X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=a6293e672bd97b726cff7dbe0eb3645680b0512e;hp=8cebf4f2d66e4e64fdafc96320b32ae5dc15fd88;hb=e69f7ec847b9dbbf88350521ccd3fd773c6aeaa8;hpb=8b0cf50a6cfbe40d485ec7d2fe63f3dd1f7225d6
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 8cebf4f..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 (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
+
+ -
+ Very long feature descriptions truncated in
+ tooltips and menus
+
+ -
+ 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
+
+ -
+ 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
+
+ -
+ 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
+ Release processes
+
+ -
+ New point release version scheme - 2.11.1.0
+
+ -
+ 'Jalview Test' installers/apps for easier access to test-release channel builds
+
+ Build System
+
+ -
+ Clover updated to 4.4.1
+
+ -
+ Test code included in Clover coverage
+ report
+
+
+ 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
+
+ -
+ ID margins for CDS and Protein views not
+ equal when split frame is first opened
+
+ -
+ Sequence position numbers in status bar not
+ correct after editing a sequence's start position
+
+ -
+ Alignment is misaligned in wrapped mode
+ with annotation and exceptions thrown when only a few
+ columns shown in wrapped mode
+
+ -
+ Sequence IDs missing in headless export of
+ wrapped alignment figure with annotations
+
+ -
+ Sorting Structure Chooser table by Sequence
+ ID fails with ClassCastException
+
+ -
+ Chimera session not restored from Jalview
+ Project
+
+ -
+ Double-click on 'Show feature' checkbox in
+ feature settings dialog also selects columns
+
+ -
+ SpinnerNumberModel causes
+ IllegalArgumentException in some circumstances
+
+ -
+ Multiple feature settings dialogs can be
+ opened for a view
+
+ -
+ Feature Settings dialog is orphaned if
+ alignment window is closed
+
+ -
+ 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
+
+ -
+ OSX - Can't view some search results in
+ PDB/Uniprot search panel
+
+ Installer
+
+ -
+ Jalview should not create file associations
+ for 3D structure files (.pdb, .mmcif. .cif)
+
+ Repository and Source Release
+
+ -
+ removed obsolete .cvsignore files from
+ repository
+
+ -
+ Clover report generation running out of
+ memory
+
+ New Known Issues
+
+ -
+ OSX - Current working directory not
+ preserved when Jalview.app launched with parameters from
+ command line
+
+ -
+ Sequence IDs aligned to wrong margin and
+ clipped in headless figure export when Right Align option
+ enabled
+
+ -
+ Jalview Installation type always reports
+ 'Source' in console output
+
+ -
+ Test Suite: Certain Functional tests fail on jalview's
+ bamboo server but run fine locally.
+
+
+ |
+
+
- 2.11
- 20/06/2019
+ 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 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)
+
+ -
+ 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
+
+
+ -
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'
-
Update of Ensembl Rest Client to API v10.0
- - Enhanced visualisation and analysis of Sequence Features
-
- -
- Sequence features can be filtered and
- shaded according to any associated attributes (e.g. variant
- attributes from VCF file, or key-value pairs imported from
- column 9 of GFF file)
-
- -
- Show synonymous codon variants on peptide
- sequences
-
- -
- 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)
-
- -
- Improved tooltips in Feature Settings
- dialog
-
-
-
- -
- Backup files created when saving Jalview project
- or alignment files
+
- Enhanced visualisation and analysis of Sequence Features
+
+ -
+ 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
+ file, or key-value pairs imported from column 9 of GFF
+ file)
+
+ -
+ Feature Attributes and shading schemes
+ stored and restored from Jalview Projects
+
+ -
+ Use full Sequence Ontology (via BioJava) to
+ recognise variant features
+
+ -
+ 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
+
+ -
+ More efficient sequence feature render
+ algorithm (Z-sort/transparency and filter aware)
+
+ -
+ Improved tooltips in Feature Settings
+ dialog
+
+
+
+ -
+ Symmetric score matrices for faster
+ tree and PCA calculations
- Principal Components Analysis Viewer
- -
- Principal Components Analysis results
- and Viewer state saved in Jalview Project
-
- - 'Change parameters' option removed from viewer's
- drop-down menus
- -
- 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
-
- -
- Speedier import of annotation rows when parsing
- Stockholm files
-
-
- - User Interface
-
- -
- Finder panel remembers last position in each
- view
-
- -
- Alignment Overview now WYSIWIS (What you see is
- what is shown)
Only visible region of alignment is shown by
- default (can be changed in user preferences)
-
- -
- File Chooser stays open after responding Cancel
- to the Overwrite Dialog
-
- -
