X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=a6293e672bd97b726cff7dbe0eb3645680b0512e;hb=e69f7ec847b9dbbf88350521ccd3fd773c6aeaa8;hp=d3f242073b1f3c83d1b7789a196b7184d7f1a9c8;hpb=2720003e4d3537f99f6c1643561cbdb3d0120d2d;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index d3f2420..a6293e6 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -1,3 +1,4 @@
+
Support for viewing 3D
+ structures with ChimeraX and Pymol in addition to Jmol and
+ Chimera.
+
+
+ New Preferences tab for adjusting Jalview's
+ memory settings at launch
+
+
+ Reverted to Jalview 'classic' drop-down
+ menu for selecting which database to fetch from in sequence
+ fetcher dialog.
+
+
+
+
+
+
+
+
+ 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
+
+
+ Updated Jalview bindings for Uniprot XML
+ schema
+
+ JalviewJS
+
+ -
+ PDB structures mapped to Uniprot Sequences with
+ SIFTS
+
+ -
+
+
+ -
+
+
+ -
+
+
+ -
+ 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
+
+
+
Development
+
+ - First integrated JalviewJS and Jalview release
+ - Updated building instructions
+ -
+ Improved JalviewJS/Jalview build process
+ for system package provided eclipse installs on linux
+
+ - Install4j 9.0.x used for installer packaging
+ - Notarized MacOS installer for compatibility with Big
+ Sur and Monterey
+ -
+ Uninstaller application for old
+ (InstallAnywhere based) Jalview installations removed from
+ the DMG
+
+ -
+ Improved use of installers for unattended
+ installation with a customizedId of "JALVIEW" in install4j's
+ Jalview Launcher
+
+
+
+
+
+
+
+ -
+ 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
+ -
+ Standard out logging broken: messages only
+ routing to stderr and appear as a raw template
+
+ JalviewJS
+
+ -
+
+
+ -
+
+
+ -
+
+
+ -
+
+
+ -
+
+
+ -
+ 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+
+
+
+
+
+
+ |
+
+
+ 2.11.1.7
+ 18/01/2022 |
+ |
+
+
+ -
+ Files open in Jalview cannot be
+ updated by Jalview or other applications (Windows, other non
+ Unix/BSD OSs)
+
+ Security
+
+ -
+ Enable AIA download of HTTPS intermediate
+ certificates.
+
+
+ |
+
+ 2.11.1.6
+ 6/01/2022 |
+
+ Security
+
+ -
+ Version bump library dependency: Log4j 2.16.0 to 2.17.0.
+
+ |
+
+ |
+
+
+ 2.11.1.5
+ 20/12/2021 |
+
+ Security
+
+ -
+ Update library dependency: Log4j 2.16.0
+ (was log4j 1.2.x).
