X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=f0b29f059c8d7a4f76de249e18ea9899db4ea3de;hb=99604d97d9c8c5ec78d6c72a29aae7c6413b6ccd;hp=485cf735ac69f009e0073038fa5444ee7897410e;hpb=0865048016e68bb32886129654a5f7f6ae2d675e;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 485cf73..f0b29f0 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -68,23 +68,367 @@ li:before {
+ |
+
+ |
+
+
+ |
+
+
+ - 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
+ |
+
+
+ |
+
+ |
+
+
+
+ -
+ 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
+
+
+ |
+
+ |
+
+
|
|
+ -
+ Show gaps in overview window by colouring
+ in grey (sequences used to be coloured grey, and gaps were
+ white)
+
+ -
+ Overview tab in Jalview Desktop
+ Preferences
+
+ -
+ Overview updates immediately on increase
+ in size and progress bar shown as higher resolution
+ overview is recalculated
+
+
|
+ -
+ Overview window redraws every hidden
+ column region row by row
+
+ -
+ duplicate protein sequences shown after
+ retrieving Ensembl crossrefs for sequences from Uniprot
+
+ -
+ Overview window throws NPE if show boxes
+ format setting is unticked
+
+ -
+ Groups are coloured wrongly in overview
+ if group has show boxes format setting unticked
+
+ -
+ Redraw problems when
+ autoscrolling whilst dragging current selection group to
+ include sequences and columns not currently displayed
+
+ -
+ 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
+
|
-
+
@@ -228,7 +572,9 @@ li:before {
Updated JABAWS client to v2.2
- Filter non-standard amino acids and nucleotides when submitting to AACon and other MSA Analysis services
+ Filter non-standard amino acids and
+ nucleotides when submitting to AACon and other MSA
+ Analysis services
URLs for viewing database
@@ -290,25 +636,23 @@ li:before {
matrix - C->R should be '-3'
Old matrix restored
with this one-line groovy script:
jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
-
- Fixed Jalview's treatment of gaps in PCA
- and substitution matrix based Tree calculations.
In
- earlier versions of Jalview, gaps matching gaps were
- penalised, and gaps matching non-gaps penalised even more.
- In the PCA calculation, gaps were actually treated as
- non-gaps - so different costs were applied, which meant
- Jalview's PCAs were different to those produced by
- SeqSpace.
Jalview now treats gaps in the same way as
- SeqSpace (ie it scores them as 0).
Enter
- the following in the Groovy console to restore pre-2.10.2
- behaviour:
+ Fixed
+ Jalview's treatment of gaps in PCA and substitution matrix
+ based Tree calculations.
In earlier versions
+ of Jalview, gaps matching gaps were penalised, and gaps
+ matching non-gaps penalised even more. In the PCA
+ calculation, gaps were actually treated as non-gaps - so
+ different costs were applied, which meant Jalview's PCAs
+ were different to those produced by SeqSpace.
Jalview
+ now treats gaps in the same way as SeqSpace (ie it scores
+ them as 0).
Enter the following in the
+ Groovy console to restore pre-2.10.2 behaviour:
jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
// for 2.10.1 mode
jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
// to restore 2.10.2 mode
Note:
these settings will affect all subsequent tree and PCA
- calculations (not recommended)
-
+ calculations (not recommended)
Fixed off-by-one bug that affected
scaling of branch lengths for trees computed using
@@ -661,7 +1005,8 @@ li:before {
doesn't always add secondary structure annotation.
- |
+
+
2.10.1
29/11/2016
@@ -1338,6 +1683,10 @@ 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.
+
|