What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=1e4fbd027c8271596dca041d4cba79eb5b951432;hb=750c116fd45133a73acd57639c8a4bdbce57578d;hp=5d00e193e35918a376d012edd2cd0629fa9d422f;hpb=0bce27989320cd0b44a13151269749614d5cd312;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 5d00e19..1e4fbd0 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,130 +1,69 @@ + * 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 some 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 +
  + 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, and RNA secondary structure + annotation.
  +
  - 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.
  - 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 +
  - 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.
  - Embedded VARNA RNA - secondary structure viewer in the Desktop -
- Parse and display T-COFFEE - alignment quality scores (thanks to Paolo 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
+
Improved support for VIENNA extended dot-bracket notation + for RNA secondary structure
Positional and selected region highlighting in VARNA + 'trimmed sequence' view now more reliable

+ The full list of bugs fixed in this release can be found in the 2.10.5 Release Notes. The + majority of improvement 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 do this ! +

+ 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.

The 'Save As' dialog for Jalview's Groovy Console remains + affected: the workaround is to create a new file outside of Jalview + and then select it when saving your groovy script. We hope to + address this in the next major release.