X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=0abd2a7b9501e9f1fffc3bc4456f39ec4af1d50a;hb=31117f8593d9c51c6238be3d40771819da96939d;hp=a090673ff8c5bdb9bc1464a6713e71432fb83a5f;hpb=c554d41a4effc6719895bda6b3abc04c032715a8;p=jalview.git
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+
What's new ?
-What's new ?
-Highlights in Jalview Version 2.4
-
- DNA and protein product highlighting
- URL links generated with regular expressions
- URL links for sequence database cross references
- New sequence fetcher dialog and DAS Sequence Fetching
- JPred Service upgraded to Jpred3
- Memory monitor
- PFAM full alignment retrieval
- Generalised sequence database reference validation
- DNA Protein Product sequence db traversal (Experimental)
- VAMSAS Interoperation Client (Experimental)
- export annotation rows as CSV for spreadsheet import
- New application command line args and optional Groovy suport
- New Applet API methods and parameters
-
-Issues Resolved (a select list)
-
- Aligned cDNA translation to aligned peptide works correctly
- selected region output includes visible annotations (for
- certain formats)
- edit label/displaychar contains existing label/char for
- editing
- Newick tree support improved for clustalW trees and preserving NHX style comments
- Pathological filechooser bug avoided by not allowing
- filenames containing a ':'
- Fixed exception when parsing GFF files containing global
- sequence features
- Reference counting for alignment datasets
- better reporting of non-fatal warnings and error messages to user when file
- parsing fails.
- Save works when Jalview project is default format
- Histidine should be midblue (not pink!) in Zappo
- Undo recovers dataset sequence metadata when sequence
- regions are cut
- PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) are read in properly
- Stockholm annotation parsing fixed and improved (PFAM records)
- Re-instated Full AMSA support and .amsa file association (MyHits)
- annotation consisting of sequence associated scores can be
- read and written correctly to annotation file
- Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet
- Applet Menus are always embedded in applet window on Macs.
- Newly shown features appear at top of stack (in Applet)
- Secondary structure lines are drawn starting from first
- column of alignment
- Uniprot XML import updated for new schema release in July 2008
- Sequence feature to sequence ID match for Features file is case-insensitive
- Sequence features read from Features file appended to all sequences with matching IDs
- PDB structure coloured correctly for associated views containing a sub-sequence
- Display name and local features preserved in results retrieved from web service
- Visual delay indication for sequence retrieval and sequence fetcher initialisation
- Updated Application to use DAS 1.53e version of dasobert DAS client
-
-
-
-See the Release History page for
-details of all new features and resolved issues.
+
+ What's new in Jalview 2.10.4 ?
+
+
+ This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
+
+
+ - Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns
+ - Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services
+ - Critical patches for running Jalview on OSX with Java 10
+ - Easier adjustment of the Alignment ID panel and Annotation panel
+ - Improved support for mapping between 3D Structures and Uniprot Protein Sequences
+ - Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs
+ - New buttons on the Structure Chooser for adding structures
+ to an existing view, and disabling automatic superposition
+ according to linked alignments
+ - Annotation transfer between Chimera and Jalview (formerly only
+ available in 'Experimental' mode)
+
+
+ The full list of bugs fixed in this release can be found in the 2.10.4
+ Release Notes.
+