X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=a090673ff8c5bdb9bc1464a6713e71432fb83a5f;hb=eea2b610bea04896964d403093df1141a16efd5f;hp=344c322233d893da5d0fd96edbcb175d510b5380;hpb=85fb1c79fd82d7eada801624f745635632be8362;p=jalview.git
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-What's new ?
+
+What's new ?
+
-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
+
-Jalview Version 2.2
-Multiple views with different styles, colours, hidden regions for one alignment
-
-Easily add, amend and delete sequence features
-
-"Reload" alignment from File or URL to revert to original
-
-"Save" to current filename or "Save As" to new filename
-
-Set different text colour for dark or light background
-
-Right align sequence ids
-
-Set colour of lower case residues in a user defined colour scheme
-
-Menu Rearrangements: New Format for alignment layout and Select for region selection.
-
-Menu item accelerator keys added
-
-Control-V pastes sequences to active window, Control-Shift-V pastes to a new window.
-
-Raise/Minimise alignment and all associated windows from desktop window's window menu
-
-Select and colour whole branches of a tree
-'New Window' button on the 'Output to Text box' alignment output
-option to open a new alignment window after editing.
-Issues Resolved
-
-
-Optimisations for large alignments: faster multithreaded calculations and Undo/Redo system.
-
-Remove empty columns - if empty columns exist at the end of the
-alignment bug fixed.
-
-DAS feature fetching slowed down, doesn't overload DAS servers
-
-DAS feature fetching can be cancelled
-
-Correct display of > and < symbols for feature descriptions without explicit <html> tags.
-
-Zoom working in PCA viewer
-
-Sequence Descriptions retained after running a web service
-
-See the Release History page for details of all
- new features and resolved issues.
+See the Release History page for
+details of all new features and resolved issues.