X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=a090673ff8c5bdb9bc1464a6713e71432fb83a5f;hb=refs%2Ftags%2FRelease_2_4_0;hp=fff6ed920d7813a8a9edc155358ec32f549eb312;hpb=bddc7dcaf05c8c66801badea47ee9b0c55ba70eb;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index fff6ed9..a090673 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -4,43 +4,62 @@
What's new ?
-Jalview Version 2.4
+Highlights in Jalview Version 2.4
- VAMSAS Interoperation Client
- DAS Sequence Fetching
- DNA/Protein Product traversal (Experimental)
- .. (more to come)
+ 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
+Issues Resolved (a select list)
- .. (more to come)
+ 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
-<--Jalview Version 2.3
-
- Jmol 11.0.2 integration
- PDB views stored in Jalview XML files
- Slide sequences
- Edit sequence in place
- EMBL CDS features
- DAS Feature mapping
- Feature ordering
- Alignment Properties
- Annotation Scores
- Sort by scores
- Feature/annotation editing in applet
-
-Issues Resolved
-
- Headless state operation in 2.2.1
- Incorrect and unstable DNA pairwise alignment
- Cut and paste of sequences with annotation
- Feature group display state in XML
- Feature ordering in XML
- 2.2.1 applet had no feature transparency
- Number pad keys can be used in cursor mode
- Structure Viewer mirror image resolved
-
-->
See the Release History page for
details of all new features and resolved issues.