X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=4723a9a622053fee395cd4f6b69a554a815f4a0a;hb=b482f8156c38c7b5ea498eec33f312375441c352;hp=0f9f7d27a3b3d156c8527ed5851ed193ddae6826;hpb=2e5b635fb5180b2da27a89f2a17a1a09f82ce055;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 0f9f7d2..4723a9a 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -1,36 +1,93 @@
-
-
-What's new ?
-
-
-What's new ?
-
-Jalview Version 2.3
-Jmol 11 integration
- PDB views stored in Jalview XML files
-Slide sequences
-Edit sequence in place
-EMBL CDS features
-DAS Feature mapping
-Feature ordering
-Alignment Properties
-Annotation Scores
-Sort by scores
-Feature/annotation editing in applet
-
-
-Issues Resolved
-
- Headless state operation in 2.2.1
- Incorrect and unstable DNA pairwise alignment
- Cut and paste of sequences with annotation
- Feature group display state in XML
- Feature ordering in XML
- 2.2.1 applet had no feature transparency
- Number pad keys can be used in cursor mode
- Structure Viewer mirror image resolved
-
-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.
+
+