X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=a090673ff8c5bdb9bc1464a6713e71432fb83a5f;hb=3e0eb5fe92f38828607594c7b70dfdf012e4d3dc;hp=bd57b81b2859697831859af7babf8ebab04729d5;hpb=b5edbd2a03d16372bc3e8019ddbf3840dcfe38ed;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index bd57b81..a090673 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -1,30 +1,67 @@
-
-What's new ?
-
-What's new ?
-Jalview Version 2.07
-Sequence Fetcher has been added to quickly
- retrieve sequences with known ids from several databases.
-Sequence Features enhanced to allow
- the user to display all features of a Uniprot file on the alignment and subsequently
- colour, hide or show overlapping features.
-Choose to omit /start-end from sequences when
- saving files. This is important for saving files to be used by some programs
- which cannot read the original Jalview sequence output with the appended /start-end.
-PDB structure viewer enhanced. Mapping
- between sequence and structure has been enhanced, colours on the alignment are
- reflected in the structure viewer.
-Jalview Applet can read
- in feature files, PDB files be used as input to HTML form See the website
- to find out the new parameters available for the Applet Version of Jalview.
-
-Issues Resolved
-Group Editing is possible with Control and mouse click. Alt key and mouse press
- does not work as this translates as the middle mouse button, which since 2.04
- is now used to scroll the alignment and change the font size.
-HTML export now writes groups and features which were previously missing.
-
-See the Release History page for details of all
- new features and resolved issues.
-
-
+
+
+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.
+
+