEW" in install4j's Jalview Launcher +- Improved compatibility of Jalview build with Java 17 (next LTS target) + + +## Issues Resolved + +- Slow structure commands can block Jalview execution +- Structure window's viewer-specific menu disappears when only one structure is shown (and many sequences:one chain mappings are present) +- Annotation file: PROPERTIES apply only to the first SEQUENCE_GROUP defined +- Selections not propagated between Linked CDS - Protein alignments and their trees (known defect from 2.11.1.3) +- Not all codon positions highlighted for overlapping exon splice sites (e.g due to RNA slippage) +- X was not being recognised as the unknown base in DNA sequences +- Removed RNAview checkbox and logic from Structure Preferences +- Tooltip behaviour improved (slightly) +- Can edit a feature so that start > end +- Cancel from Amend Features doesn't reset a modified graduated colour +- New View with automatic 'Show Overview' preference enabled results in Null Pointer Exceptions when clustal colouring is enabled +- Can open multiple Preferences panels +- Properly configure HTTPS proxy settings from Preferences +- Standard out logging broken: messages only routing to stderr and appear as a raw template +- Entering web service parameter values in numerical field doesn't update the value of the parameter until return is pressed. +- Resolved known issue (from 2.11.1.1) concerning duplicate CDS sequences generated when protein products for certain ENA records are repeatedly shown via Calculate->Show Cross Refs + + +### JalviewJS +- Consensus profile may include zero (rounded down) percentage values causing a divide by zero +- JalviewJS doesn't honour arguments passed via Info.args when there are arguments on the URL +- gradle closure-compiler not using UTF-8 +- Annotation file fails to load from URL in JalviewJS + + +### Development +- Gradle + - Fixed non-fatal gradle errors during build + - Updated build.gradle for use with Gradle v.6.6+ + + +### Known Issues +- Display of RESNUM sequence features are not suppressed when structures associated with a sequence are viewed with an external viewer (Regression from 2.11.1 series)