X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=c83741a1082d50a442bb8a250dd0d84aa378bc49;hb=a39aca0519f2fba1c0706e295831008da951608d;hp=13e2ae80a9e2deda1835c9d81550761a695cfac8;hpb=325d9af46f90ec58df53d6a0384bf3afbff6d5ab;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 13e2ae8..c83741a 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,18 +57,91 @@ li:before {
2.11.1.0
- 16/2/2020 |
+ id="Jalview.2.11.1">2.11.1.1
+ 13/07/2020
+ |
+
+
+ - Escape does not clear highlights on the alignment (Since Jalview 2.10.3)
+
+ |
+
+
+ 2.11.1.0
+ 22/04/2020 |
+
+
+ -
+ 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
+
+ -
+ Capture VCF "fixed column" values
+ POS, ID, QUAL, FILTER as Feature Attributes
+
+ -
+ More robust VCF numeric data field
+ validation while parsing
+
+ -
+ Feature Settings dialog keeps same screen
+ position if reopened
+
+ -
+ Feature Settings dialog title includes name
+ of associated view
+
+ -
+ Font anti-aliasing in alignment views
+ enabled by default
+
+ -
+ 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
+
+ -
+ Versions for install4j and getdown and installer template version reported
+ in console (may be null when Jalview launched as executable jar or via conda)
+
+ -
+ Layout improvements for OSX .dmg Finder and higher quality background images
+
+ -
+ New installer/application launcher generated with install4j 8.0.4
+
+ -
+ Jalview File Associations shown for Unix Platforms
+ -
+ Improved defaults for maximum memory setting when running on large memory machines
Release processes
-
New point release version scheme - 2.11.1.0
+ -
+ 'Jalview Test' installers/apps for easier access to test-release channel builds
+
Build System
-
@@ -78,18 +151,57 @@ li:before {
Test code included in Clover coverage
report
- Deprecations
+
+ 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
-
-
+ 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
+
+ -
+ Alignment is misaligned in wrapped mode
+ with annotation and exceptions thrown when only a few
+ columns shown in wrapped mode
+
+ -
+ Sequence IDs missing in headless export of
+ wrapped alignment figure with annotations
-
Sorting Structure Chooser table by Sequence
@@ -104,24 +216,68 @@ li:before {
feature settings dialog also selects columns
-
- SpinnerNumberModel causing
+ SpinnerNumberModel causes
IllegalArgumentException in some circumstances
-
+ Multiple feature settings dialogs can be
+ opened for a view
+
+ -
+ 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 results in PDB/Uniprot FTS
+ OSX - Can't view some search results in
+ PDB/Uniprot search panel
+
+ Installer
+
+ -
+ Jalview should not create file associations
+ for 3D structure files (.pdb, .mmcif. .cif)
Repository and Source Release
-
- removed redundant .gitignore files from
+ removed obsolete .cvsignore files from
repository
+ -
+ Clover report generation running out of
+ memory
+
+ New Known Issues
+
+ -
+ OSX - Current working directory not
+ preserved when Jalview.app launched with parameters from
+ command line
+
+ -
+ Sequence IDs aligned to wrong margin and
+ clipped in headless figure export when Right Align option
+ enabled
+
+ -
+ Jalview Installation type always reports
+ 'Source' in console output
+
+ -
+ Test Suite: Certain Functional tests fail on jalview's
+ bamboo server but run fine locally.
+
|