What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=9eaf83e4352208e8889381ece559ac222f88481d;hb=80c223c45fde0899c9794e887801dd82fffd3452;hp=75afae872444fa133618b222e0fdd898faa8f6ab;hpb=dc6f1dbbd2c3e951c94f969703d595ea22e33f73;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 75afae8..9eaf83e 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,36 +1,130 @@ - - -What's new ? - - -

What's new ?

- -

Jalview Version 2.3

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-

-

Issues Resolved

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- Headless state operation in 2.2.1
- Incorrect and unstable DNA pairwise alignment
- Cut and paste of sequences with annotation
- Feature group display state in XML
- Feature ordering in XML
- 2.2.1 applet had no feature transparency
- Number pad keys can be used in cursor mode
- Structure Viewer mirror image resolved

-

-

See the Release History page for -details of all new features and resolved issues.

- - + + + +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 +
- 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

+ +