X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=dfbbde578871ee5a1b8290f733560827564cad78;hb=0805157df366ff8c386f03f020cd2d54b372e314;hp=082146ef5a4b439580cb85bad1316d1cbbd15c88;hpb=e1932a723036ee3a5814c840ccaaa5f13029e821;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 082146e..dfbbde5 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,45 +57,107 @@ li:before {
2.11.1.1
+ 13/07/2020 |
+
+
+
+ -
+ Shift+arrow keys navigate to next gap or
+ residue in cursor mode
+
+ -
+ Support import of VCF 4.3 by updating
+ HTSJDK from 2.12 to 2.23
+
+ -
+ IntervalStore library updated to v.1.1:
+ optimisations and improvements suggested by Bob Hanson and
+ improved compatibility with JalviewJS
+
+ -
+ Retrieve GZipped stockholm formatted alignments from Pfam and Rfam
+
+ -
+ Recognise GZipped content fetched via URL
+
+
+
+ |
+
+
+ -
+ Escape does not clear highlights on the
+ alignment (Since Jalview 2.10.3)
+
+ -
+ Alt+Left or Right arrow in cursor mode
+ doesn't slide selected sequences
+
+ -
+ Peptide-to-CDS tracking broken when
+ multiple EMBL gene products shown for a single contig
+
+ -
+ Errors encountered when processing variants
+ from VCF files yield "Error processing VCF: Format specifier
+ '%s'" on the console
+
+ -
+ Count of features not shown can be wrong
+ when there are both local and complementary features mapped
+ to the position under the cursor
+
+
+ |
+
+
+ 2.11.1.0
- 27/03/2020 |
+ 22/04/2020
-
- Option to show 'virtual' codon features on
- protein (or vice versa)
-
- -
- Option to export virtual features if
- shown
-
- -
- Option to transfer virtual features to
- Chimera
-
-
+ Map
+ 'virtual' codon features shown on protein (or vice versa)
+ for display in alignments, on structure views (including
+ transfer to UCSF chimera), in feature reports and for
+ export.
-
- Feature attributes from VCF files can be exported and re-imported as GFF3 files
+ Feature attributes from VCF files can be
+ exported and re-imported as GFF3 files
-
- Capture VCF "fixed column" values POS,
- ID, QUAL, FILTER as Feature Attributes
+ Capture VCF "fixed column" values
+ POS, ID, QUAL, FILTER as Feature Attributes
-
- More robust VCF numeric data field validation while parsing
+ More robust VCF numeric data field
+ validation while parsing
-
- Feature Settings dialog keeps same screen position if reopened
-
+ Feature Settings dialog keeps same screen
+ position if reopened
+
-
- Font anti-aliasing in alignment views enabled by default
-
+ Feature Settings dialog title includes name
+ of associated view
+
-
- Very long feature descriptions truncated in tooltips and menus
-
+ Font anti-aliasing in alignment views
+ enabled by default
+
-
- Warn if Sort by Score or Density attempted with no feature types visible
+ Very long feature descriptions truncated in
+ tooltips and menus
+
+ -
+ Warn if Sort by Score or Density attempted
+ with no feature types visible
+
+ -
+ Improved support for filtering feature attributes with large integer values
Jalview Installer
@@ -118,6 +180,9 @@ li:before {
-
New point release version scheme - 2.11.1.0
+ -
+ 'Jalview Test' installers/apps for easier access to test-release channel builds
+
Build System
-
@@ -128,20 +193,36 @@ li:before {
report
-
- Groovy Scripts
-
- -
- exportconsensus.groovy prints a FASTA
- file to stdout containing the consensus sequence for each
- alignment in a Jalview session
-
-
+ Groovy Scripts
+
+ -
+ exportconsensus.groovy prints a FASTA file
+ to stdout containing the consensus sequence for each
+ alignment in a Jalview session
+
+ -
+ ComputePeptideVariants.groovy to translate
+ genomic sequence_variant annotation from CDS as
+ missense_variant or synonymous_variant on protein products.
+
|
-
+ Hidden sequence markers still visible when
+ 'Show hidden markers' option is not ticked
+
+ -
+ Hidden sequence markers not shown in EPS and
+ PNG output when 'Automatically set ID width' is set in
+ jalview preferences or properties file
+
+ -
+ Feature Editor dialog can be opened when
+ 'Show Sequence Features' option is not ticked
+
+ -
Undo 'Null' operation shown after sort by
buttons in Feature Settings dialog are clicked when no
features are visible
@@ -191,6 +272,11 @@ li:before {
Credits missing some authors in Jalview
help documentation for 2.11.0 release
+ -
+ Export of Pfam alignment as Stockholm
+ includes Pfam ID as sequence's accession rather than its
+ Uniprot Accession
+
Java 11 Compatibility issues
-
@@ -229,6 +315,10 @@ li:before {
Jalview Installation type always reports
'Source' in console output
+ -
+ Test Suite: Certain Functional tests fail on jalview's
+ bamboo server but run fine locally.
+
|