What's new ?

2.6.1 diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index c260b5a..d9b6360 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -20,43 +20,184 @@ 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 Desktop Version 2.8 -
-
+
+ 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 +
+
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 +
-
New Purine/Pyrimidine colour scheme
-
Colouring of RNA secondary structure by helices. See Nucleic Acid Support
-
Embedded VARNA RNA secondary structure viewer. -
+
-
- Issues Resolved (a select list - see the release history for full details) - -
-
- Issues in the Jalview Desktop -
-
- Issues specific to the JalviewLite Applet -
-
- Issues affecting both applet and application -
-
+ 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 +
+