X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=4723a9a622053fee395cd4f6b69a554a815f4a0a;hb=b482f8156c38c7b5ea498eec33f312375441c352;hp=9c13b59d5a5643b8b2a2b6a72f80a3f8a3782325;hpb=90255554ddb63f5474c11afcaba96d23ffd88a46;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 9c13b59..4723a9a 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -1,56 +1,93 @@
-
-
What's new ?
-
-What's new ?
-Jalview Version 2.08
-Editing can be locked to the
- selection area so that any edits made within the locked area do
- not unexpectedly shift other parts 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 features 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 2.5
+
+ Linked viewing of nucleic acid sequences and structures
+ Automatic Scrolling option in View menu to display the
+ currently highlighted region of an alignment.
+ Order an alignment by sequence length, or using the average score or total feature count for each sequence.
+ Shading features by score or associated description
+ Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).
+ New hide/show options including Shift+Control+H to hide everything but the currently selected region.
+
+Jalview Desktop:
+
+ Fetch DB References capabilities and UI expanded to support
+ retrieval from DAS sequence sources
+ Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in application.
+ Group-associated consensus, sequence logos and conservation
+ plots
+ Symbol distributions for each column can be exported and
+ visualized as sequence logos
+ Jalview Java Console
+ New webservice for submitting sequences and IDs to Envision2 Workflows
+ Improved VAMSAS synchronization and sharing of selections.
+
+JalviewLite:
+
+ Middle button resizes annotation row height
+ New Parameters - including default tree display settings.
+ Non-positional features displayed in ID tooltip
+
+Issues Resolved (a select list)
+
+
+ Source field in GFF files parsed as feature source rather
+ than description
+ Non-positional features are now included in sequence feature
+ and gff files (controlled via non-positional feature visibility in
+ tooltip).
+ URL links generated for all feature links (bugfix)
+ Codons containing ambiguous nucleotides translated as 'X' in
+ peptide product
+ Match case switch in find dialog box works for both sequence
+ ID and sequence string and query strings do not have to be in upper
+ case to match case-insensitively.
+ Jalview Annotation File generation/parsing consistent with
+ documentation (e.g. Stockholm annotation can be exported and
+ re-imported)
+ Find incrementally searches ID string matches as well as
+ subsequence matches, and correctly reports total number of both.
+
+ Desktop Issues
+
+ Better handling of exceptions during sequence retrieval
+ PDB files retrieved from URLs are cached properly
+ Sequence description lines properly shared via VAMSAS
+ Sequence fetcher fetches multiple records for all data
+ sources
+ Ensured that command line das feature retrieval completes
+ before alignment figures are generated.
+ Reduced time taken when opening file browser for first time.
+ User defined group colours properly recovered from Jalview projects.
+
+
+
+
+See the Release History page for
+details of all new features and resolved issues.
+
+