X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=b9a27ff9e02f0fb2d53a8e01f25f195229692221;hp=d3f242073b1f3c83d1b7789a196b7184d7f1a9c8;hb=639c433bf1162d8219b12813753c9ba38446b52e;hpb=2720003e4d3537f99f6c1643561cbdb3d0120d2d
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index d3f2420..b9a27ff 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.
+
+
+ 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)
+
+ -
+ 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)
+
+
+
+
+
+ -
+ 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)
+
+
+ |
+
+
+ 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+)
+
+ -
+ RESNUM sequence features (the
+ green ones) are not automatically displayed when associated
+ structures are displayed or for sequences retrieved from the
+ PDB.
+
+ 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.)
+
+ -
+ Dragging a PDB file onto an alignment with
+ sequence features displayed causes displayed features to be
+ hidden.
+
+ -
+ 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
@@ -98,30 +792,43 @@ li:before {
Warn if Sort by Score or Density attempted
with no feature types visible
- Jalview Installer
-
-
- Versions for install4j and getdown and installer template version reported
- in console (may be null when Jalview launched as executable jar or via conda)
+ Improved support for filtering feature
+ attributes with large integer values
+
+
+ Jalview Installer
+
+ -
+ Versions for install4j and getdown and
+ installer template version reported in console (may be null
+ when Jalview launched as executable jar or via conda)
+
+ -
+ Layout improvements for OSX .dmg Finder and
+ higher quality background images
-
- Layout improvements for OSX .dmg Finder and higher quality background images
+ New installer/application launcher
+ generated with install4j 8.0.4
-
- New installer/application launcher generated with install4j 8.0.4
+ Jalview File Associations shown for Unix
+ Platforms
+
+ -
+ Improved defaults for maximum memory
+ setting when running on large memory machines
- -
- Jalview File Associations shown for Unix Platforms
- -
- Improved defaults for maximum memory setting when running on large memory machines
Release processes
-
New point release version scheme - 2.11.1.0
-
- 'Jalview Test' installers/apps for easier access to test-release channel builds
-
+ 'Jalview Test' installers/apps for easier
+ access to test-release channel builds
+
Build System
-
@@ -131,14 +838,18 @@ li:before {
Test code included in Clover coverage
report
-
- Groovy Scripts
- 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.
+
|
@@ -148,6 +859,11 @@ 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
@@ -245,60 +961,69 @@ li:before {
'Source' in console output
- 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
+ Test Suite: Certain Functional tests fail
+ on jalview's bamboo server but run fine locally.
|
-
- 2.11.0
- 04/07/2019
- |
+ 2.11.0
04/07/2019 |
-
- Jalview Native Application and
- Installers built with install4j (licensed to the Jalview open
- source project) rather than InstallAnywhere
+ Jalview Native
+ Application and Installers built with install4j
+ (licensed to the Jalview open source project) rather than
+ InstallAnywhere
-
- Jalview Launcher System to auto-configure memory
- settings, receive over the air updates and launch specific
- versions via (Three
+ Jalview Launcher System to auto-configure
+ memory settings, receive over the air updates and launch
+ specific versions via (Three
Rings' GetDown)
-
- File type associations for
- formats supported by Jalview (including .jvp project files)
+ File type associations
+ for formats supported by Jalview (including .jvp project
+ files)
-
- Jalview launch files (.jvl) to pass command line
- arguments and switch between different getdown channels
+ Jalview launch files (.jvl) to pass command
+ line arguments and switch between different getdown channels
-
- Backup files created when saving Jalview project
- or alignment files
+ Backup files created when saving Jalview
+ project or alignment files
-
- Annotate nucleotide alignments from VCF data files
- - Version of HTSJDK shipped with Jalview updated to version 2.12.0
+ Annotate nucleotide alignments from VCF
+ data files
+
+ -
+ Version of HTSJDK shipped with Jalview
+ updated to version 2.12.0
+
-
Alternative genetic code tables for
- 'Translate as cDNA'
+ 'Translate as cDNA'
+
-
- Update of Ensembl Rest Client to API v10.0
- - Enhanced visualisation and analysis of Sequence Features
+ Update of Ensembl Rest Client to API v10.0
