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+ * 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 2.5
-
- 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.
+
+ What's new in Jalview 2.10.2 ?
+
+
+ Full details about Jalview 2.10.2 are in the Release Notes, but the
+ highlights are below.
+
+
+ - New UI, and faster and more configurable implementation for PCA, Neighbour-Joining and UPGMA Trees
+ Menu entries for calculating PCA and different types of tree have
+ been replaced by a single Calculations dialog box. The
+ underlying implementation for the PCA and tree calculations have been
+ made faster and more memory efficient. A new framework has also been
+ created for the score models used to calculate distances between
+ sequences. This framework allows import of substitution matrices in
+ NCBI and AAIndex format, and custom score models to be created via a
+ groovy script.
+ - Update to JABAWS 2.2
Jalview's
+ alignment, protein conservation analysis, and protein disorder and
+ RNA secondary structure prediction services are now provided by JABAWS 2.2.
+ Several of the programs provided as services have been updated, so
+ their options and parameters have changed.
+ - New preferences for opening
+ web pages for database cross-references via the UK Elixir's
+ EMBL-EBI's MIRIAM database and identifiers.org services.
+
+ - Showing and hiding regions
+
+ - Hide
+ insertions in the PopUp menu has changed its behaviour.
+ Prior to 2.10.2, columns were only shown or hidden according
+ to gaps in the sequence under the popup menu. Now, only
+ columns that are gapped in all selected sequences as well as
+ the sequence under the popup menu are hidden, and column
+ visibility outside the selected region is left as is. This
+ makes it easy to filter insertions from the alignment view
+ (just select the region containing insertions to remove)
+ without affecting the rest of the hidden columns.
+
+
+
+ Experimental Features
+
+
+ This release of Jalview includes a new option in the Jalview Desktop
+ that allows you to try out features that are still in development.
+ To access the features described below, please first enable the Tools→Enable
+ Experimental Features option, and then restart Jalview.
+
+