X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=cffa10f692c88b13d3b8400aae8ab9556f447153;hb=07addcb8a9c7904b60e19f637c5258849987c2a6;hp=3e701f93b46d038c07e907ba2a85de5980877825;hpb=11ca0240a5792724d5e890de9fbd63cb2f11093a;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 3e701f9..cffa10f 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -67,11 +67,546 @@ li:before {
+
+
+
+ 2.11
+ 14/05/2019 (final due date !)
+ |
+
+
+ -
+ Optional automatic backups when saving
+ Jalview project or alignment files
+ -
+ Principal Components Analysis and
+ Viewer state is saved in Jalview Project
The 'Change
+ parameters' option has also been removed from the PCA viewer
+ -
+ New 'Colour by Sequence ID' (subgroup) option
+ -
+ Alternative genetic code tables supported for
+ 'Translate as cDNA'
+ -
+ Finder panel remembers last position in each view
+ -
+ More efficient creation of selections and
+ multiple groups when working with large alignments
+ -
+ Speedier import of annotation rows when
+ parsing stockholm files
+ -
+ Update of Ensembl Rest Client to API v10.0
+ -
+ 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)
+ -
+ More efficient sequence feature render
+ algorithm (Z-sort/transparency and filter aware)
+ -
+ Alignment Overview now by default shows
+ only visible region of alignment (this can be changed in
+ user preferences)
+ -
+ File Chooser stays open after Cancel overwrite
+ -
+ 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
+ -
+ Show annotation tooltips and popup menus in wrapped mode
+ -
+ Can select columns by dragging left/right in annotations
+ -
+ Improved tooltips in Feature Settings dialog
+ -
+ Help button on Uniprot and PDB search panels
+ -
+ Cursor changes over draggable box in Overview panel
+ -
+ Overview panel default changed to not show hidden regions
+ -
+ Consistent ordering of links in sequence id popup menu
+ -
+ Sequence Details report opens positioned to top of report
+ -
+ Scale panel popup menu allows Hide selected columns adjacent
+ to a hidden column marker
+
+ Deprecations
+
+ -
+ DAS sequence retrieval and annotation
+ capabilities removed from the Jalview Desktop
+
+
+ Release Processes
+
+ -
+ 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
+ unmarshalling has been replaced by JAXB for Jalview projects
+ and XML based data retrieval clients
+
+ |
+
+
+
+ -
+ Timeouts when retrieving data from Ensembl
+ -
+ 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
+ -
+ Error message for trying to load in invalid
+ URLs doesn't tell users the invalid URL
+ -
+ Nonpositional features lose feature group
+ on export as Jalview features file
+ -
+ Status bar updates beyond visible columns
+ -
+ Blank extra columns drawn or
+ printed when columns are hidden
+ -
+ Regular expression error in Select Columns by Annotation description
+ -
+ Scroll doesn't stop on mouse up after
+ dragging out of Scale or Annotation Panel
+ -
+ Display is incorrect after Page Down and Up in wrapped mode
+ -
+ Help page can be opened twice
+ -
+ Finder doesn't skip hidden regions
+ -
+ Column selection incorrect after scrolling out of scale panel
+ -
+ Tree calculation fails on a selection dragged to left of alignment
+ -
+ '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
+ -
+ Value input for graduated feature colour threshold gets 'unrounded'
+
+ 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)
+
+ New Known Defects
+
+ -
+ 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'
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ Default memory for Jalview webstart and
+ InstallAnywhere increased to 1G.
+
+ -
+ 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
+ properties file.
+
+ -
+ Ensembl client updated to Version 7 REST
+ API and sequence data now imported as JSON.
+
+ -
+ Change in recommended way of starting
+ Jalview via a Java command line: add jars in lib directory
+ to CLASSPATH, rather than via the deprecated java.ext.dirs
+ property.
+
+
+ Development
+
+ -
+ Support added to execute test suite
+ instrumented with Open
+ Clover
+
+
+ |
+
+
+
+ -
+ Poorly scaled bar in quality annotation
+ row shown in Feredoxin Structure alignment view of example
+ alignment.
+
+ -
+ Annotation obscures sequences if lots of
+ annotation displayed.
+
+ -
+ Group conservation/consensus not shown
+ for newly created group when 'Apply to all groups'
+ selected
+
+ -
+ Corrupted display when switching to
+ wrapped mode when sequence panel's vertical scrollbar is
+ visible.
