X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=a090673ff8c5bdb9bc1464a6713e71432fb83a5f;hb=ddb0a809c051b4e2506aafe9efacbd57868742db;hp=b099c3b142e676a55f94a5e7b02980c082d85cd8;hpb=2eeea2f43d7bbaafd79ebd4185b42fc60646d9e3;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 existing 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 ?
+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.
+
+