X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;fp=help%2Fhtml%2Freleases.html;h=471e12a5dcb2056da476c5945a98cbad232b26aa;hb=4f9c22055c3cdbfc9c4375dcb74755a89ec32b62;hp=89a39a32698ac269d7fddac823fb99eef4d647bb;hpb=64c7a281bdc5c7eb342e477302164979f15a8d5d;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 89a39a3..471e12a 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -122,10 +122,6 @@ 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 +163,10 @@ 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 +180,10 @@ 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 +201,7 @@ 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
@@ -237,7 +241,7 @@ li:before {
Documentation
-
- Release notes reformatted for readibility
+ Release notes reformatted for readability
with the built-in Java help viewer
-
@@ -268,21 +272,24 @@ 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
@@ -415,10 +422,6 @@ 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
@@ -624,11 +627,11 @@ 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