X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=9eaf83e4352208e8889381ece559ac222f88481d;hb=80c223c45fde0899c9794e887801dd82fffd3452;hp=d9b63608533b67a993ef7586aa719e8820b03946;hpb=32254db18cc678b675db8d0cd72a525a6034bf01;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index d9b6360..9eaf83e 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -21,183 +21,110 @@

- 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 + 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 JABA client and new JABAWS 2.0 Services +
Improved JABAWS + 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 +
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 - secondary structure notation from stockholm and clustalW files or - as jalview annotation.

RFAM

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 +
RNA canonical base pair consensus + score and sequence logo +
Embedded VARNA RNA secondary structure viewer in the Desktop

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

+ +

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 (a select list - see the release history for full details) - + Issues resolved in the Jalview Desktop

- 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 + 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
- 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.
- 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. +
- 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 +

+ 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 -
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 +

+ 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 -
- Choosing - fonts without letter symbols defined causes exceptions and redraw - errors -
- Initial - PCA plot view is not same as manually reconfigured view -
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