+
Development
+
+ - Updated building instructions
+ |
+
+
+ -
+ Occupancy calculation is incorrect for
+ alignment columns with over -1+2^32 gaps (breaking filtering
+ and display)
+
+ -
+ Caps on Hi-DPI scaling to prevent crazy
+ scale factors being set with buggy window-managers (linux
+ only)
+
+ Development
+
+ - Fixed non-fatal gradle errors during build
+
+ |
+
+
+ 2.11.1.4
+ 09/03/2021 |
+ Improved control of
+ Jalview's use of network services via jalview_properties
+
+ -
+ New .jalview_properties token controlling
+ launch of the news browser (like -nonews argument)
+
+ -
+ New .jalview_properties token controlling
+ download of linkout URLs from
+ www.jalview.org/services/identifiers
+
+ -
+ New .jalview_properties token controlling
+ download of BIOJSHTML templates
+
+ -
+ New 'Discover Web Services' option to
+ trigger a one off JABAWS discovery if autodiscovery was
+ disabled
+
+ |
+
+
+ -
+ Intermittent deadlock opening structure in
+ Jmol
+
+ New Known defects
+
+ -
+ Protein Cross-Refs for Gene Sequence not
+ always restored from project (since 2.10.3)
+
+ -
+ Selections from tree built from CDS aren't
+ propagated to Protein alignment (since 2.11.1.3)
+
+
+ |
+
+
+ 2.11.1.3
+ 29/10/2020 |
+
+
+ |
+
+
+ -
+ Find doesn't always highlight all matching
+ positions in a sequence (bug introduced in 2.11.1.2)
+
+ -
+ Alignments containing one or more protein
+ sequences can be classed as nucleotide
+
+ -
+ CDS alignment doesn't match original CDS
+ sequences after alignment of protein products (known defect
+ first reported for 2.11.1.0)
+
+ -
+ No tooltip or popup menu for genomic
+ features outwith CDS shown overlaid on protein
+
+ -
+ Overlapping CDS in ENA accessions are not
+ correctly mapped by Jalview (e.g. affects viral CDS with
+ ribosomal slippage, since 2.9.0)
+
+ -
+ Spliced transcript CDS sequences don't show
+ CDS features
+
+ -
+ Selections in CDS sequence panel don't
+ always select corresponding protein sequences
+
+ -
+ Make groups from selection for a
+ column selection doesn't always ignore hidden columns
+
+ Installer
+
+ -
+ Space character in Jalview install path on
+ Windows prevents install4j launching getdown
+
+ Development
+
+ -
+ Fixed typos and specified compatible gradle
+ version numbers in doc/building.md
+
+
+ |
+
+
+ 2.11.1.2
+ 25/09/2020 |
+
+
+ |
+
+
+ -
+ Fresh install of Jalview 2.11.1.1 reports
+ "Encountered problems opening
+ https://www.jalview.org/examples/exampleFile_2_7.jvp"
+
+
+ |
+
+
+ 2.11.1.1
+ 17/09/2020 |
+
+
+ -
+ Shift+arrow keys navigate to next gap or
+ residue in cursor mode
+
+ -
+ Support import of VCF 4.3 by updating
+ HTSJDK from 2.12 to 2.23
+
+ -
+ IntervalStore library updated to v.1.1:
+ optimisations and improvements suggested by Bob Hanson and
+ improved compatibility with JalviewJS
+
+ -
+ Retrieve GZipped stockholm formatted
+ alignments from Pfam and Rfam
+
+ -
+ Recognise GZipped content for URLs and File
+ import (no longer based on .gz extension)
+
+ -
+ Updated Spanish Translation for 2.11.1
+
+ -
+ Migrate EMBL record retrieval to use latest
+ ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
+ EMBL flat file
+
+ -
+ Improved warning messages, debug logging
+ and fixed Retry action when Jalview encounters errors when
+ saving or making backup files.
+
+ -
+ Enhanced Jalview Java Console:
+
+ - Jalview's logging level can be configured
+ - Copy to Clipboard Buttion
+
+
+ -
+ Improved support for Hi-DPI (4K) screens
+ when running on Linux (Requires Java 11+)
+
+ Launching Jalview
+
+ -
+ Configure Jalview Desktop's look and feel
+ through a system property
+
+ -
+ Improved built-in documentation and command
+ line help for configuring Jalview's memory
+
+
+ |
+
+
+ -
+ Conservation and Quality tracks are shown
+ but not calculated and no protein or DNA score models are
+ available for tree/PCA calculation when launched with
+ Turkish language locale
+
+ -
+ Escape does not clear highlights on the
+ alignment (Since Jalview 2.10.3)
+
+ -
+ Alt+Left or Right arrow in cursor mode
+ doesn't slide selected sequences, just sequence under cursor
+
+ -
+ Alt+Up/Down in cursor mode doesn't move
+ sequence under the cursor
+
+ -
+ Peptide-to-CDS tracking broken when
+ multiple EMBL gene products shown for a single contig
+
+ -
+ Errors encountered when processing variants
+ from VCF files yield "Error processing VCF: Format specifier
+ '%s'" on the console
+
+ -
+ Count of features not shown can be wrong
+ when there are both local and complementary features mapped
+ to the position under the cursor
+
+ -
+ Sequence ID for reference sequence is
+ clipped when Right align Sequence IDs enabled
+
+ -
+ Slider with negative range values not
+ rendered correctly in VAqua4 (Since 2.10.4)
+
+ -
+ Single quotes not displayed correctly in
+ internationalised text for some messages and log output
+
+ -
+ Find doesn't report matches that span
+ hidden gapped columns
+
+ -
+ Resolved memory leaks in Tree and PCA
+ panels, Alignment viewport and annotation renderer.
