X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2FwhatsNew.html;h=a090673ff8c5bdb9bc1464a6713e71432fb83a5f;hb=b94df7cbe375db4a0df5c351dda035ae8e9c10f7;hp=b5f5c7876eead6be00bda53d2434f747f09c3d2d;hpb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;p=jalview.git
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-
-
What's new ?
-
-What's new ?
-Jalview Version 2.08
- Editing can be locked to the selection area.
- Any edits made within the locked area do not affect the rest of the alignment.
- Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list
- of keyboard controls, look here.
- Create sequence features from searches.
- Previously, the regions of sequences highlighted as the result of
- searches were added as new regions in the alignment. Now, the sequence region
- selected by a search can be used to define named sequences features
- attached to the sequence, rather than the alignment.
-
-Sequence feature display and rendering has also been enhanced, with
- the addition of sequence feature groups (which can be used to show
- or hide a set of feature types en masse) and user defined
- feature colours as well as transparency controls, using the Sequence Feature Settings
- window. The Features file
- has also been extended to accomodate these enhancements.
-Alignment annotation and colouring is also considerably
- enhanced. Precalculated symbolic and quantitative annotations (text labels,
- secondary structure symbols and multiple scalar graphs) can now be
- loaded onto alignments via the Annotation
- File. Additionally, the Annotation
- Colouring dialog box allows an alignment to be coloured based on
- any of the graphed quantities with which it is annotated.
-Rendering speed has been improved by disabling anti-aliasing via
- the Smooth Fonts
- option in the View
- menu (its default set in Preferences). In addition, response
- times when editing alignments can be reduced by turning off the automatic
- calculation of amino acid property Consensus (which has been
- reintroduced to the Calculate menu as Autocalculate Consensus).
-
-Issues Resolved
-
-- Drag & Drop now works on common Linux desktops (at least KDE
-and Gnome)
-- Jalview XML Archive Input/Output is now faster (using an
-internal Jalview schema), and sequence description strings are now
-preserved in the archive.
-- Jalview can now correctly read and write MODELLER style
-PIR description lines for proteins with a PDB reference.
-
-
-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.
+
+