+
+ -
+ Alignment is black in exported EPS file
+ when sequences are selected in exported view.
+
+ -
+ Groups with different coloured borders
+ aren't rendered with correct colour.
+
+ -
+ Jalview could hang when importing certain
+ types of knotted RNA secondary structure.
+
+ -
+ Sequence highlight and selection in
+ trimmed VARNA 2D structure is incorrect for sequences that
+ do not start at 1.
+
+ -
+ '.' inserted into RNA secondary structure
+ annotation when columns are inserted into an alignment,
+ and when exporting as Stockholm flatfile.
+
+ -
+ Jalview annotation rows containing upper
+ and lower-case 'E' and 'H' do not automatically get
+ treated as RNA secondary structure.
+
+ -
+ .jvp should be used as default extension
+ (not .jar) when saving a jalview project file.
+
+ -
+ Mac Users: closing a window correctly
+ transfers focus to previous window on OSX
+
+
+ Java 10 Issues Resolved
+
+ -
+ OSX - Can't save new files via the File
+ or export menus by typing in a name into the Save dialog
+ box.
+
+ -
+ Jalview now uses patched version
+ of the VAqua5
+ 'look and feel' which has improved compatibility with the
+ latest version of OSX.
+
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ Use HGVS nomenclature for variant
+ annotation retrieved from Uniprot
+
+ -
+ Windows File Shortcuts can be dragged
+ onto the Jalview Desktop
+
+
+ |
+
+
+
+ -
+ Cannot import features with multiple
+ variant elements (blocks import of some Uniprot records)
+
+ -
+ Clustal files with sequence positions in
+ right-hand column parsed correctly
+
+ -
+ Wrap view - export to SVG - IDs shown but
+ not alignment area in exported graphic
+
+ -
+ F2/Keyboard mode edits work when Overview
+ window has input focus
+
+ -
+ Annotation panel set too high when
+ annotation added to view (Windows)
+
+ -
+ Jalview Desktop is slow to start up when
+ network connectivity is poor
+
+ -
+ Drag URL from chrome, firefox, IE to
+ Jalview desktop on Windows doesn't open file
Dragging
+ the currently open URL and links from a page viewed in
+ Firefox or Chrome on Windows is now fully supported. If
+ you are using Edge, only links in the page can be
+ dragged, and with Internet Explorer, only the currently
+ open URL in the browser can be dropped onto Jalview.
+
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ New Structure Chooser control
+ for disabling automatic superposition of multiple
+ structures and open structures in existing views
+
+ -
+ Mouse cursor changes to indicate Sequence
+ ID and annotation area margins can be click-dragged to
+ adjust them.
+
+ -
+ Jalview uses HTTPS for Uniprot, Xfam and
+ Ensembl services
+
+ -
+ Improved performance for large alignments
+ and lots of hidden columns
+
+ -
+ Improved performance when rendering lots
+ of features (particularly when transparency is disabled)
+
+
+ |
+
+
+ -
+ Structure and Overview aren't updated
+ when Colour By Annotation threshold slider is adjusted
+
+ -
+ Slow redraw when Overview panel shown
+ overlapping alignment panel
+
+ -
+ Overview doesn't show end of unpadded
+ sequence as gaps
+
+ -
+ Cross-reference handling
+ improved: CDS not handled correctly if transcript has no
+ UTR
+
+ -
+ Secondary structure and temperature
+ factor annotation not added to sequence when local PDB
+ file associated with it by drag'n'drop or structure
+ chooser
+
+ -
+ Answering 'No' to PDB Autoassociate
+ dialog doesn't import PDB files dropped on an alignment
+
+ -
+ Linked scrolling via protein horizontal
+ scroll bar doesn't work for some CDS/Protein views
+
+ -
+ Trackpad scrolling is broken on OSX on
+ Java 1.8u153 onwards and Java 1.9u4+.
