X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=b3d98c9a6207318618fedd292c85a0283d341cfa;hb=235ee12229b39c41085229f5375ff6dc8c93b19d;hp=b56442829556bfb5dc38f401cfce65f988575762;hpb=bbd978c6c697b2a4591d984e011198d7d4b5afc5;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index b564428..b3d98c9 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,6 +70,200 @@ li:before {
|
+ |
+
+
+
+ -
+ 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
+
+ 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
+
+ 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 only aligns selected regions of each selected sequence
+ - 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)
+
+ Applet
+
+ - Concurrent modification exception when closing alignment panel
+
+ BioJSON
+
+ -
+ BioJSON export does not preserve non-positional 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
+
+
+ |
+
+
+ |
+
|
@@ -122,10 +316,6 @@ li:before {
with alignment and overview windows
- Linked scrolling of CDS/Protein views
- via Overview or sequence motif search operations
-
-
Scrolling of wrapped alignment views via
overview
@@ -167,6 +357,10 @@ li:before {
the application.
+ Linked scrolling of CDS/Protein views
+ via Overview or sequence motif search operations
+
+
Amend sequence features dialog box can be
opened by double clicking gaps within sequence feature
extent
@@ -180,6 +374,10 @@ li:before {
3D Structure
-
+ Hidden regions in alignment views are not
+ coloured in linked structure views
+
+ -
Faster Chimera/Jalview communication by
file-based command exchange
@@ -206,7 +404,9 @@ 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
@@ -268,25 +468,23 @@ 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
@@ -418,10 +616,6 @@ li:before {
Rendering
-
- Hidden regions in alignment views are not
- coloured in linked structure views
-
- -
Overview window visible region moves
erratically when hidden rows or columns are present
@@ -643,7 +837,8 @@ li:before {
doesn't always add secondary structure annotation.
-
+
+
2.10.1
29/11/2016
@@ -1320,6 +1515,10 @@ 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.
+
|