X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp%2Fhtml%2Freleases.html;h=0a2065078ea442303ffd285e300519094389fbaa;hb=5fded65dab76ae9214716a59e2bfad03e64053ed;hp=0e13dabf9d7156685cd54792629403a47abeffb9;hpb=19a35562dfd8e4e534681d2d4163e7b07117bd7c;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 0e13dab..0a20650 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,8 +57,8 @@ li:before {
- 2.11
- 20/06/2019
+ 2.11.0
+ 04/07/2019
|
@@ -75,7 +75,7 @@ li:before {
-
File type associations for
- formats supported by jalview (including .jvp project files)
+ formats supported by Jalview (including .jvp project files)
-
Jalview launch files (.jvl) to pass command line
@@ -98,17 +98,25 @@ li:before {
-
IntervalStoreJ (NCList
- implementation that alows updates) used for Sequence Feature collections
+ implementation that allows updates) used for Sequence Feature collections
-
-
-
- Sequence features can be filtered and
- shaded according to any associated attributes (e.g. variant
- attributes from VCF file, or key-value pairs imported from
- column 9 of GFF file)
+ Sequence
+ features can be filtered and shaded according to any
+ associated attributes (e.g. variant attributes from VCF
+ file, or key-value pairs imported from column 9 of GFF
+ file)
+
+ -
+ Feature Attributes and shading schemes
+ stored and restored from Jalview Projects
+
+ -
+ Use full Sequence Ontology (via BioJava) to
+ recognise variant features
-
- Show synonymous codon variants on peptide
- sequences
+ Show synonymous codon variants on peptide
+ sequences (also coloured red by default)
-
Popup window to show full report for a selected sequence feature's
@@ -134,7 +142,7 @@ li:before {
Principal Components Analysis results
and Viewer state saved in Jalview Project
- - 'Change parameters' option removed from viewer's
+
- 'Change parameters' option removed from viewer's
drop-down menus
-
Can use shift + arrow keys to rotate PCA image
@@ -167,7 +175,7 @@ li:before {
-
Alignment Overview now WYSIWIS (What you see is
- what is shown)
Only visible region of alignment is shown by
+ what is shown) Only visible regions of alignment are shown by
default (can be changed in user preferences)
-
@@ -195,7 +203,7 @@ li:before {
annotation
-
- Help button on Uniprot and PDB search panels
+ Help button on Uniprot and PDB search panels
-
Cursor changes over draggable box in Overview
@@ -223,40 +231,55 @@ li:before {
Deprecations
- -
- DAS sequence retrieval and annotation
+
- DAS sequence retrieval and annotation
capabilities removed from the Jalview Desktop
- -
- Castor library for XML marshalling and
+
- Castor library for XML marshalling and
unmarshalling has been replaced by JAXB for Jalview projects
and XML based data retrieval clients
- Disable VAMSAS menu in preparation for removal
- Jalview Desktop no longer distributed via Java Web Start
Documentation
- -
- Added remarks about transparent rendering effects
+
- Added remarks about transparent rendering effects
not supported in EPS figure export
+ - Typos in documentation for Preferences dialog
Development and Release Processes
-
- Build system migrated from Ant to Gradle
-
- - Enhanced checks for missing and duplicated keys in Message bundles
- -
- Eclipse project configuration managed with
- gradle-eclipse
+ Build system migrated from Ant to Gradle
- -
- Atlassian Bamboo continuous integration for
- unattended Test Suite execution
+ -
+ Enhanced checks for missing and duplicated keys in Message bundles
+ -
+ Eclipse project configuration managed with
+ gradle-eclipse
+
+ -
+ Atlassian
+ Bamboo continuous integration for unattended Test Suite
+ execution
+
+ -
+ Memory test suite to detect leaks in common
+ operations
+
+ -
+ More unit test coverage, and minor
+ issues resolved
+
+ -
+ Developer documentation migrated to
+ markdown (with HTML rendering)
+
-
- Memory test suite to detect leaks in common
- operations
- - More unit test coverage, and minor issues resolved.
- - Developer documentation migrated to markdown (with HTML rendering)
+ HelpLinksChecker runs on Windows
+
+ -
+ New URLs for publishing development
+ versions of Jalview
+
|
@@ -299,8 +322,8 @@ li:before {
Settings and Jalview Preferences panels
- Jalview hangs when closing windows or the
- overview updates with large alignments
+ Jalview hangs when closing windows, or redrawing the
+ overview with large alignments
Tree and PCA calculation fails for selected
@@ -316,16 +339,21 @@ li:before {
doesn't tell users the invalid URL
- Nonpositional features lose feature group on
- export as Jalview features file
-
-
Tooltips displayed for features filtered by
score from view
+ Sequence Variants retrieved from Ensembl during
+ show cross references or Fetch Database References are shown in
+ red in original view
+
+
+ stop_gained variants not shown correctly on
+ peptide sequence (computed variant shown as p.Res.null)
+
+
'Graduated colour' option not offered for
- manually created features (where if feature score is Float.NaN)
+ manually created features (where feature score is Float.NaN)
Blank extra columns drawn or printed
@@ -408,20 +436,19 @@ li:before {
shown in complementary view
- stop_gained variants not shown correctly on
- peptide sequence
-
-
Codon consensus incorrectly scaled when shown
without normalisation
- Sequence Details report opens positioned to top
+ Sequence Details report should open positioned at top
of report
Help page can be opened twice
+
+ Fuzzy text in web service status menu on OSX Mojave
+
Editing
-
@@ -442,10 +469,23 @@ li:before {
Structure colours not updated when associated tree
repartitions the alignment view (Regression in 2.10.5)
-
-
- New Known Defects
- Datamodel
+
+ -
+ Sequence.findIndex returns wrong value when
+ sequence's End is greater than its length
+
+ Bugs fixed for Java 11 Support (not yet on
+ general release)
+
+ -
+ Menus work properly in split-screen
+
+ New Known Defects
+
+ -
+ Select columns containing feature by double clicking ignores bounds of an existing selected region
+
-
Codon consensus logo incorrectly scaled in gapped
regions of protein alignment.
@@ -473,14 +513,23 @@ li:before {
not shown as thresholded features in 2.11. To workaround please
create a Score filter instead.
- - Java 11 Specific defects
+
-
+ Cancel on Feature Settings dialog doesn't reset group visibility
+ -
+ F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
+
+ -
+ Closing tree windows with CMD/CTRL-W for
+ alignments with multiple views can close views unexpectedly
+
+
+ Java 11 Specific defects
-
- Jalview Properties file is not sorted alphabetically when saved
-
-
-
-
+ Jalview Properties file is not sorted
+ alphabetically when saved
+
+
|