X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=94426410bbe90b8ec4ec8fbbbaff9ef6b84f4214;hb=0b6d277e8fc98b1bc61d040932dba670340db344;hp=8ef92b9bdabba84b6684a23505450259a4003770;hpb=fa265315cce1d9329ab4db8d464e991847927474;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 8ef92b9..9442641 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -56,318 +56,687 @@ li:before {
| Issues Resolved |
+ 2.11.1.0
+ 22/04/2020 |
+
+
+ -
+ Map 'virtual'
+ codon features shown on protein (or vice versa) for display
+ in alignments, on structure views, in feature reports and for export.
+
+ -
+ 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
+
+ -
+ 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.
+
+ -
+ Filtering features by genomic location (POS) is broken by rounding
+
+
+ |
+
+
- 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 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
-
-
-
- - 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
- -
- 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
-
- 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 for
- unattended Test Suite execution
- -
- Memory test suite to detect leaks in common
- operations
- -
- IntervalStoreJ (NCList
- implementation that alows updates) used for Sequence Feature collections
+
+ - 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
+
-
- 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
- -
- '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
+ 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)
+
-
- Regular expression error for '(' in Select Columns by Annotation description
+ Blank extra columns drawn or printed
+ when columns are hidden
+
-
- Scroll doesn't stop on mouse up after
- dragging out of Scale or Annotation Panel
+ Regular expression error for '(' in Select
+ Columns by Annotation description
+
-
- Column selection incorrect after scrolling out of scale panel
+ Scroll doesn't stop on mouse up after dragging
+ out of Scale or Annotation Panel
+
-
- Left/right drag in annotation can scroll alignment down
+ Column selection incorrect after scrolling out of
+ scale panel
+
-
- Error if mouse moved before clicking Reveal in scale panel
+ Left/right drag in annotation can scroll
+ alignment down
+
-
- Column display is out by one after Page Down, Page Up in wrapped mode
+ Error if mouse moved before clicking Reveal in
+ scale panel
+
-
- Finder doesn't skip hidden regions
+ Column display is out by one after Page Down,
+ Page Up in wrapped mode
+
-
- Finder searches in minimised alignments
+ Finder doesn't skip hidden regions
+
-
- 'Apply Colour to All Groups' not always selected on
- opening an alignment
+ Finder searches in minimised alignments
+
-
- 'Colour by Annotation' not marked selected in Colour menu
+ 'Apply Colour to All Groups' not always selected
+ on opening an alignment
+
-
- Per-group Clustal colour scheme changes when
- different groups in the alignment are selected
+ 'Colour by Annotation' not marked selected in
+ Colour menu
+
-
- Internationalised colour scheme names not shown correctly in menu
+ Per-group Clustal colour scheme changes when
+ different groups in the alignment are selected
+
-
- Colour by Annotation can go black at min/max threshold limit
+ Internationalised colour scheme names not shown
+ correctly in menu
+
-
- Value input for graduated feature colour threshold gets 'unrounded'
+ Colour by Annotation can go black at min/max
+ threshold limit
+
-
- PCA image export doesn't respect background colour
+ Value input for graduated feature colour
+ threshold gets 'unrounded'
+
-
- PCA points don't dim when rotated about y axis
+ PCA image export doesn't respect background
+ colour
+
-
- PCA Print dialog continues after Cancel
+ PCA points don't dim when rotated about y axis
+
-
- Cancel in Tree Font dialog resets alignment, not Tree font
+ PCA Print dialog continues after Cancel
+
-
- Associate Tree with All Views not restored from project file
+ Cancel in Tree Font dialog resets alignment, not
+ Tree font
+
-
- Scrolling of split frame is sluggish if Overview shown in complementary view
+ Associate Tree with All Views not restored from
+ project file
+
-
- stop_gained variants not shown correctly on peptide sequence
+ Scrolling of split frame is sluggish if Overview
+ shown in complementary view
+
-
- Sequence Details report opens positioned to top of report
+ Codon consensus incorrectly scaled when shown
+ without normalisation
+
-
- Help page can be opened twice
-
- Editing
+ 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
+ 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
+
-
- Delete/Cut selection doesn't relocate
- sequence features correctly when start of sequence is
- removed (Known defect since 2.10)
- New Known Defects
+ Structure colours not updated when associated tree
+ repartitions the alignment view (Regression in 2.10.5)
+
+ Datamodel
-
- Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
+ 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)
+
-
- 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
-
-
+ 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
+
+
|
@@ -387,7 +756,7 @@ 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.
@@ -461,7 +830,7 @@ 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
@@ -542,6 +911,10 @@ li:before {
open URL in the browser can be dropped onto Jalview.
+ New Known Defects
+
+ - Cancel option doesn't reset Colour by Annotation
+
@@ -575,12 +948,12 @@ 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
-
-
+
+ Experimental features in 2.10.2 for
+ exchange of Jalview features and Chimera attributes made
+ generally available
+
+
@@ -701,6 +1074,10 @@ 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
+
|
@@ -1453,6 +1830,15 @@ 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