+
+ -
+ Jalview ignores file format parameter
+ specifying output format when exporting an alignment via the
+ command line
+
+ -
+ Windows 10: For a minority of users, if
+ backups are not enabled, Jalview sometimes fails to
+ overwrite an existing file and raises a warning dialog. (in
+ 2.11.0, and 2.11.1.0, the workaround is to try to save the
+ file again, and if that fails, delete the original file and
+ save in place.)
+
+ -
+ Cannot process alignments from HTTPS urls
+ via command line
+
+ -
+ References to http://www.jalview.org in
+ program and documentation
+
+ Launching Jalview
+
+ -
+ Jalview application fails when launched the
+ first time for a version that has different jars to the
+ previous launched version.
+
+ Developing Jalview
+
+ -
+ Fixed issue with cleaning up old coverage
+ data, causing cloverReport gradle task to fail with an
+ OutOfMemory error.
+
+ -
+ Migrated the Jalview Version Checker to
+ monitor the release channel
+
+ New Known defects
+
+ -
+ CDS shown in result of submitting proteins
+ in a CDS/Protein alignment to a web service is wrong when
+ proteins share a common transcript sequence (e.g.
+ genome of RNA viruses)
+
+ -
+ Co-located features exported and re-imported
+ are ordered differently when shown on alignment and in
+ tooltips. (Also affects v2.11.1.0)
+
+ -
+ Drag and drop of alignment file onto
+ alignment window when in a HiDPI scaled mode in Linux only
+ works for the top left quadrant of the alignment window
+
+ -
+ Stale build data in jalview standalone jar
+ builds (only affects 2.11.1.1 branch)
+
+ -
+ Sequence ID colourscheme not re-applied
+ when alignment view restored from project (since Jalview 2.11.0)
+
+ -
+ Duplicate CDS sequences are generated when
+ protein products for certain ENA records are repeatedly
+ shown via Calculate->Show Cross Refs
+
+
+ |
+
+
+ 2.11.1.0
22/04/2020 |
-
- Map 'virtual'
- codon features shown on protein (or vice versa) for display
- in alignments, on structure views, in feature reports and for export.
+ 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.
-
Feature attributes from VCF files can be
@@ -98,6 +671,9 @@ li:before {
Warn if Sort by Score or Density attempted
with no feature types visible
+ -
+ Improved support for filtering feature attributes with large integer values
+
Jalview Installer
-
@@ -139,6 +715,11 @@ li:before {
to stdout containing the consensus sequence for each
alignment in a Jalview session
+ -
+ ComputePeptideVariants.groovy to translate
+ genomic sequence_variant annotation from CDS as
+ missense_variant or synonymous_variant on protein products.
+
|
@@ -148,6 +729,11 @@ li:before {
'Show hidden markers' option is not ticked
+ Hidden sequence markers not shown in EPS and
+ PNG output when 'Automatically set ID width' is set in
+ jalview preferences or properties file
+
+
Feature Editor dialog can be opened when
'Show Sequence Features' option is not ticked
@@ -248,9 +834,6 @@ li:before {
Test Suite: Certain Functional tests fail on jalview's
bamboo server but run fine locally.
-
- Filtering features by genomic location (POS) is broken by rounding
-
|