X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=a21d3f10af372cd4baa0fd81273e84ac405fde68;hb=6b546f7bffb732ae50a927f4c0ad796f4e137e74;hp=082146ef5a4b439580cb85bad1316d1cbbd15c88;hpb=e1932a723036ee3a5814c840ccaaa5f13029e821;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 082146e..a21d3f1 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -1,3 +1,4 @@
+
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)
+
+
+ |
+
2.11.1.0
- 27/03/2020 |
+ id="Jalview.2.11.1">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 |
-
- Option to show 'virtual' codon features on
- protein (or vice versa)
+ 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:
- -
- Option to export virtual features if
- shown
-
- -
- Option to transfer virtual features to
- Chimera
-
+ - Jalview's logging level can be configured
+ - Copy to Clipboard Buttion
-
- Feature attributes from VCF files can be exported and re-imported as GFF3 files
+ 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)
-
- Capture VCF "fixed column" values POS,
- ID, QUAL, FILTER as Feature Attributes
+ 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
-
- More robust VCF numeric data field validation while parsing
+ Stale build data in jalview standalone jar
+ builds (only affects 2.11.1.1 branch)
-
- Feature Settings dialog keeps same screen position if reopened
-
+ 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 (including
+ transfer to UCSF chimera), in feature reports and for
+ export.
+
+ -
+ Feature attributes from VCF files can be
+ exported and re-imported as GFF3 files
+
+ -
+ Capture VCF "fixed column" values
+ POS, ID, QUAL, FILTER as Feature Attributes
+
+ -
+ More robust VCF numeric data field
+ validation while parsing
+
+ -
+ Feature Settings dialog keeps same screen
+ position if reopened
+
+ -
+ Feature Settings dialog title includes name
+ of associated view
+
+ -
+ Font anti-aliasing in alignment views
+ enabled by default
+
-
- Font anti-aliasing in alignment views enabled by default
-
+ Very long feature descriptions truncated in
+ tooltips and menus
+
-
- Very long feature descriptions truncated in tooltips and menus
-
+ Warn if Sort by Score or Density attempted
+ with no feature types visible
+
-
- 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
@@ -118,6 +436,9 @@ li:before {
-
New point release version scheme - 2.11.1.0
+ -
+ 'Jalview Test' installers/apps for easier access to test-release channel builds
+
Build System
-
@@ -128,20 +449,36 @@ li:before {
report
-
- Groovy Scripts
-
- -
- exportconsensus.groovy prints a FASTA
- file to stdout containing the consensus sequence for each
- alignment in a Jalview session
-
-
+ Groovy Scripts
+
+ -
+ exportconsensus.groovy prints a FASTA file
+ 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.
+
|
-
+ Hidden sequence markers still visible when
+ '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
+
+ -
Undo 'Null' operation shown after sort by
buttons in Feature Settings dialog are clicked when no
features are visible
@@ -191,6 +528,11 @@ li:before {
Credits missing some authors in Jalview
help documentation for 2.11.0 release
+ -
+ Export of Pfam alignment as Stockholm
+ includes Pfam ID as sequence's accession rather than its
+ Uniprot Accession
+
Java 11 Compatibility issues
-
@@ -229,6 +571,10 @@ li:before {
Jalview Installation type always reports
'Source' in console output
+ -
+ Test Suite: Certain Functional tests fail on jalview's
+ bamboo server but run fine locally.
+
|