+
+ - Enhanced visualisation and analysis
+ of Sequence Features
- -
- IntervalStoreJ (NCList
- implementation that allows updates) used for Sequence Feature collections
- -
+
-
+ IntervalStoreJ (NCList
+ implementation that allows updates) used for Sequence
+ Feature collections
+
+ -
Sequence
features can be filtered and shaded according to any
associated attributes (e.g. variant attributes from VCF
@@ -310,173 +1035,200 @@ li:before {
stored and restored from Jalview Projects
-
- Use full Sequence Ontology (via BioJava) to
- recognise variant features
+ Use full Sequence Ontology (via
+ BioJava) to recognise variant features
-
- Show synonymous codon variants on peptide
- sequences (also coloured red by default)
+ Show synonymous codon variants
+ on peptide sequences (also coloured red by default)
-
- Popup window to show full report for a selected sequence feature's
- details
+ Popup window to show full report for a
+ selected sequence feature's details
-
- More efficient sequence feature render
- algorithm (Z-sort/transparency and filter aware)
+ More efficient
+ sequence feature render algorithm (Z-sort/transparency
+ and filter aware)
-
- Improved tooltips in Feature Settings
- dialog
+ Improved tooltips in Feature
+ Settings dialog
-
-
+
- Symmetric score matrices for faster
- tree and PCA calculations
+ Symmetric score matrices for faster tree
+ and PCA calculations
Principal Components Analysis Viewer
-
- Principal Components Analysis results
- and Viewer state saved in Jalview Project
+ Principal Components Analysis
+ results and Viewer state saved in Jalview Project
+
+ -
+ 'Change parameters' option removed from
+ viewer's drop-down menus
- - 'Change parameters' option removed from viewer's
- drop-down menus
-
- Can use shift + arrow keys to rotate PCA image
- incrementally
+ Can use shift + arrow keys to rotate
+ PCA image incrementally
-
PCA plot is depth cued
-
-
+
New 'Colour by Sequence ID' option
Speed and Efficiency
-
+
-
- More efficient creation of selections and
- multiple groups when working with large alignments
+ More efficient creation of
+ selections and multiple groups when working with large
+ alignments
-
- Speedier import of annotation rows when parsing
- Stockholm files
+ Speedier import of annotation rows when
+ parsing Stockholm files
- User Interface
-
+
-
- Finder panel remembers last position in each
- view
+ Finder panel remembers last position in
+ each view
-
- Alignment Overview now WYSIWIS (What you see is
- what is shown)
Only visible regions of alignment are shown by
- default (can be changed in user preferences)
+ Alignment Overview now WYSIWIS
+ (What you see is what is shown)
Only visible
+ regions of alignment are shown by default (can be
+ changed in user preferences)
-
- File Chooser stays open after responding Cancel
- to the Overwrite Dialog
+ File Chooser stays open after
+ responding Cancel to the Overwrite Dialog
-
- Better popup menu behaviour when all
- sequences are hidden
+ Better popup menu behaviour
+ when all sequences are hidden
-
Status bar shows bounds when dragging a
- selection region, and gap count when inserting or deleting gaps
+ selection region, and gap count when inserting or
+ deleting gaps
-
- Status bar updates over sequence and annotation
- labels
+ Status bar updates over sequence and
+ annotation labels
-
- Annotation tooltips and popup menus are shown
- when in wrapped mode
+ Annotation tooltips and popup menus are
+ shown when in wrapped mode
-
- Can select columns by dragging left/right in a graph or histogram
- annotation
+ Can select columns by dragging
+ left/right in a graph or histogram annotation
-
- Help button on Uniprot and PDB search panels
+ Help button on Uniprot and PDB
+ search panels
-
- Cursor changes over draggable box in Overview
- panel
+ Cursor changes over draggable box in
+ Overview panel
-
- Consistent ordering of links in sequence id
- popup menu
+ Consistent ordering of links in
+ sequence id popup menu
-
- Red line indicating tree-cut position not shown if no subgroups are created
+ Red line indicating tree-cut position
+ not shown if no subgroups are created
+
-
- Removed ability to configure length of search history by right-clicking search box
-
-
+ Removed ability to configure length of
+ search history by right-clicking search box
+
+
+
- Jalview Groovy Scripting Console updated to Groovy v2.5
- Java 11 Support (not yet on general release)
+
+ Jalview Groovy Scripting Console updated to
+ Groovy v2.5
+
+ Java 11 Support (not yet on general
