X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Freleases.html;h=09595b08b570208fa9b15a0187499f8a263249cf;hb=2e78324ac6e6dba9f3db8939df4e777a0b097300;hp=ef68578a779ebabf52fd0bf0d4d4c7c83e6754db;hpb=d3d0238b6f894febe960e9f99742bea4289f70aa;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index ef68578..09595b0 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,7 +70,175 @@ 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
+
+ - 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
+
+ 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
+ - 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
+
+ Applet
+
+ - Concurrent modification exception when closing alignment panel
+
+ |
+
+
+ |
+
+ |
+
+ 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 +290,6 @@ 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 +331,10 @@ 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 +348,10 @@ 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
@@ -197,7 +369,7 @@ li:before {
New entries in the Chimera menu
to transfer Chimera's structure attributes as Jalview
features, and vice-versa (Experimental
- Feauture)
+ Feature)
Web Services
@@ -206,6 +378,11 @@ li:before {
Updated JABAWS client to v2.2
+ Filter non-standard amino acids and
+ nucleotides when submitting to AACon and other MSA
+ Analysis services
+
+
URLs for viewing database
cross-references provided by identifiers.org and the
EMBL-EBI's MIRIAM DB
@@ -234,7 +411,7 @@ li:before {
Documentation
-
- Release notes reformatted for readibility
+ Release notes reformatted for readability
with the built-in Java help viewer
-
@@ -265,22 +442,23 @@ 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). To restore pre-2.10.2
- behaviour
- jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
- 2.10.1 mode
- jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
- restore 2.10.2 mode
-
+ - 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)
-
Fixed off-by-one bug that affected
scaling of branch lengths for trees computed using
@@ -412,10 +590,6 @@ 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
@@ -621,15 +795,15 @@ li:before {
-
Importing annotation file with rows
containing just upper and lower case letters are
- interpreted as WUSS rna secondary structure symbols
+ interpreted as WUSS RNA secondary structure symbols
-
- Cannot load Newick trees from eggnog
- ortholog database
+ Cannot load and display Newick trees
+ reliably from eggnog Ortholog database
-
Status bar shows 'Marked x columns
- containing features of type Highlight' when 'B" is pressed
+ containing features of type Highlight' when 'B' is pressed
to mark columns containing highlighted regions.
-
@@ -637,7 +811,8 @@ li:before {
doesn't always add secondary structure annotation.
- |
+
+
2.10.1
29/11/2016
@@ -1314,6 +1489,10 @@ 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.
+
|