X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=485cf735ac69f009e0073038fa5444ee7897410e;hb=0865048016e68bb32886129654a5f7f6ae2d675e;hp=0bc5ea7adf6777e9601b050d43bcc38e0476e649;hpb=66a8ed3a7914afb8e312c7a1e4a4726ae8b9d690;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 0bc5ea7..485cf73 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,7 +70,25 @@ li:before {
+
+
|
@@ -122,10 +140,6 @@ 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 +181,10 @@ 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 +198,10 @@ 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 +219,7 @@ 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 +228,9 @@ li:before {
Updated JABAWS client to v2.2
+ Filter non-standard amino acids and nucleotides when submitting to AACon and other MSA Analysis services
+
+
URLs for viewing database
cross-references provided by identifiers.org and the
EMBL-EBI's MIRIAM DB
@@ -234,7 +259,7 @@ li:before {
Documentation
-
- Release notes reformatted for readibility
+ Release notes reformatted for readability
with the built-in Java help viewer
-
@@ -265,21 +290,24 @@ 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
+ 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
+ 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
@@ -412,10 +440,6 @@ 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
@@ -621,11 +645,11 @@ 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
|