X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=556b49e391e7c72efb4bb9ca167dea6c55f70e71;hb=c42bc457ef9b3a5606f309268d4a644ef113c390;hp=5bb50f9eb0e177707442c3bc1fd76fad58414dc2;hpb=20bddfcf8ef1a53bce455b7599f8066b8ccba0d4;p=jalview.git
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-
-
What's new ?
-
-What's new ?
-Jalview Version 2.1
-The multiple sequence alignment program MAFFT
- is available from the default Web Service list.
-The sequence feature retrieval system using DBFetch from EBI has been replaced
- with DAS Feature fetching capabilities.
-Hide sequences and columns
-Export Annotations and Features
-GFF file reading / writing
-Associate structures with sequences from local PDB files
-Add sequences to exisiting alignment
-Recently opened files / URL lists
-Applet can launch the full application
-Applet has transparency for features (Java 1.2 required)
-Applet has user defined colours parameter
-
-Issues Resolved
-Redundancy Panel reinstalled in the Applet
-Monospaced font - EPS / rescaling bug fixed
-Annotation files with sequence references bug fixed
-
-See the Release History page for details of all
- new features and resolved issues.
-
-
+
+
+
+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.
+
+