X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=13fe656793c44b226851761ef5bed6d16a8ca710;hb=3f62f10ab0f8985945e460c70c89b530446d6afa;hp=a090673ff8c5bdb9bc1464a6713e71432fb83a5f;hpb=c554d41a4effc6719895bda6b3abc04c032715a8;p=jalview.git
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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.
+
+ What's new in Jalview 2.10.5 ?
+
+ Jalview 2.10.5 is a minor release that includes critical
+ patches for users working with Ensembl, RNA secondary structure
+ annotation, and those running Jalview on OSX with Java 10.
+
+ - Jalview's default memory limit increased to 1G.
If you have
+ problems starting Jalview 2.10.5 and you have 1G or less
+ physical memory on your machine, you will need to reduce the memory allocated to
+ Jalview.
+
+ - EPS, PNG and SVG export now includes hidden sequence
+ markers, and representative sequences are marked in bold.
+ - Ensembl Client updated for Ensembl Rest API v7.
The
+ latest Ensembl API is not backwards compatible with earlier
+ versions of Jalview, so if you require Ensembl functionality you
+ will need to install this release.
+
+ - Improved support for VIENNA extended dot-bracket notation
+ for RNA secondary structure.
+ - Positional and selected region highlighting in VARNA
+ 'trimmed sequence' view made more reliable.
+
+
+ The full list of bugs fixed in this release can be found in the 2.10.5 Release Notes. The
+ majority of bug fixes and improvements in 2.10.5 are due to Jalview users
+ contacting us via the jalview-discuss email list. Thanks to everyone
+ who took the time to help make Jalview better !
+
+
+ Jalview and Java 10
+
+ This release addresses a critical bug for OSX users who are
+ running Jalview with Java 10 which can prevent files being saved
+ correctly through the 'Save As' dialog box.
+ Known Issues
+
+ - OSX: The 'Open File' dialog for Jalview's Groovy Console
+ appears with the title 'Save As', and attempting to select a file to load yields a FileNotFound exception.The workaround is to first clear the 'Untitled' filename before selecting the file you wish to load.
+
+ - OSX: Links don't open when clicked on or via the Sequence or Alignment window popup menu.
+ - OSX (Webstart): Jalview only displays old news feed items
+