X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Freleases.html;h=d1a1c599553bb21684f16ecd4fa9d982db900443;hb=dfdd9065b253d59b628b6b778105979c8e10444b;hp=cfc6a7545ba3a8ee72874713ac024a3ea12f56f0;hpb=afa0eead37d52f0969fa24fca4b35b0358f434a8;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index cfc6a75..d1a1c59 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -96,6 +96,10 @@ li:before {
+ Tree/PCA calculation menu items merged to
+ a calculation dialog box
+
+
More robust colours and shader
model for alignments and groups
@@ -133,6 +137,25 @@ li:before {
Graduated feature colour style example
included in the example feature file
+
+ Occupancy annotation row shows number of
+ ungapped positions in each column of the alignment.
+
+
+ File extension pruned from Sequence ID
+ for sequences derived from structure files without
+ embedded database accession
+
+
+ Status bar message shown when not enough
+ aligned positions were available to create a 3D structure
+ superposition.
+
+
+ More robust per-sequence positional
+ annotation input/output via stockholm flatfile
+
+
Application
@@ -162,6 +185,17 @@ li:before {
Drag and drop load of AAIndex and NCBI
format sequence substitution matrices
+ -
+ Structure chooser automatically shows
+ Cached Structures rather than querying the PDBe if
+ structures are already available for sequences
+
+ -
+ Structures imported via URL are cached in
+ the Jalview project rather than downloaded again when the
+ project is reopened.
+
+
Experimental features
@@ -187,6 +221,10 @@ li:before {
during tests
-
+ External service integration tests for
+ Uniprot REST Free Text Search Client
+
+ -
Scripting
-
@@ -195,8 +233,11 @@ li:before {
constants)
-
-
+ FeatureCounter script refactored for
+ efficiency when counting all displayed features (not
+ backwards compatible with 2.10.1)
+
@@ -227,6 +268,11 @@ li:before {
restore 2.10.2 mode
-
+ Fixed off-by-one bug that affected
+ scaling of branch lengths for trees computed using
+ Sequence Feature Similarity.
+
+ -
Reopening Colour by annotation dialog
doesn't reselect a specific sequence's associated
annotation after it was used for colouring a view
@@ -338,16 +384,71 @@ li:before {
overview when features overlaid on alignment
-
-
+ Minimum size set for Jalview windows so
+ widgets don't permanently disappear
-
-
+ Cannot select or filter quantitative
+ annotation that are shown only as column labels (e.g.
+ T-Coffee column reliability scores)
-
-
+ Gap colours in user-defined colourschemes
+ are not shown
-
-
+ Exception thrown if trying to create a
+ sequence feature on gaps only
+
+ -
+ Sort by features includes features to
+ right of selected region when gaps present on right-hand
+ boundary
+
+ -
+ Features created with 'New feature'
+ button from a Find inherit previously defined feature type
+ rather than the Find query string
+
+ -
+ incorrect title in output window when
+ exporting tree calculated in Jalview
+
+ -
+ Per-sequence RNA secondary structures
+ added after a sequence was imported are not written to
+ Stockholm File
+
+ -
+ WUSS notation for simple pseudoknots lost
+ when importing RNA secondary structure via Stockholm
+
+ -
+ Secondary structure arrows for [] and {}
+ not shown in correct direction for simple pseudoknots
+
+ -
+ Hiding sequences at bottom of alignment
+ and then revealing them reorders sequences on the
+ alignment
+
+ -
+ Group panel in sequence feature settings
+ doesn't update to reflect available set of groups after
+ interactively adding or modifying features
+
+ -
+ Sequence Database chooser unusable on
+ Linux
+
+ -
+
+
+ -
+
+
+ -
+
Documentation
@@ -356,10 +457,26 @@ li:before {
Release notes reformatted for readibility
with the built-in Java help viewer
+
+ Find documentation updated with 'search
+ sequence description' option
+
Application
-
+ Sequence Database chooser doesn't show
+ available databases panel on Linux
+
+ -
+ EnsemblGenomes example failing after
+ release of Ensembl v.88
+
+ -
+ User Defined Colours not added to Colour
+ menu
+
+ -
Easier creation of colours for all 'Lower
case' residues (button in colourscheme editor debugged and
new documentation and tooltips added)
@@ -373,6 +490,15 @@ li:before {
new features are added to alignment
-
+ Cancel in feature settings reverts
+ changes to feature colours via the Amend features dialog
+
+ -
+ Null pointer exception when attempting to
+ edit graduated feature colour via amend features dialog
+ box
+
+ -
Structure viewer's View -> Colour By view
selection menu changes colours of alignment views
@@ -406,9 +532,9 @@ li:before {
when alignment view imported from project
-
- No mappings generated between structure
- and sequences extracted from structure files imported via
- URL
+ No mappings generated between
+ structure and sequences extracted from structure files
+ imported via URL and viewed in Jmol
-
Structures loaded via URL are saved in
@@ -438,7 +564,8 @@ li:before {
proteins
-
- cDNA Consensus not shown
+ SIFTs mappings not created for some
+ structures
@@ -489,10 +616,19 @@ li:before {
jalview.ws.jabaws.RNAStructExportImport setup fails
-
-
+ Unit test failure:
+ jalview.ws.sifts.SiftsClientTest due to compatibility
+ problems with deep array comparison equality asserts in
+ successive versions of TestNG
+
+ -
+ Relocated StructureChooserTest and
+ ParameterUtilsTest Unit tests to Network suite
+
+
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