X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2FwhatsNew.html;h=a090673ff8c5bdb9bc1464a6713e71432fb83a5f;hb=eea2b610bea04896964d403093df1141a16efd5f;hp=7fa98068aeb4b86d2713b5985d58fa64e8061ba5;hpb=4e377b5c02352a12537100dddd2f8a2b84536205;p=jalview.git
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-
-
What's new ?
-
-What's new ?
-Jalview Version 2.08
- Editing can be locked to the selection area.
- Any edits made within the locked area do not affect the rest of the alignment.
- Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list
- of keyboard controls, look here.
- Create sequence features from searches.
- Previously results from searches were added as alignment positions, which was
- wrong. Now the search results are saved as sequence features and their visibility
- and colour can be modified using the Sequence
- Feature Settings window.
- Precalculated annotations can be loaded onto alignments. The Annotation
- File format is a tab delimited set of values.
- Features file allows grouping of
- features. The Sequence Feature Settings
- window then makes it very easy to set the visibility of groups of features.
-
- Annotation Colouring
- scheme added. A new colour scheme which colours columns on a per-column value.
- Smooth fonts off by default - faster rendering. Toggle on / off from the View
- menu, or can be set in Preferences.
- Choose to toggle Autocalculate Consensus On/Off from the Calculate menu.
-
-Issues Resolved
- Drag & Drop fixed on Linux
- Jalview Archive file faster to load/save, sequence descriptions saved.
-
-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.
+
+