+
+ -
+ Tooltip shouldn't be displayed for empty
+ columns in annotation row
+
+ -
+ Preferences panel's ID Width control is not
+ honored in batch mode
+
+ -
+ Linked sequence highlighting doesn't work
+ for structures added to existing Jmol view
+
+ -
+ 'View Mappings' includes duplicate
+ entries after importing project with multiple views
+
+ -
+ Viewing or annotating Uniprot
+ protein sequences via SIFTS from associated PDB entries
+ 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)
+
+ -
+ Uniprot 'sequence variant' features
+ tooltip doesn't include a text description of mutation
+
+ -
+ Invert displayed features very slow when
+ structure and/or overview windows are also shown
+
+ -
+ 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
+
+ -
+ Adding a structure to existing structure
+ view appears to do nothing because the view is hidden behind the alignment view
+
+
+ Applet
+
+ -
+ Copy consensus sequence option in applet
+ should copy the group consensus when popup is opened on it
+
+
+ Batch Mode
+
+ -
+ Fixed ID width preference is not respected
+
+
+ New Known Defects
+
+ -
+ Exceptions occasionally raised when
+ editing a large alignment and overview is displayed
+
+ -
+ 'Overview updating' progress bar is shown
+ repeatedly after a series of edits even when the overview
+ is no longer reflecting updates
+
+ -
+ 'SIFTS Mapping Error' when viewing
+ structures for protein subsequence (if 'Trim Retrieved
+ Sequences' enabled) or Ensembl isoforms (Workaround in
+ 2.10.4 is to fail back to N&W mapping)
+
+
+ |
+
|
+ |
+
+ - 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
+
+ |
+
+
+ |
+
|
@@ -89,91 +624,227 @@ li:before {
Structure views don't get updated unless
their colours have changed
- All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)
- 'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
+
+ All linked sequences are highlighted for
+ a structure mousover (Jmol) or selection (Chimera)
+
+
+ 'Cancel' button in progress bar for
+ JABAWS AACon, RNAAliFold and Disorder prediction jobs
+
+
+ Stop codons are excluded in CDS/Protein
+ view from Ensembl locus cross-references
+
+
+ Start/End limits are shown in Pairwise
+ Alignment report
+
+
+ Sequence fetcher's Free text 'autosearch'
+ feature can be disabled
+
+
+ Retrieve IDs tab added for UniProt and
+ PDB easier retrieval of sequences for lists of IDs
+
+
+ Short names for sequences retrieved from
+ Uniprot
-
- Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references
- Start/End limits are shown in Pairwise Alignment report
- Sequence fetcher's Free text 'autosearch' feature can be disabled
- Retrieve IDs tab added for UniProt and PDB easier retrieval of sequences for lists of IDs
- Short names for sequences retrieved from Uniprot
Scripting
- Groovy interpreter updated to 2.4.12
- - Example groovy script for generating a matrix of percent identity scores for current alignment.
+ - Example groovy script for generating a matrix of
+ percent identity scores for current alignment.
Testing and Deployment
- - Test to catch memory leaks in Jalview UI
+ -
+ Test to catch memory leaks in Jalview UI
+
- |
+
General
- - Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view
- - Race condition when parsing sequence ID strings in parallel
- - Overview windows are also closed when alignment window is closed
- - Export of features doesn't always respect group visibility
- - Jumping from column 1 to column 100,000 takes a long time in Cursor mode
+ -
+ Pressing tab after updating the colour
+ threshold text field doesn't trigger an update to the
+ alignment view
+
+ -
+ Race condition when parsing sequence ID
+ strings in parallel
+
+ -
+ Overview windows are also closed when
+ alignment window is closed
+
+ -
+ Export of features doesn't always respect
+ group visibility
+
+ -
+ Jumping from column 1 to column 100,000
+ takes a long time in Cursor mode
+
Desktop
- - Structures with whitespace chainCode cannot be viewed in Chimera
- - Protein annotation panel too high in CDS/Protein view
-
- - Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
-
- - Slow EnsemblGenome ID lookup
- - Revised Ensembl REST API CDNA query
- - Hidden column marker in last column not rendered when switching back from Wrapped to normal view
- - Annotation display corrupted when scrolling right in unwapped alignment view
- - Existing features on subsequence incorrectly relocated when full sequence retrieved from database
- - Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)
- - Amend Features dialog doesn't allow features of same type and group to be selected for amending
- - Jalview becomes sluggish in wide alignments when hidden columns are present
