X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;fp=help%2Fhtml%2Freleases.html;h=8f5a024c5179cbe4cfe347f2803cdd32f8b8b731;hp=471e12a5dcb2056da476c5945a98cbad232b26aa;hb=a435323c67f5dd67ab887bb0c71cf493d04c9272;hpb=d9ec1e848018a92a6d0883b13a25038e279e4ee9
diff --git a/help/html/releases.html b/help/html/releases.html
index 471e12a..8f5a024 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,6 +70,37 @@ li:before {
+ |
+
+
+
+ -
+ Show gaps in overview window by colouring
+ in grey (sequences used to be coloured grey, and gaps were
+ white)
+
+
+ |
+
+
+
+ -
+ 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
+
+
+ |
+
+
+
+
|
@@ -210,7 +241,9 @@ 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 +305,23 @@ 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 +674,8 @@ li:before {
doesn't always add secondary structure annotation.
-
+
+
|