X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=0382f2225f7b83d424b1b6b660b6eef0c7673e3f;hb=33342a9ee15da4873f9fd94bc2330bc73e7bc51f;hp=e6ab69520eb599fea0ced93a73e300673f272971;hpb=c43a1ee36b2679fd972599186e4d6e45fda87623;p=jalview.git
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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 ?
-Jalview 2.5.1 is a bug fix release for the 2.5 version of
-Jalview. See the release
-history for the bugs that this release resolves.
-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 2.10.3b1 ?
+
+
+ This release - Jalview 2.10.3b1 is the January 2018 patch release for Version 2.10.3 was released in November 2017. The major focus was to
+ improve Jalview's sequence features datamodel and the scalability of
+ the alignment rendering system. The bugs fixed in this release can be found in the 2.10.3b1
+ Release Notes.
+
+ The highlights for Jalview 2.10.3 include:
+
+
+ - Faster and more responsive UI when importing and working
+ with wide alignments and handling hundreds and thousands of
+ sequence features
+ - Improved usability with PDB and UniProt Free Text
+ Search dialog, and new tab for retrieval of sequences for lists of
+ IDs.
+
+ - Short names assigned to sequences retrieved from UniProt
+ - Groovy console upgraded to 2.4.12 (improved support for Java 9)
+
+
+ Experimental Features
+
+
+ Remember, please enable the Experimental Features option in
+ the Jalview Desktop's Tools menu, and then restart Jalview
+ if you want to try out features below:
+
+
+