X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=b264a3f12fe0139e876b0fa577ef22a71dd25bd4;hb=303cf24674d8cb8200c6d2880d6ff72d25ba32da;hp=e7b2f471bc294fe342c12aa1dbac9127ab3d87df;hpb=4a383fcb88588a8425c7bb2ebfb70d4de24ec80a;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index e7b2f47..b264a3f 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -56,218 +56,760 @@ li:before {
| Issues Resolved |
-
- 2.11
- tbc/06/2019
- |
+ 2.11.1.1
+ 13/07/2020 |
+
-
- Annotate nucleotide alignments from VCF data files
+ Shift+arrow keys navigate to next gap or
+ residue in cursor mode
+
-
- Optional automatic backups when saving
- Jalview project or alignment files
+ Support import of VCF 4.3 by updating
+ HTSJDK from 2.12 to 2.23
+
-
- Principal Components Analysis and
- Viewer state is saved in Jalview Project
The 'Change
- parameters' option has also been removed from the PCA viewer
+ IntervalStore library updated to v.1.1:
+ optimisations and improvements suggested by Bob Hanson and
+ improved compatibility with JalviewJS
+
-
- New 'Colour by Sequence ID' (subgroup) option
+ Retrieve GZipped stockholm formatted
+ alignments from Pfam and Rfam
+
-
- Alternative genetic code tables supported for
- 'Translate as cDNA'
+ Recognise GZipped content for URLs and File
+ import (no longer based on .gz extension)
+
+ -
+ Updated Spanish Translation for 2.11.1
+
+ Launching Jalview
+
+ -
+ Configure Jalview Desktop's look and feel
+ through a system property
+
+
+ |
+
+
-
- Finder panel remembers last position in each view
+ Escape does not clear highlights on the
+ alignment (Since Jalview 2.10.3)
+
-
- More efficient creation of selections and
- multiple groups when working with large alignments
+ Alt+Left or Right arrow in cursor mode
+ doesn't slide selected sequences
+
-
- Speedier import of annotation rows when
- parsing stockholm files
+ Peptide-to-CDS tracking broken when
+ multiple EMBL gene products shown for a single contig
+
-
- Update of Ensembl Rest Client to API v10.0
+ 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 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)
+ Slider with negative range values not
+ rendered correctly in VAqua4 (Since 2.10.4)
+
+
+ |
+
+
+ 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.
+
-
- Show synonymous codon variants on peptide sequences
+ Feature attributes from VCF files can be
+ exported and re-imported as GFF3 files
+
-
- Popup report of a selected sequence feature's details
+ Capture VCF "fixed column" values
+ POS, ID, QUAL, FILTER as Feature Attributes
+
-
- More efficient sequence feature render
- algorithm (Z-sort/transparency and filter aware)
+ More robust VCF numeric data field
+ validation while parsing
+
-
- Alignment Overview now by default shows
- only visible region of alignment (this can be changed in
- user preferences)
+ Feature Settings dialog keeps same screen
+ position if reopened
+
-
- File Chooser stays open after Cancel overwrite
+ Feature Settings dialog title includes name
+ of associated view
+
-
- Better popup menu behaviour when
- all sequences are hidden
+ Font anti-aliasing in alignment views
+ enabled by default
+
-
- Status bar shows bounds when dragging a selection
- region, and gap count when inserting or deleting gaps
+ Very long feature descriptions truncated in
+ tooltips and menus
+
-
- Status bar updates over sequence and annotation labels
+ Warn if Sort by Score or Density attempted
+ with no feature types visible
+
-
- Show annotation tooltips and popup menus in wrapped mode
+ Improved support for filtering feature attributes with large integer values
+
+ Jalview Installer
+
-
- Can select columns by dragging left/right in annotations
+ 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 tooltips in Feature Settings dialog
+ Layout improvements for OSX .dmg Finder and higher quality background images
+
-
- Help button on Uniprot and PDB search panels
- -
- Cursor changes over draggable box in Overview panel
+ 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
+
-
- Overview panel default changed to not show hidden regions
+ New point release version scheme - 2.11.1.0
+
-
- Consistent ordering of links in sequence id popup menu
+ 'Jalview Test' installers/apps for easier access to test-release channel builds
+
+ Build System
+
-
- Sequence Details report opens positioned to top of report
+ Clover updated to 4.4.1
+
-
- Scale panel popup menu allows Hide selected columns adjacent
- to a hidden column marker
+ Test code included in Clover coverage
+ report
+
+
+ Groovy Scripts
+
-
- Can use shift + arrow keys to rotate PCA image incrementally
+ exportconsensus.groovy prints a FASTA file
+ to stdout containing the consensus sequence for each
+ alignment in a Jalview session
+
-
- PCA depth cueing with graduated colours
+ ComputePeptideVariants.groovy to translate
+ genomic sequence_variant annotation from CDS as
+ missense_variant or synonymous_variant on protein products.
+
- Deprecations
+ |
+
-
- DAS sequence retrieval and annotation
- capabilities removed from the Jalview Desktop
+ 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.
