X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=e16949e9709ef0a36e22945c21cb632fbfd748da;hb=3d5d8043f5eaa6e5ca903289a7d136125d3ed1c1;hp=4723a9a622053fee395cd4f6b69a554a815f4a0a;hpb=d8e0a824988ef34a5ffdf0bd7347f27f0ec16d46;p=jalview.git
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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)
-
+
+ What's new ?
Jalview 2.8.1 includes a range of new features developed in the last 12 months.
As usual you can find the
+ highlights below, and the comprehensive list is given in the Jalview 2.8.1 Release Notes.
+
+ Internationalisation
+
+ In August 2013, David Róldan-Martinez took on the task of
+ internationalising Jalview's user interface. He also recruited Sara
+ Hernández DÃaz and Laura Ferrandis Martinez who created Jalview's
+ first spanish user interface translation.
If you notice any
+ problems, or would like to help translate Jalview's user interface
+ into other languages, please sign up at issues.jalview.org and put in
+ a feature request for your translation to the i18n component, and
+ David or Jim will get in contact with you.
+
+ Enhancements and new features
- 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.
+ -
+
- Extended the feature settings dialog to allow columns to be selected containing particular sequence features.
- Desktop Issues
+ Bug fixes
- 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.
+