X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=5f109ef9217e602be9e103551dd0aa5de3893052;hb=ed671cc6c671a3f225f28311b2745d576bbe3c82;hp=471e12a5dcb2056da476c5945a98cbad232b26aa;hpb=438f101f56c8bcfe5422a54328d7bad60e9c07eb;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 471e12a..5f109ef 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,6 +70,148 @@ 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
+
+
+ - Example groovy script for generating a matrix of percent identity scores for current alignment.
+ |
+
+
+
+ - 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
+ - Race condition when parsing sequence ID strings in parallel
+ - 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
+
+ |
+
+
+ |
+
+ |
+
+ 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
+
+
+ |
+
+
+ |
+
|
@@ -210,7 +352,9 @@ 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
@@ -272,25 +416,23 @@ 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
@@ -643,7 +785,8 @@ li:before {
doesn't always add secondary structure annotation.
-
+
+
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