X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2FwhatsNew.html;h=a090673ff8c5bdb9bc1464a6713e71432fb83a5f;hb=eea2b610bea04896964d403093df1141a16efd5f;hp=c6389d942242997534d11828f6dc5f9ed436718b;hpb=a05186c1168e5e0a96a8825fe4c53d439079fdb3;p=jalview.git
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-
-
-What's new ?
-
-
-What's new ?
-
-Jalview Version 2.2.1
-Non standard characters can be read and displayed
-Annotations/Features can be imported/exported to the applet via textbox
-Applet allows editing of sequence/annotation/group name & description
-Preference setting to display sequence name in italics
-Annotation file format extended to allow Sequence_groups to be defined
-
-Issues Resolved
-
- Applet crash under certain Linux OS with Java 1.6 installed
-Annotation file export / import bugs fixed
-PNG / EPS image output bugs fixed
-
-
-See the Release History page for
-details of all new features and resolved issues.
-
-
+
+
+What's new ?
+
+
+What's new ?
+Highlights in Jalview Version 2.4
+
+ 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
+
+
+
+See the Release History page for
+details of all new features and resolved issues.
+
+