+ release)
-
- OSX GUI integrations for App menu's 'About' entry and
- trapping CMD-Q
+ OSX GUI integrations for App menu's 'About'
+ entry and trapping CMD-Q
-
- Deprecations
+ Deprecations
- - DAS sequence retrieval and annotation
+
-
+ DAS sequence retrieval and annotation
capabilities removed from the Jalview Desktop
- - Castor library for XML marshalling and
- unmarshalling has been replaced by JAXB for Jalview projects
- and XML based data retrieval clients
- - Disable VAMSAS menu in preparation for removal
- - Jalview Desktop no longer distributed via Java Web Start
+ -
+ Castor library for XML marshalling
+ and unmarshalling has been replaced by JAXB for Jalview
+ projects and XML based data retrieval clients
+
+ -
+ Disable VAMSAS menu in preparation for
+ removal
+
+ -
+ Jalview Desktop no longer distributed via Java Web
+ Start
+
Documentation
- - Added remarks about transparent rendering effects
- not supported in EPS figure export
+
-
+ Added remarks about transparent rendering
+ effects not supported in EPS figure export
+
+ -
+ Typos in documentation for Preferences
+ dialog
- - Typos in documentation for Preferences dialog
Development and Release Processes
-
- Build system migrated from Ant to Gradle
+ Build system migrated
+ from Ant to Gradle
+
+ -
+ Enhanced checks for missing and duplicated
+ keys in Message bundles
- -
- Enhanced checks for missing and duplicated keys in Message bundles
-
- Eclipse project configuration managed with
+ Eclipse project configuration managed with
gradle-eclipse
-
- Atlassian
- Bamboo continuous integration for unattended Test Suite
- execution
+ Atlassian Bamboo
+ continuous integration for unattended Test Suite execution
-
- Memory test suite to detect leaks in common
+ Memory test suite to detect leaks in common
operations
-
- More unit test coverage, and minor
+ More unit test coverage, and minor
issues resolved
-
- Developer documentation migrated to
+ Developer documentation migrated to
markdown (with HTML rendering)
-
- HelpLinksChecker runs on Windows
+ HelpLinksChecker runs on Windows
-
- New URLs for publishing development
+ New URLs for publishing development
versions of Jalview
@@ -491,16 +1243,17 @@ li:before {
superposition in Jmol fail on Windows
- Blank error dialog is displayed when discovering
- structures for sequences with lots of PDB structures
+ Blank error dialog is displayed when
+ discovering structures for sequences with lots of PDB
+ structures
- Text misaligned in EPS or SVG image export with
- monospaced font
+ Text misaligned in EPS or SVG image export
+ with monospaced font
- Warning of 'Duplicate entry' when saving Jalview
- project involving multiple views
+ Warning of 'Duplicate entry' when saving
+ Jalview project involving multiple views
Overview for complementary view in a linked
@@ -508,79 +1261,81 @@ li:before {
Annotation dialog hides columns
- Selection highlighting in the complement of a
- CDS/Protein alignment stops working after making a selection in
- one view, then making another selection in the other view
+ Selection highlighting in the complement of
+ a CDS/Protein alignment stops working after making a
+ selection in one view, then making another selection in the
+ other view
Annotations tooltip changes beyond visible
columns
- Table Columns could be re-ordered in Feature
- Settings and Jalview Preferences panels
+ Table Columns could be re-ordered in
+ Feature Settings and Jalview Preferences panels
- Jalview hangs when closing windows, or redrawing the
- overview with large alignments
+ Jalview hangs when closing windows, or
+ redrawing the overview with large alignments
Tree and PCA calculation fails for selected
- region if columns were selected by dragging right-to-left and the
- mouse moved to the left of the first column
+ region if columns were selected by dragging right-to-left
+ and the mouse moved to the left of the first column
- Couldn't hide selected columns adjacent to a
- hidden column marker via scale popup menu
+ Couldn't hide selected columns adjacent to
+ a hidden column marker via scale popup menu
- Error message for trying to load in invalid URLs
- doesn't tell users the invalid URL
+ Error message for trying to load in invalid
+ URLs doesn't tell users the invalid URL
Tooltips displayed for features filtered by
score from view
- Sequence Variants retrieved from Ensembl during
- show cross references or Fetch Database References are shown in
- red in original view
+ Sequence Variants retrieved from Ensembl
+ during show cross references or Fetch Database References
