X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=dfbbde578871ee5a1b8290f733560827564cad78;hb=0805157df366ff8c386f03f020cd2d54b372e314;hp=36d13e43f87b0a75af785fbdf7f5326e4e82c83f;hpb=b9f0dfb7fdd3b3d2eba566eae75ecadc3da35369;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 36d13e4..dfbbde5 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,40 +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)
+ 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.
-
- Option to export virtual features if shown
+ Feature attributes from VCF files can be
+ exported and re-imported as GFF3 files
-
- Option to transfer virtual features to Chimera
+ Capture VCF "fixed column" values
+ POS, ID, QUAL, FILTER as Feature Attributes
-
- Feature attributes from VCF files can be exported and re-imported as GFF3 files
+ More robust VCF numeric data field
+ validation while parsing
-
- Capture VCF "fixed column" values POS,
- ID, QUAL, FILTER as Feature Attributes
+ Feature Settings dialog keeps same screen
+ position if reopened
-
- More robust VCF numeric data field validation while parsing
+ Feature Settings dialog title includes name
+ of associated view
-
- Feature Settings dialog keeps same screen position if reopened
-
+ Font anti-aliasing in alignment views
+ enabled by default
+
-
- Font anti-aliasing in alignment views enabled by default
-
+ Very long feature descriptions truncated in
+ tooltips and menus
+
-
- Very long feature descriptions truncated in tooltips and menus
-
+ Warn if Sort by Score or Density attempted
+ with no feature types visible
+
-
- 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
@@ -113,6 +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
-
@@ -123,14 +193,47 @@ li:before {
report
+ 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.
+
+
|
-
- ID margins for CDS and Protein views not equal when split frame is first opened
+ 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
+
+ -
+ ID margins for CDS and Protein views not
+ equal when split frame is first opened
-
- Sequence position numbers in status bar not correct after editing a sequence's start position
+ Sequence position numbers in status bar not
+ correct after editing a sequence's start position
-
Alignment is misaligned in wrapped mode
@@ -158,34 +261,45 @@ li:before {
IllegalArgumentException in some circumstances
-
- Multiple feature settings dialogs can be opened for a view
+ Multiple feature settings dialogs can be
+ opened for a view
-
- Feature Settings dialog is orphaned if alignment window is closed
+ Feature Settings dialog is orphaned if
+ alignment window is closed
-
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
-
- OSX - Can't view some search results in PDB/Uniprot search panel
+ OSX - Can't view some search results in
+ PDB/Uniprot search panel
- Installer
+ Installer
- - Jalview should not create file associations for 3D structure files (.pdb, .mmcif. .cif)
+
-
+ Jalview should not create file associations
+ for 3D structure files (.pdb, .mmcif. .cif)
Repository and Source Release
-
- removed obsolete .cvsignore files from repository
+ removed obsolete .cvsignore files from
+ repository
-
- Clover report generation running out of memory
+ Clover report generation running out of
+ memory
-
- New Known Issues
+ New Known Issues
-
OSX - Current working directory not
@@ -198,7 +312,12 @@ li:before {
enabled
-
- Jalview Installation type always reports 'Source' in console output
+ Jalview Installation type always reports
+ 'Source' in console output
+
+ -
+ Test Suite: Certain Functional tests fail on jalview's
+ bamboo server but run fine locally.
|