X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=d9b63608533b67a993ef7586aa719e8820b03946;hb=32254db18cc678b675db8d0cd72a525a6034bf01;hp=e2c6cdbdc2b01825fda2ce80f85e9a0105f044d9;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index e2c6cdb..d9b6360 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -1,84 +1,203 @@
+-->
What's new ?
-What's new ?
-Highlights in Jalview Version 2.4
-
- 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
-
-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
-
+
+ What's new ?
+
+ Jalview 2.8 includes a brand new logo, which you'll see in file
+ browsers, splash screens, and also on the new look Jalview site.
+
+ In addition to our new look, Jalview 2.8 includes a number of new
+ features.. some of which have been in development since July 2010. The
+ highlights are below, and - as usual, for a comprehensive list, take a
+ look at the Jalview 2.8 Release
+ Notes.
+
+
+ Highlights in Jalview Version 2.8
+
+
+ - Improved JABA client and new JABAWS 2.0 Services
+
+ - AACon alignment conservation
+ - Protein disorder - DisEMBL, RONN, GlobPlot and IUPred
+ - Clustal Omega - huge protein alignments
+
+
+ - Support for RNA
+
+ - Import sequence and alignment associated WUSS or VIENNA
+ secondary structure notation from stockholm and clustalW files or
+ as jalview annotation.
+ - Interactive editing of RNA secondary structure annotation
+ - Colour scheme for purine/pyrimidine and to highlight RNA
+ helices
+ - RNA canonical base pair consensus score and sequence logo
+ - Embedded VARNA RNA
+ secondary structure viewer in the Desktop
+
+
See Nucleic Acid Support for full
+ details.
+ - Parse and display T-COFFEE alignment quality scores
+ - Shade individual sequence positions according to alignment
+ annotation scores
+ - Enhanced PCA viewer: more export options, and switch between
+ different PCA modes and residue score models
+ - New Jalview Desktop database fetcher GUI
+ - Support for DAS 1.6 and DAS 2.0 sources
+ - Export sequence database annotation as HTML report
+ - Normalised Sequence Logo Display
+
+
+ Issues Resolved (a select list - see the release history for full details)
+
+
+
+ Issues in the Jalview Desktop
+
+ - PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
+ REST service
+
+ -
+
+ Stop
+ windows being moved outside desktop on OSX
+
+ -
+ Filetype
+ associations not installed for webstart launch
+
+ -
+ Jalview
+ does not always retrieve progress of a JABAWS job execution in full
+ once it is complete
+
+ -
+ View
+ all structures superposed fails with exception
+
+ -
+ Jnet
+ job queues forever if a very short sequence is submitted for
+ prediction
+
+ -
+ Structure
+ view highlighting doesn't work on windows 7
+
+ -
+ Jalview
+ desktop fails to launch with exception when using proxy
+
+ -
+ Tree
+ calculation reports 'you must have 2 or more sequences
+ selected' when selection is empty
+
+ -
+ DAS
+ Sequence retrieval with range qualification results in sequence xref
+ which includes range qualification
+
+ -
+ Cannot
+ close news reader when JABAWS server warning dialog is shown
+
+ -
+ Edited
+ sequence not submitted to web service
+
+ -
+ Jalview
+ 2.7 Webstart and InstallAnywhere installer doesn't unpack and run
+ on OSX Mountain Lion
+
+ - The workaround for webstart is to go into the Security
+ panel (gatekeeper symbol) under System settings, and select the
+ 'allow any code to run' setting.
+
+
+ -
+ Annotation
+ panel not given a scroll bar when sequences with alignment annotation
+ are pasted into the alignment
+
+ -
+ Sequence
+ associated annotation rows not associated when loaded from jalview
+ project
+
+ -
+ Exceptions
+ when copy/paste sequences with grouped annotation rows to new window
+
+ -
+ Browser
+ launch fails with NPE on java 1.7
+
+
+
-
-See the Release History page for
-details of all new features and resolved issues.
+ Issues specific to the JalviewLite Applet
+
+ -
+ Sequence
+ features are momentarily displayed before they are hidden using
+ hidefeaturegroups applet parameter
+
+ -
+ loading
+ features via javascript API automatically enables feature display
+
+ -
+ scrollToColumnIn
+ javascript API method doesn't work
+
+
+ Issues affecting both applet and application
+ General
+
+ -
+ Redundancy
+ removal fails for rna alignment
+
+ -
+ PCA
+ window shows grey box when first opened on OSX
+
+ -
+ Letters
+ coloured pink in sequence logo when alignment coloured with clustalx
+
+ -
+ Choosing
+ fonts without letter symbols defined causes exceptions and redraw
+ errors
+
+ -
+ Initial
+ PCA plot view is not same as manually reconfigured view
+
+