X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=4723a9a622053fee395cd4f6b69a554a815f4a0a;hb=b482f8156c38c7b5ea498eec33f312375441c352;hp=6b7a758b35f3c05ad26b69e60c89f0539da93153;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
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What's new ?
-Highlights in Jalview Version 2.4
+Highlights in Jalview Version 2.5
- DNA and protein product highlighting
- URL links generated with regular expressions
- URL links for sequence database cross references
- New sequence fetcher dialog and DAS Sequence Fetching
- JPred Service upgraded to Jpred3
- Memory monitor
- PFAM full alignment retrieval
- Generalised sequence database reference validation
- DNA Protein Product sequence db traversal (Experimental)
- VAMSAS Interoperation Client (Experimental)
- export annotation rows as CSV for spreadsheet import
- New application command line args and optional Groovy suport
- New Applet API methods and parameters
+ 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)
- Aligned cDNA translation to aligned peptide works correctly
- selected region output includes visible annotations (for
- certain formats)
- edit label/displaychar contains existing label/char for
- editing
- Newick tree support improved for clustalW trees and preserving NHX style comments
- Pathological filechooser bug avoided by not allowing
- filenames containing a ':'
- Fixed exception when parsing GFF files containing global
- sequence features
- Reference counting for alignment datasets
- better reporting of non-fatal warnings and error messages to user when file
- parsing fails.
- Save works when Jalview project is default format
- Histidine should be midblue (not pink!) in Zappo
- Undo recovers dataset sequence metadata when sequence
- regions are cut
- PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) are read in properly
- Stockholm annotation parsing fixed and improved (PFAM records)
- Re-instated Full AMSA support and .amsa file association (MyHits)
- annotation consisting of sequence associated scores can be
- read and written correctly to annotation file
- Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet
- Applet Menus are always embedded in applet window on Macs.
- Newly shown features appear at top of stack (in Applet)
- Secondary structure lines are drawn starting from first
- column of alignment
- Uniprot XML import updated for new schema release in July 2008
- Sequence feature to sequence ID match for Features file is case-insensitive
- Sequence features read from Features file appended to all sequences with matching IDs
- PDB structure coloured correctly for associated views containing a sub-sequence
- Display name and local features preserved in results retrieved from web service
- Visual delay indication for sequence retrieval and sequence fetcher initialisation
- Updated Application to use DAS 1.53e version of dasobert DAS client
+
+ 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.
+