- 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
-
- -
- Status bar updates over sequence and annotation
- labels
-
- -
- Annotation tooltips and popup menus are shown
- when in wrapped mode
-
- -
- Can select columns by dragging left/right in
- annotations
-
- -
- Help button on Uniprot and PDB search panels
-
- -
- Cursor changes over draggable box in Overview
- panel
-
- -
- Consistent ordering of links in sequence id
- popup menu
-
- -
- Sequence Details report opens positioned to top
- of report
-
-
- - Java 11 Support
-
- -
- Java 11 Native Desktop installer, standalone JAR
- and getdown release channels
-
- -
- OSX GUI integrations for App menu's 'About' entry and
- trapping CMD-Q
-
-
-
+
+ Principal Components Analysis results
+ and Viewer state saved in Jalview Project
+
+ 'Change parameters' option removed from viewer's
+ drop-down menus
+
+ 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
+
+ -
+ Speedier import of annotation rows when parsing
+ Stockholm files
+
+
+ User Interface
+
+ -
+ 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)
+
+ -
+ File Chooser stays open after responding Cancel
+ to the Overwrite Dialog
+
+ -
+ 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
+
+ -
+ Status bar updates over sequence and annotation
+ labels
+
+ -
+ Annotation tooltips and popup menus are shown
+ when in wrapped mode
+
+ -
+ Can select columns by dragging left/right in a graph or histogram
+ annotation
+
+ -
+ Help button on Uniprot and PDB search panels
+
+ -
+ Cursor changes over draggable box in Overview
+ panel
+
+ -
+ Consistent ordering of links in sequence id
+ popup menu
+
+ -
+ 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
+
+
+
+ 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
+
+
+
Deprecations
- -
- DAS sequence retrieval and annotation
+
- DAS sequence retrieval and annotation
capabilities removed from the Jalview Desktop
- - Jalview Desktop no longer distributed via Java Web Start
-
- Development and Release Processes
-
- -
- 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
- Rings' GetDown)
-
- -
- Build system migrated from Ant to Gradle
-
- -
- Eclipse project configuration managed with
- gradle-eclipse
-
- -
- Atlassian Bamboo continuous integration server for
- unattended Test Suite execution
- -
- Memory test suite to detect leaks in common
- operations
- -
- IntervalStoreJ (new updatable NCList
- implementation) used for Sequence Feature collections
- -
- Castor library for XML marshalling and
+
- 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
+
+ - Typos in documentation for Preferences dialog
+ Development and Release Processes
+
+ -
+ Build system migrated from Ant to Gradle
+
+ -
+ Enhanced checks for missing and duplicated keys in Message bundles
+ -
+ Eclipse project configuration managed with
+ gradle-eclipse
+
+ -
+ Atlassian
+ Bamboo continuous integration for unattended Test Suite
+ execution
+
+ -
+ Memory test suite to detect leaks in common
+ operations
+
+ -
+ More unit test coverage, and minor
+ issues resolved
+
+ -
+ Developer documentation migrated to
+ markdown (with HTML rendering)
+
+ -
+ HelpLinksChecker runs on Windows
+
+ -
+ New URLs for publishing development
+ versions of Jalview
+
|
-
+ |
-
- Timeouts when retrieving data from Ensembl
+ Timeouts when retrieving data from Ensembl
+
+ -
+ 'View [Structure] Mappings' and structure
+ superposition in Jmol fail on Windows
+
-
- 'View [Structure] Mappings' and structure superposition in Jmol fail on Windows
+ 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
CDS/Protein alignment is not updated when Hide Columns by
- Annotation dialog hides columns
+ 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
+ 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 the overview updates 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
- -
- Couldn't hide selected columns adjacent
- to a hidden column marker via scale popup menu
+ 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
+
+ -
+ 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
+
-
- Nonpositional features lose feature group
- on export as Jalview features file
+ Sequence Variants retrieved from Ensembl during
+ show cross references or Fetch Database References are shown in
+ red in original view
+
-
- Blank extra columns drawn or
- printed when columns are hidden
+ stop_gained variants not shown correctly on
+ peptide sequence (computed variant shown as p.Res.null)
+
-
- Regular expression error for '(' in Select Columns by Annotation description
+ 'Graduated colour' option not offered for
+ manually created features (where feature score is Float.NaN)
+
-
- Scroll doesn't stop on mouse up after
- dragging out of Scale or Annotation Panel
+ Blank extra columns drawn or printed
+ when columns are hidden
+
-
- Column selection incorrect after scrolling out of scale panel
+ Regular expression error for '(' in Select