- Release Processes
+ |
+
+
+
+ 2.11.0
+ 04/07/2019
+ |
+
-
- Atlassian Bamboo continuous integration server for
- unattended Test Suite execution
+ 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)
+
-
- Memory test suite to detect leaks in common
- operations
+ 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
+
+
+
-
- IntervalStoreJ (new updatable NCList
- implementation) used for Sequence Feature collections
+ 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
+
+
+
-
- Castor library for XML marshalling and
+ 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
+ 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
+ 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
+
-
- Text misaligned in EPS or SVG image export with monospaced font
+ 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
+ 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
+ region if columns were selected by dragging right-to-left and the
+ mouse moved to the left of the first column
+
-
- Error message for trying to load in invalid
- URLs doesn't tell users the invalid URL
+ Couldn't hide selected columns adjacent to a
+ hidden column marker via scale popup menu
+
-
- Nonpositional features lose feature group
- on export as Jalview features file
+ Error message for trying to load in invalid URLs
+ doesn't tell users the invalid URL
+
-
- Blank extra columns drawn or
- printed when columns are hidden
+ Tooltips displayed for features filtered by
+ score from view
+
-
- Regular expression error for '(' in Select Columns by Annotation description
+ Sequence Variants retrieved from Ensembl during
+ show cross references or Fetch Database References are shown in
+ red in original view
+
-
- Scroll doesn't stop on mouse up after
- dragging out of Scale or Annotation Panel
+ stop_gained variants not shown correctly on
+ peptide sequence (computed variant shown as p.Res.null)
+
-
- Column selection incorrect after scrolling out of scale panel
+ 'Graduated colour' option not offered for
+ manually created features (where feature score is Float.NaN)
+
-
- Left/right drag in annotation can scroll alignment down
+ Blank extra columns drawn or printed
+ when columns are hidden
+
-
- Error if mouse moved before clicking Reveal in scale panel
+ 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 display is out by one after Page Down, Page Up in wrapped mode
+ Column selection incorrect after scrolling out of
+ scale panel
+
-
- Finder doesn't skip hidden regions
+ Left/right drag in annotation can scroll
+ alignment down
+
-
- Finder searches in minimised alignments
+ Error if mouse moved before clicking Reveal in
+ scale panel
+
-
- 'Apply Colour to All Groups' not always selected on
- opening an alignment
+ Column display is out by one after Page Down,
+ Page Up in wrapped mode
+
-
- 'Colour by Annotation' not marked selected in Colour menu
+ Finder doesn't skip hidden regions
+
-
- Per-group Clustal colour scheme changes when
- different groups in the alignment are selected
+ Finder searches in minimised alignments
+
-
- Internationalised colour scheme names not shown correctly in menu
+ 'Apply Colour to All Groups' not always selected
+ on opening an alignment
+
-
- Colour by Annotation can go black at min/max threshold limit
+ 'Colour by Annotation' not marked selected in
+ Colour menu
+
-
- Value input for graduated feature colour threshold gets 'unrounded'
+ Per-group Clustal colour scheme changes when
+ different groups in the alignment are selected
+
-
- PCA image export doesn't respect background colour
+ Internationalised colour scheme names not shown
+ correctly in menu
+
-
- PCA points don't dim when rotated about y axis
+ Colour by Annotation can go black at min/max
+ threshold limit
+
-
- PCA Print dialog continues after Cancel
+ Value input for graduated feature colour
+ threshold gets 'unrounded'
+
-
- Cancel in Tree Font dialog resets alignment, not Tree font
+ PCA image export doesn't respect background
+ colour
+
-
- Associate Tree with All Views not restored from project file
+ PCA points don't dim when rotated about y axis
+
-
- Scrolling of split frame is sluggish if Overview shown in complementary view
+ PCA Print dialog continues after Cancel
+
-
- stop_gained variants not shown correctly on peptide sequence
+ Cancel in Tree Font dialog resets alignment, not
+ Tree font
+
-
- Help page can be opened twice
-
- Editing
-
+ Associate Tree with All Views not restored from
+ project file
+
-
- Start and End should be updated when
- sequence data at beginning or end of alignment added/removed
- via 'Edit' sequence
+ Scrolling of split frame is sluggish if Overview
+ shown in complementary view
+
-
- Delete/Cut selection doesn't relocate
- sequence features correctly when start of sequence is
- removed (Known defect since 2.10)
-
- New Known Defects
+ 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
-
- 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
+
-
- Alignment panel height can be too small after 'New View'
+ Delete/Cut selection doesn't
+ relocate sequence features correctly when start of sequence is
+ removed (Known defect since 2.10)
+
-
- Display is incorrect after removing gapped columns within hidden columns
+ 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
+
|
@@ -288,7 +830,7 @@ 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.
@@ -362,7 +904,7 @@ 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
@@ -443,6 +985,10 @@ li:before {
open URL in the browser can be dropped onto Jalview.
+ New Known Defects
+
+ - Cancel option doesn't reset Colour by Annotation
+
@@ -476,6 +1022,11 @@ 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
+
@@ -597,6 +1148,10 @@ 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
+
@@ -1349,6 +1904,15 @@ 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