X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=ac4831328124a5a75e88481af90d5c2fa058f5a3;hb=908fd2853ff088e3e3ad68ffc803b390d8d40d29;hp=6b7a758b35f3c05ad26b69e60c89f0539da93153;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 6b7a758..ac48313 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -1,84 +1,74 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
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
-
+
+ What's new ?
+
+
+ Jalview 2.10 is the next major release in the Jalview 2 series. Full
+ details are in the Jalview
+ 2.10 Release Notes, but the highlights are below.
+
+
+ Highlights in Jalview 2.10
+
+ - Ensembl sequence fetcher. Annotated Genes,
+ transcripts and proteins can be retrieved via Jalview's new Ensembl REST
+ client. Support for import of Ensembl data also allows:
+
+ - Sequence variant data. Jalview
+ propagates variant annotation imported via Ensembl onto
+ protein products, complete with associated metadata such as
+ clinical significance.
+ - Aligned locus view. Transcripts
+ retrieved for a gene identifier via the Ensembl or
+ EnsemblGenomes sequence databases are automatically aligned to
+ their reference genome.
+
+ - Working with structures.
+
+ - More accurate structure mappings.
+ Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
+ to match structures to UniProt sequences, even for structures
+ containing multiple copies of a sequence.
+ - Import structures as mmCIF. Jalview
+ now downloads data from the EMBL-EBI's PDBe site as mmCIF.
+ mmCIF files allow Jalview to handle very large structures,
+ such as the HIV virus capsid assembly.
+
+ - UniProt Free Text Search. The new search
+ dialog for UniProt allows you to browse and retrieve sequences
+ from UniProt with free-text search and more structured queries
+ - Reference sequence based alignment
+ visualisation.. When a reference sequence is defined for the
+ alignment, the alignment column ruler is now numbered according to
+ the reference sequence. The reference sequence for alignment views
+ can also be saved and restored from Jalview projects.
+
+
-
-See the Release History page for
-details of all new features and resolved issues.