What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=3538ff4b1738f95e0516332b803c139306ed7206;hb=5115c19374566cc46eaac00f5ea0dbda5ff39b09;hp=9eaf83e4352208e8889381ece559ac222f88481d;hpb=e2b0b250d21b61c876bdb2303c34d66922336a86;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 9eaf83e..3538ff4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,130 +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 number of enhancements and new features that - have been in development since July 2010. It is also the first Jalview - release to incorporate RNA visualization features developed by Lauren - Lui and Jan Engelhart during their Google Summer of Code projects - (http://code.google.com/soc/). As usual you can find the highlights - below, but to see the comprehensive list take a look at the look at - the Jalview 2.8 Release Notes. -

- Highlights in Jalview Version 2.8 -

Improved JABAWS - client and new JABAWS 2.0 Services - -
- AACon alignment - conservation
- Protein - disorder - DisEMBL, RONN, GlobPlot and IUPred
- Clustal Omega for creating huge protein alignments
RNA -
- Import sequence and alignment associated WUSS or VIENNA - dot-bracket notation from files and the RFAM - database +
  + 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.
  - 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 -
- Parse and display T-COFFEE - alignment quality scores (thanks to Paolo di Tomasso of the Notredame - Group) -
- Per - sequence alignment annotation shading
- 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 (thanks to the new - JDAS Distributed Annotation client library (see - http://code.google.com/p/jdas))
- Export sequence database annotation as an HTML report
- Normalised Sequence - Logo Display
-
- Issues resolved in the Jalview Desktop -
-
- PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch - REST service
- Stop windows being moved outside desktop on OSX
- 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
- 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 InstallAnywhere installer doesn't unpack and run - on OSX Mountain Lion -
  - If you use webstart then you may need to go into the - Security panel (a.k.a the gatekeeper) in your System - Settings, and select the 'allow any code to run' option. -
  -
-
- 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 -
-
- 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
+
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