What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=8a0436dd0e6c35df296aefaed837cf04b8ff0f65;hb=ce6edf5c9421ce38f625886885ed2cd8f506f08d;hp=d9b63608533b67a993ef7586aa719e8820b03946;hpb=32254db18cc678b675db8d0cd72a525a6034bf01;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index d9b6360..8a0436d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,203 +1,84 @@ + * 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 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 +
  + What's new in Jalview 2.10.2 ? +
  +
  + Full details about Jalview 2.10.2 are in the Release Notes, but the + highlights are below. +
  +
  - New UI, and faster and more configurable implementation for PCA, Neighbour-Joining and UPGMA Trees
    + Menu entries for calculating PCA and different types of tree have + been replaced by a single Calculations dialog box. The + underlying implementation for the PCA and tree calculations have been + made faster and more memory efficient. A new framework has also been + created for the score models used to calculate distances between + sequences. This framework allows import of substitution matrices in + NCBI and AAIndex format, and custom score models to be created via a + groovy script.
  - Update to JABAWS 2.2
    Jalview's + alignment, protein conservation analysis, and protein disorder and + RNA secondary structure prediction services are now provided by JABAWS 2.2. + Several of the programs provided as services have been updated, so + their options and parameters have changed.
  - New preferences for opening + web pages for database cross-references via the UK Elixir's + EMBL-EBI's MIRIAM database and identifiers.org services.
  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 -
- - 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 -
+
Showing and hiding regions +
- Hide + insertions in the PopUp menu has changed its behaviour. + Prior to 2.10.2, columns were only shown or hidden according + to gaps in the sequence under the popup menu. Now, only + columns that are gapped in all selected sequences as well as + the sequence under the popup menu are hidden, and column + visibility outside the selected region is left as is. This + makes it easy to filter insertions from the alignment view + (just select the region containing insertions to remove) + without affecting the rest of the hidden columns.

+ Experimental Features +

+ This release of Jalview includes a new option in the Jalview Desktop + that allows you to try out features that are still in development. + To access the features described below, please first enable the Tools→Enable + Experimental Features option, and then restart Jalview. +

Annotation transfer between Chimera and Jalview
Two + new entries in + the Chimera viewer's Chimera menu allow positional annotation to + be exchanged between Chimera and Jalview.