+ are shown in red in original view
- stop_gained variants not shown correctly on
- peptide sequence (computed variant shown as p.Res.null)
+ stop_gained variants not shown
+ correctly on peptide sequence (computed variant shown as
+ p.Res.null)
'Graduated colour' option not offered for
manually created features (where feature score is Float.NaN)
- Blank extra columns drawn or printed
- when columns are hidden
+ Blank extra columns drawn or
+ printed when columns are hidden
Regular expression error for '(' in Select
Columns by Annotation description
- Scroll doesn't stop on mouse up after dragging
- out of Scale or Annotation Panel
+ Scroll doesn't stop on mouse up after
+ dragging out of Scale or Annotation Panel
- Column selection incorrect after scrolling out of
- scale panel
+ Column selection incorrect after scrolling
+ out of scale panel
Left/right drag in annotation can scroll
alignment down
- Error if mouse moved before clicking Reveal in
- scale panel
+ Error if mouse moved before clicking Reveal
+ in scale panel
- Column display is out by one after Page Down,
- Page Up in wrapped mode
+ Column display is out by one after Page
+ Down, Page Up in wrapped mode
Finder doesn't skip hidden regions
@@ -589,24 +1344,24 @@ li:before {
Finder searches in minimised alignments
- 'Apply Colour to All Groups' not always selected
- on opening an alignment
+ 'Apply Colour to All Groups' not always
+ selected on opening an alignment
- 'Colour by Annotation' not marked selected in
- Colour menu
+ 'Colour by Annotation' not marked selected
+ in Colour menu
- Per-group Clustal colour scheme changes when
- different groups in the alignment are selected
+ Per-group Clustal colour scheme changes
+ when different groups in the alignment are selected
- Internationalised colour scheme names not shown
- correctly in menu
+ Internationalised colour scheme names not
+ shown correctly in menu
- Colour by Annotation can go black at min/max
- threshold limit
+ Colour by Annotation can go black at
+ min/max threshold limit
Value input for graduated feature colour
@@ -617,56 +1372,59 @@ li:before {
colour
- PCA points don't dim when rotated about y axis
+ PCA points don't dim when rotated about y
+ axis
PCA Print dialog continues after Cancel
- Cancel in Tree Font dialog resets alignment, not
- Tree font
+ Cancel in Tree Font dialog resets
+ alignment, not Tree font
- Associate Tree with All Views not restored from
- project file
+ Associate Tree with All Views not restored
+ from project file
- Scrolling of split frame is sluggish if Overview
- shown in complementary view
+ Scrolling of split frame is sluggish if
+ Overview shown in complementary view
- Codon consensus incorrectly scaled when shown
- without normalisation
+ Codon consensus incorrectly scaled when
+ shown without normalisation
- Sequence Details report should open positioned at top
- of report
+ Sequence Details report should open
+ positioned at top of report
Help page can be opened twice
- Fuzzy text in web service status menu on OSX Mojave
+ Fuzzy text in web service status menu on
+ OSX Mojave
Editing
-
- Start and End should be updated when sequence
- data at beginning or end of alignment added/removed via 'Edit'
- sequence
+ Start and End should be updated when
+ sequence data at beginning or end of alignment added/removed
+ via 'Edit' sequence
-
- Delete/Cut selection doesn't
- relocate sequence features correctly when start of sequence is
- removed (Known defect since 2.10)
+ Delete/Cut selection
+ doesn't relocate sequence features correctly when start of
+ sequence is removed (Known defect since 2.10)
-
- Inserting gap sequence via the Edit Sequence
- dialog corrupts dataset sequence
+ Inserting gap sequence via the Edit
+ Sequence dialog corrupts dataset sequence
-
- Structure colours not updated when associated tree
- repartitions the alignment view (Regression in 2.10.5)
+ Structure colours not updated when
+ associated tree repartitions the alignment view (Regression
+ in 2.10.5)
Datamodel
@@ -674,72 +1432,75 @@ li:before {
Sequence.findIndex returns wrong value when
sequence's End is greater than its length
- Bugs fixed for Java 11 Support (not yet on
- general release)
+ Bugs fixed for Java 11 Support (not yet on general
+ release)
-
Menus work properly in split-screen
New Known Defects
- -
- Select columns containing feature by double clicking ignores bounds of an existing selected region
-
- -
- Codon consensus logo incorrectly scaled in gapped
- regions of protein alignment.