- - Jalview freezes when loading and displaying several structures
- - Black outlines left after resizing or moving a window
- - Unable to minimise windows within the Jalview desktop on OSX
- - Mouse wheel doesn't scroll vertically when in wrapped alignment mode
- - Scale mark not shown when close to right hand end of alignment
- - Pairwise alignment of selected regions of each selected sequence do not have correct start/end positions
- - Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog
- - Show cross-references not enabled after restoring project until a new view is created
- - Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2)
- - Overview redraws whole window when box position is adjusted
- - Structure viewer doesn't map all chains in a multi-chain structure when viewing alignment involving more than one chain (since 2.10)
- - Double residue highlights in cursor mode if new selection moves alignment window
- - Alignment vanishes when using arrow key in cursor mode to pass hidden column marker
-
- > Applet
-
- - Concurrent modification exception when closing alignment panel
+ -
+ Structures with whitespace chainCode
+ cannot be viewed in Chimera
+
+ -
+ Protein annotation panel too high in
+ CDS/Protein view
+
+ -
+ Can't edit the query after the server
+ error warning icon is shown in Uniprot and PDB Free Text
+ Search Dialogs
+
+ -
+ Slow EnsemblGenome ID lookup
+
+ -
+ Revised Ensembl REST API CDNA query
+
+ -
+ Hidden column marker in last column not
+ rendered when switching back from Wrapped to normal view
+
+ -
+ Annotation display corrupted when
+ scrolling right in unwapped alignment view
+
+ -
+ Existing features on subsequence
+ incorrectly relocated when full sequence retrieved from
+ database
+
+ -
+ Last reported memory still shown when
+ Desktop->Show Memory is unticked (OSX only)
+
+ -
+ Amend Features dialog doesn't allow
+ features of same type and group to be selected for
+ amending
+
+ -
+ Jalview becomes sluggish in wide
+ alignments when hidden columns are present
+
+ -
+ Jalview freezes when loading and
+ displaying several structures
+
+ -
+ Black outlines left after resizing or
+ moving a window
+
+ -
+ Unable to minimise windows
+ within the Jalview desktop on OSX
+
+ -
+ Mouse wheel doesn't scroll vertically
+ when in wrapped alignment mode
+
+ -
+ Scale mark not shown when close to right
+ hand end of alignment
+
+ -
+ Pairwise alignment of selected regions of
+ each selected sequence do not have correct start/end
+ positions
+
+ -
+ Alignment ruler height set incorrectly
+ after canceling the Alignment Window's Font dialog
+
+ -
+ Show cross-references not enabled after
+ restoring project until a new view is created
+
+ -
+ Warning popup about use of SEQUENCE_ID in
+ URL links appears when only default EMBL-EBI link is
+ configured (since 2.10.2b2)
+
+ -
+ Overview redraws whole window when box
+ position is adjusted
+
+ -
+ Structure viewer doesn't map all chains
+ in a multi-chain structure when viewing alignment
+ involving more than one chain (since 2.10)
+
+ -
+ Double residue highlights in cursor mode
+ if new selection moves alignment window
+
+ -
+ Alignment vanishes when using
+ arrow key in cursor mode to pass hidden column marker
+
+ -
+ Ensembl Genomes example ID changed to one
+ that produces correctly annotated transcripts and products
+
+ -
+ Toggling a feature group after first time
+ doesn't update associated structure view
+
- BioJSON
+ Applet
- -
- BioJSON export does not preserve non-positional features
-
+ -
+ Concurrent modification exception when
+ closing alignment panel
+
- New Known Issues
+ BioJSON
- - Delete/Cut selection doesn't relocate sequence features correctly (for many previous versions of Jalview)
- - Cursor mode unexpectedly scrolls when using cursor in wrapped panel other than top
- - Select columns containing feature ignores graduated colour threshold
- - Edit sequence operation doesn't always preserve numbering and sequence features
+ -
+ BioJSON export does not preserve
+ non-positional features
+
+
+ New Known Issues
+
+ -
+ Delete/Cut selection doesn't relocate
+ sequence features correctly (for many previous versions of
+ Jalview)
+
+ -
+ Cursor mode unexpectedly scrolls when
+ using cursor in wrapped panel other than top
+
+ -
+ Select columns containing feature ignores
+ graduated colour threshold
+
+ -
+ Edit sequence operation doesn't
+ always preserve numbering and sequence features
+
- Known Java 9 Issues
+ Known Java 9 Issues
- - Groovy Console very slow to open and is
- not responsive when entering characters (Webstart, Java 9.01,
- OSX 10.10)
+
-
+ Groovy Console very slow to open and is
+ not responsive when entering characters (Webstart, Java
+ 9.01, OSX 10.10)
-
- |
+
|
|