X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=29f2ee186772e9c88d0d5448bacaae8545f82c7b;hb=0e8fccceb3460c9a6bd611472549c3c985e5143e;hp=2f09fef4f4ce21a5264b9d76355c468ba61b2627;hpb=def03896e8452bac544cabe09b154c18c3940a6b;p=jalview.git diff --git a/help/help/html/releases.html b/help/help/html/releases.html index 2f09fef..29f2ee1 100755 --- a/help/help/html/releases.html +++ b/help/help/html/releases.html @@ -1,3 +1,4 @@ + Distribution Tarball includes git commit + and branch details + + + + +

+ Residue selection using keyboard input + stops working after first "Create sequence feature" +
+ 3D Structure chooser fails to select + structures from 3D-beacons and pops up a 'null' dialog +
+ Cannot build Jalview 2.11.2.0 via gradle + from its source tarball +

New Known Issues +

+ Colour by->all views doesn't allow + colouring same structure from different views (since + 2.11.2.0) +
+ Sequence ID tooltip not showing during + long running retrieval/crossref operations (affects at least + 2.11.1 onwards) +
+ Pfam and Rfam alignment retrieval as + gzipped stockholm doesn't work on JalviewJS build of 2.11.2 +
+ Java 11 Only: Jalview 2.11.2.0 OSX install + not working due to VAqua requiring + sun.awt.image.MultiResolutionImage +
+ Sequence Details can take a long time to be + displayed for heavily annotated sequences (all versions) +

+ + + + 2.11.2 .0
+ 10/03/2022 + +

+ 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 forÂ 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 (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. +

+ + + + 2.11.0
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 +
- + 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 + 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 +

- Release History -

- 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
+ Export Annotations from File Menu with + CSV option gives blank output +

Release	New Features	Issues Resolved
- 2.11.0 - 02/07/2019 -	+ + + 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 - Jalview Native Application and - Installers built with install4j (licensed to the Jalview open - source project) rather than InstallAnywhere + DAS sequence retrieval and annotation + capabilities removed from the Jalview Desktop - Jalview Launcher System to auto-configure memory - settings, receive over the air updates and launch specific - versions via (Three - Rings' GetDown) + Castor library for XML marshalling + and unmarshalling has been replaced by JAXB for Jalview + projects and XML based data retrieval clients - - 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' + Disable VAMSAS menu in preparation for + removal + - 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 + Jalview Desktop no longer distributed via Java Web + Start + + Documentation + - - 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 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 + Added remarks about transparent rendering + effects not supported in EPS figure export + + + Typos in documentation for Preferences + dialog + + Development and Release Processes - DAS sequence retrieval and annotation - capabilities removed from the Jalview Desktop + Build system migrated + from Ant to Gradle - 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 + 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 + Atlassian Bamboo + continuous integration for unattended Test Suite execution Memory test suite to detect leaks in common @@ -270,7 +1274,7 @@ li:before { More unit test coverage, and minor - issues resolved. + issues resolved Developer documentation migrated to @@ -283,265 +1287,276 @@ li:before { New URLs for publishing development versions of Jalview + +	+ + + Timeouts when retrieving data from Ensembl + + + '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 + + + 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 + + + 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 + + + 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 + + + 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 + + + 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 + + + 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 + + + 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 + + + Column display is out by one after Page + Down, Page Up in wrapped mode + + + Finder doesn't skip hidden regions + + + Finder searches in minimised alignments + + + 'Apply Colour to All Groups' not always + selected on opening an alignment + + + 'Colour by Annotation' not marked selected + in Colour menu + + + Per-group Clustal colour scheme changes + when different groups in the alignment are selected + + + Internationalised colour scheme names not + shown correctly in menu + + + Colour by Annotation can go black at + min/max threshold limit + + + Value input for graduated feature colour + threshold gets 'unrounded' + + + PCA image export doesn't respect background + colour + + + 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 + + + Associate Tree with All Views not restored + from project file + + + Scrolling of split frame is sluggish if + Overview shown in complementary view + + + Codon consensus incorrectly scaled when + shown without normalisation + + + 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 + + + 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 + + + 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) + + + 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 +	- - - Timeouts when retrieving data from Ensembl - - - '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 - - - 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 - - - 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 - - - Jalview hangs when closing windows or the - overview updates 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 - - - 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 - - - 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 if feature score is Float.NaN) - - - 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 - - - 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 - - - Column display is out by one after Page Down, - Page Up in wrapped mode - - - Finder doesn't skip hidden regions - - - Finder searches in minimised alignments - - - 'Apply Colour to All Groups' not always selected - on opening an alignment - - - 'Colour by Annotation' not marked selected in - Colour menu - - - Per-group Clustal colour scheme changes when - different groups in the alignment are selected - - - Internationalised colour scheme names not shown - correctly in menu - - - Colour by Annotation can go black at min/max - threshold limit - - - Value input for graduated feature colour - threshold gets 'unrounded' - - - PCA image export doesn't respect background - colour - - - 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 - - - Associate Tree with All Views not restored from - project file - - - Scrolling of split frame is sluggish if Overview - shown in complementary view - - - Codon consensus incorrectly scaled when shown - without normalisation - - - 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 - - - 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 - - - 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) - - - 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 - - Java 11 Specific defects - - - Jalview Properties file is not sorted alphabetically when saved - - - - -
- - 2.10.5 10/09/2018 - -	- - +	+ + 2.10.5 10/09/2018 + +	+ + Default memory for Jalview webstart and InstallAnywhere increased to 1G. @@ -550,7 +1565,7 @@ 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. @@ -573,9 +1588,9 @@ li:before {	- - +	+ + Poorly scaled bar in quality annotation row shown in Feredoxin Structure alignment view of example @@ -624,7 +1639,7 @@ 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 @@ -645,8 +1660,7 @@ li:before { latest version of OSX. - -
@@ -707,7 +1721,10 @@ li:before { New Known Defects - Cancel option doesn't reset Colour by Annotation + + Cancel option doesn't reset Colour by + Annotation +
@@ -792,8 +1808,8 @@ 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 @@ -809,9 +1825,9 @@ 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 @@ -822,20 +1838,22 @@ 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 @@ -847,9 +1865,10 @@ li:before { Batch Mode - - Fixed ID width preference is not respected - + + Fixed ID width preference is not + respected + New Known Defects @@ -868,36 +1887,65 @@ 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 - - - -
- 2.10.3b1 24/1/2018 + 2.10.3b1 + 24/1/2018	- 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 + + +
@@ -1153,14 +2201,16 @@ 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	-
@@ -1629,9 +2679,9 @@ 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 @@ -2507,7 +3557,7 @@ li:before { column. - Null Pointer Exception raised when + Null Pointer Exception raised when pressing Add on an orphaned cut'n'paste window.