-
- -
- Input Data menu entry is greyed out when PCA View
- is restored from a Jalview 2.11 project
-
- -
- Alignment panel height can be too small after
- 'New View'
-
- -
- Display is incorrect after removing gapped
- columns within hidden columns
-
- -
- Rightmost selection is lost when mouse re-enters
- window after dragging left to select columns to left of visible
- region
-
- -
- Features coloured according to their description
- string and thresholded by score in earlier versions of Jalview are
- not shown as thresholded features in 2.11. To workaround please
- create a Score filter instead.
-
- -
- Cancel on Feature Settings dialog doesn't reset group visibility
- -
- F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
-
- -
- Closing tree windows with CMD/CTRL-W for
- alignments with multiple views can close views unexpectedly
-
-
- Java 11 Specific defects
-
- -
- Jalview Properties file is not sorted
- alphabetically when saved
-
+ -
+ Select columns containing feature by double
+ clicking ignores bounds of an existing selected region
+
+ -
+ Codon consensus logo incorrectly scaled in
+ gapped regions of protein alignment.
+
+ -
+ Input Data menu entry is greyed out when
+ PCA View is restored from a Jalview 2.11 project
+
+ -
+ Alignment panel height can be too small
+ after 'New View'
+
+ -
+ Display is incorrect after removing gapped
+ columns within hidden columns
+
+ -
+ Rightmost selection is lost when mouse
+ re-enters window after dragging left to select columns to
+ left of visible region
+
+ -
+ Features coloured according to their
+ description string and thresholded by score in earlier
+ versions of Jalview are not shown as thresholded features in
+ 2.11. To workaround please create a Score filter instead.
+
+ -
+ Cancel on Feature Settings dialog doesn't
+ reset group visibility
+
+ -
+ F2 doesn't enable/disable keyboard mode in
+ linked CDS/Protein view
+
+ -
+ Closing tree windows with CMD/CTRL-W for
+ alignments with multiple views can close views unexpectedly
+
+ Java 11 Specific defects
+
+ -
+ Jalview Properties file is not sorted
+ alphabetically when saved
+
|
- |
-
- |
-
-
-
+ |
+
+ |
+
+
+
-
Default memory for Jalview webstart and
InstallAnywhere increased to 1G.
@@ -771,9 +1532,9 @@ li:before {
|
-
-
-
+
+
+
-
Poorly scaled bar in quality annotation
row shown in Feredoxin Structure alignment view of example
@@ -843,8 +1604,7 @@ li:before {
latest version of OSX.
- |
+ |
|
@@ -905,7 +1665,10 @@ li:before {
New Known Defects
- - Cancel option doesn't reset Colour by Annotation
+ -
+ Cancel option doesn't reset Colour by
+ Annotation
+
|
@@ -941,13 +1704,12 @@ li:before {
of features (particularly when transparency is disabled)
- Experimental features in 2.10.2 for
- exchange of Jalview features and Chimera attributes made
- generally available
+ Experimental features in 2.10.2
+ for exchange of Jalview features and Chimera attributes
+ made generally available
-
-
+
-
@@ -990,8 +1752,8 @@ li:before {
columns in annotation row
-
- Preferences panel's ID Width control is not
- honored in batch mode
+ Preferences panel's ID Width control is
+ not honored in batch mode
-
Linked sequence highlighting doesn't work
@@ -1007,9 +1769,9 @@ li:before {
with negative residue numbers or missing residues fails
-
- Exception when shading sequence with negative
- Temperature Factor values from annotated PDB files (e.g.