+ Columns by Annotation description
+
-
- Left/right drag in annotation can scroll alignment down
+ Scroll doesn't stop on mouse up after dragging
+ out of Scale or Annotation Panel
+
-
- Error if mouse moved before clicking Reveal in scale panel
+ Column selection incorrect after scrolling out of
+ scale panel
+
-
- Column display is out by one after Page Down, Page Up in wrapped mode
+ Left/right drag in annotation can scroll
+ alignment down
+
-
- Finder doesn't skip hidden regions
+ Error if mouse moved before clicking Reveal in
+ scale panel
+
-
- Finder searches in minimised alignments
+ Column display is out by one after Page Down,
+ Page Up in wrapped mode
+
-
- 'Apply Colour to All Groups' not always selected on
- opening an alignment
+ Finder doesn't skip hidden regions
+
-
- 'Colour by Annotation' not marked selected in Colour menu
+ Finder searches in minimised alignments
+
-
- Per-group Clustal colour scheme changes when
- different groups in the alignment are selected
+ 'Apply Colour to All Groups' not always selected
+ on opening an alignment
+
-
- Internationalised colour scheme names not shown correctly in menu
+ 'Colour by Annotation' not marked selected in
+ Colour menu
+
-
- Colour by Annotation can go black at min/max threshold limit
+ Per-group Clustal colour scheme changes when
+ different groups in the alignment are selected
+
-
- Value input for graduated feature colour threshold gets 'unrounded'
+ Internationalised colour scheme names not shown
+ correctly in menu
+
-
- PCA image export doesn't respect background colour
+ Colour by Annotation can go black at min/max
+ threshold limit
+
-
- PCA points don't dim when rotated about y axis
+ Value input for graduated feature colour
+ threshold gets 'unrounded'
+
-
- PCA Print dialog continues after Cancel
+ PCA image export doesn't respect background
+ colour
+
-
- Cancel in Tree Font dialog resets alignment, not Tree font
+ PCA points don't dim when rotated about y axis
+
-
- Associate Tree with All Views not restored from project file
+ PCA Print dialog continues after Cancel
+
-
- Scrolling of split frame is sluggish if Overview shown in complementary view
+ Cancel in Tree Font dialog resets alignment, not
+ Tree font
+
-
- stop_gained variants not shown correctly on peptide sequence
+ Associate Tree with All Views not restored from
+ project file
+
-
- Help page can be opened twice
-
- Editing
-
+ Scrolling of split frame is sluggish if Overview
+ shown in complementary view
+
-
- Start and End should be updated when
- sequence data at beginning or end of alignment added/removed
- via 'Edit' sequence
+ Codon consensus incorrectly scaled when shown
+ without normalisation
+
-
- Delete/Cut selection doesn't relocate
- sequence features correctly when start of sequence is
- removed (Known defect since 2.10)
-
- New Known Defects
+ 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
+
+ Editing
-
- Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
+ 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)
+
+ -
+ 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)
+
+ Datamodel
+
-
- Alignment panel height can be too small after 'New View'
+ 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)
+
-
- Display is incorrect after removing gapped columns within hidden columns
+ 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
+
|
@@ -367,7 +1331,7 @@ li:before {
Hidden sequence markers and representative
sequence bolding included when exporting alignment as EPS,
SVG, PNG or HTML. Display is configured via the
- Format menu, or for command-line use via a jalview
+ Format menu, or for command-line use via a Jalview
properties file.
@@ -441,7 +1405,7 @@ li:before {
.jvp should be used as default extension
- (not .jar) when saving a jalview project file.
+ (not .jar) when saving a Jalview project file.
Mac Users: closing a window correctly
@@ -522,6 +1486,10 @@ li:before {
open URL in the browser can be dropped onto Jalview.
+ New Known Defects
+
+ - Cancel option doesn't reset Colour by Annotation
+
@@ -555,6 +1523,11 @@ li:before {
Improved performance when rendering lots
of features (particularly when transparency is disabled)
+
+ Experimental features in 2.10.2 for
+ exchange of Jalview features and Chimera attributes made
+ generally available
+
@@ -676,6 +1649,10 @@ li:before {
Sequences' enabled) or Ensembl isoforms (Workaround in
2.10.4 is to fail back to N&W mapping)
+
+ Export Annotations from File Menu with CSV
+ option gives blank output
+
@@ -1428,6 +2405,15 @@ li:before {
User defined gap colour not shown in
overview when features overlaid on alignment
+
+ Feature settings for different views not
+ recovered correctly from Jalview project file
+
+
+ Feature colours in overview when first opened
+ (automatically via preferences) are different to the main
+ alignment panel
+
Data import/export