X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=993fcd50737ddd23a69d7594308531d254efeda0;hb=576d2415673f37bb083d88e3c5702fb7d71d9b7b;hp=925efdba98a60440a943c95a10bbc35466712d99;hpb=c4b2cda477ade69b8db58f60f905d310723763d3;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 925efdb..993fcd5 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,8 +70,446 @@ li:before {
|
+ |
+
+
+
+ -
+ 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)
+
+ -
+ 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
+
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ Faster and more efficient management and
+ rendering of sequence features
+
+ -
+ More reliable Ensembl fetching with HTTP
+ 429 rate limit request hander
+
+ -
+ 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
+
+ -
+ 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.
+
+ Testing and Deployment
+
+ -
+ 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
+
+
+ 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
+
+ -
+ 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
+
+
+ Applet
+
+ -
+ Concurrent modification exception when
+ closing alignment panel
+
+
+ BioJSON
+
+ -
+ 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
+
+ -
+ Groovy Console very slow to open and is
+ not responsive when entering characters (Webstart, Java
+ 9.01, OSX 10.10)
+
+
+ |
+
+
+ |
+
+ |
+
+ New features in Jalview Desktop
+
+ -
+ Uniprot Sequence Fetcher now uses web API at uniprot.org
+
+ - HTTPS used for all connections to ebi.ac.uk
+
+
+ |
+
+ |
+
+
+ |
+
|
@@ -122,9 +560,32 @@ li:before {
Not all chains are mapped when multimeric
assemblies are imported via CIF file
+
+ Gap colour in custom colourscheme is not
+ displayed when threshold or conservation colouring is also
+ enabled.
+
+
+ JABAWS 2.2 services report wrong JABAWS
+ server version
+
+
+ Jalview continues to scroll after
+ dragging a selected region off the visible region of the
+ alignment
+
+
+ Cannot apply annotation based
+ colourscheme to all groups in a view
+
+
+ IDs don't line up with sequences
+ initially after font size change using the Font chooser or
+ middle-mouse zoom
+
|
-
+
|
@@ -1379,6 +1840,10 @@ li:before {
after clicking on it to create new annotation for a
column.
+
+ Null Pointer Exception raised when
+ pressing Add on an orphaned cut'n'paste window.
+
|