- as generated by CONSURF)
+ Exception when shading sequence with
+ negative Temperature Factor values from annotated PDB
+ files (e.g. as generated by CONSURF)
-
Uniprot 'sequence variant' features
@@ -1020,20 +1782,22 @@ li:before {
structure and/or overview windows are also shown
-
- Selecting columns from highlighted regions
- very slow for alignments with large numbers of sequences
+ Selecting columns from highlighted
+ regions very slow for alignments with large numbers of
+ sequences
-
Copy Consensus fails for group consensus
with 'StringIndexOutOfBounds'
-
- VAqua(4) provided as fallback Look and Feel for OSX
- platforms running Java 10
+ VAqua(4) provided as fallback Look and
+ Feel for OSX platforms running Java 10
-
Adding a structure to existing structure
- view appears to do nothing because the view is hidden behind the alignment view
+ view appears to do nothing because the view is hidden
+ behind the alignment view
Applet
@@ -1045,9 +1809,10 @@ li:before {
Batch Mode
- -
- Fixed ID width preference is not respected
-
+ -
+ Fixed ID width preference is not
+ respected
+
New Known Defects
@@ -1067,35 +1832,64 @@ li:before {
2.10.4 is to fail back to N&W mapping)
-
- Export Annotations from File Menu with CSV
- option gives blank output
+ Export Annotations from File Menu with
+ CSV option gives blank output
-
- |
+
|
|
- - Updated Certum Codesigning Certificate
- (Valid till 30th November 2018)
|
-
- Desktop
- - Only one structure is loaded when several sequences and structures are selected for viewing/superposing
- - Alignment doesn't appear to scroll vertically via trackpad and scrollwheel
- - Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment
- - Helix annotation has 'notches' when scrolled into view if columns are hidden
- - Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns
- - User preference for disabling inclusion of sequence limits when exporting as flat file has no effect
- - Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes
+ - Updated Certum Codesigning Certificate (Valid till
+ 30th November 2018)
- |
+
+
+ Desktop
+
+
+ -
+ Only one structure is loaded when
+ several sequences and structures are selected for
+ viewing/superposing
+
+ -
+ Alignment doesn't appear to scroll
+ vertically via trackpad and scrollwheel
+
+ -
+ Jalview hangs if up/down arrows pressed
+ in cursor mode when cursor lies in hidden region at
+ start of alignment
+
+ -
+ Helix annotation has 'notches' when
+ scrolled into view if columns are hidden
+
+ -
+ Annotation column filter can be slow to
+ reset (ie after hitting cancel) for large numbers of
+ hidden columns
+
+ -
+ User preference for disabling inclusion
+ of sequence limits when exporting as flat file has no
+ effect
+
+ -
+ Reproducible cross-reference
+ relationships when retrieving sequences from
+ EnsemblGenomes
+
+
+ |
@@ -1351,14 +2145,16 @@ li:before {
New features in Jalview Desktop
-
- Uniprot Sequence Fetcher now uses web API at uniprot.org
+ Uniprot Sequence Fetcher now uses web API
+ at uniprot.org
- - HTTPS used for all connections to ebi.ac.uk
+
-
+ HTTPS used for all connections to
+ ebi.ac.uk
|
-
- |
+ |
|
@@ -1827,9 +2623,9 @@ li:before {
recovered correctly from Jalview project file
- Feature colours in overview when first opened
- (automatically via preferences) are different to the main
- alignment panel
+ Feature colours in overview when first
+ opened (automatically via preferences) are different to
+ the main alignment panel
Data import/export
@@ -2705,7 +3501,7 @@ li:before {
column.
- Null Pointer Exception raised when
+ Null Pointer Exception raised when
pressing Add on an orphaned cut'n'paste window.
|