What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=3538ff4b1738f95e0516332b803c139306ed7206;hb=5115c19374566cc46eaac00f5ea0dbda5ff39b09;hp=d9b63608533b67a993ef7586aa719e8820b03946;hpb=32254db18cc678b675db8d0cd72a525a6034bf01;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index d9b6360..3538ff4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,203 +1,71 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> What's new ? -

- What's new ? -

Jalview 2.8 includes a brand new logo, which you'll see in file - browsers, splash screens, and also on the new look Jalview site.

- In addition to our new look, Jalview 2.8 includes a number of new - features.. some of which have been in development since July 2010. The - highlights are below, and - as usual, for a comprehensive list, take a - look at the Jalview 2.8 Release - Notes. -

- Highlights in Jalview Version 2.8 -

Improved JABA client and new JABAWS 2.0 Services -
- AACon alignment conservation
- Protein disorder - DisEMBL, RONN, GlobPlot and IUPred
- Clustal Omega - huge protein alignments
-
Support for RNA -
- Import sequence and alignment associated WUSS or VIENNA - secondary structure notation from stockholm and clustalW files or - as jalview annotation.
- Interactive editing of RNA secondary structure annotation
- Colour scheme for purine/pyrimidine and to highlight RNA - helices
- RNA canonical base pair consensus score and sequence logo
- Embedded VARNA RNA - secondary structure viewer in the Desktop +
  + Jalview 2.11 - major and minor new features +
  +
  Jalview 2.11 introduces support for loading VCF files, and new + filters and shading models for sequence features. Under the hood, + we've addressed many bugs, and also made some important changes in + the way the Jalview desktop is installed and launched.
  +
  - VCF Support. Proteins and genomic contigs with + chromosomal location annotation (such as protein coding genes + retrieved from Ensembl) can be annotated with variants imported + from a local VCF file.
  - The Jalview Launcher and Update System
    + Jalview's new installation model means you'll only need to + download and install Jalview once. After installation, Jalview + will automatically keep itself up to date. The launcher also sets + Jalview's memory automatically, so you'll never again have to + manually configure Java's memory settings.
    We are grateful to + Install4J who provided us with a free license for their + installation system, and Jalview's over the air update system is + via Getdown.
  +
  + The full list of bugs fixed in this release can be found in the 2.11 Release Notes. +
  +
  + Jalview and Java 11, 13, and onwards +
  +
  Java 11 provides improved performance and better OS + integration, so we now recommend users select our Java 11 Jalview + distribution rather than the legacy Java 8 build.
  + Known Issues - update for 211 +
  - 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.
  See Nucleic Acid Support for full - details.
- Parse and display T-COFFEE alignment quality scores
- Shade individual sequence positions according to alignment - annotation scores
- Enhanced PCA viewer: more export options, and switch between - different PCA modes and residue score models
- New Jalview Desktop database fetcher GUI
- Support for DAS 1.6 and DAS 2.0 sources
- Export sequence database annotation as HTML report
- Normalised Sequence Logo Display
-
- Issues Resolved (a select list - see the release history for full details) - -
-
- Issues in the Jalview Desktop -
- PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch - REST service -
- - - Stop - windows being moved outside desktop on OSX -
- - Filetype - associations not installed for webstart launch -
- - Jalview - does not always retrieve progress of a JABAWS job execution in full - once it is complete -
- - View - all structures superposed fails with exception -
- - Jnet - job queues forever if a very short sequence is submitted for - prediction -
- - Structure - view highlighting doesn't work on windows 7 -
- - Jalview - desktop fails to launch with exception when using proxy -
- - Tree - calculation reports 'you must have 2 or more sequences - selected' when selection is empty -
- - DAS - Sequence retrieval with range qualification results in sequence xref - which includes range qualification -
- - Cannot - close news reader when JABAWS server warning dialog is shown -
- - Edited - sequence not submitted to web service -
- - Jalview - 2.7 Webstart and InstallAnywhere installer doesn't unpack and run - on OSX Mountain Lion -
  - The workaround for webstart is to go into the Security - panel (gatekeeper symbol) under System settings, and select the - 'allow any code to run' setting.
  -
- - Annotation - panel not given a scroll bar when sequences with alignment annotation - are pasted into the alignment -
- - Sequence - associated annotation rows not associated when loaded from jalview - project -
- - Exceptions - when copy/paste sequences with grouped annotation rows to new window -
- - Browser - launch fails with NPE on java 1.7 -
- - Issues specific to the JalviewLite Applet -
- - Sequence - features are momentarily displayed before they are hidden using - hidefeaturegroups applet parameter -
- - loading - features via javascript API automatically enables feature display -
- - scrollToColumnIn - javascript API method doesn't work -
- Issues affecting both applet and application - General -
- - Redundancy - removal fails for rna alignment -
- - PCA - window shows grey box when first opened on OSX -
- - Letters - coloured pink in sequence logo when alignment coloured with clustalx -
- - Choosing - fonts without letter symbols defined causes exceptions and redraw - errors -
- - Initial - PCA plot view is not same as manually reconfigured view -
+
OSX: Links don't open when clicked on or via the Sequence + or Alignment window popup menu.
OSX (Webstart): JalviewÂ only displays old news feed items