What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=cf96d474e209855f2d8c501f9bb9c81286f6b97b;hb=7a9adf94a201d360b215b0bab0178a656e52148e;hp=b099c3b142e676a55f94a5e7b02980c082d85cd8;hpb=2eeea2f43d7bbaafd79ebd4185b42fc60646d9e3;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index b099c3b..cf96d47 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,28 +1,103 @@ - -What's new ? - -

What's new ?

Jalview Version 2.1

The multiple sequence alignment program MAFFT - is available from the default Web Service list.

The sequence feature retrieval system using DBFetch from EBI has been replaced - with DAS Feature fetching capabilities.

Hide sequences and columns

Export Annotations and Features

GFF file reading / writing

Associate structures with sequences from local PDB files

Add sequences to existing alignment

Recently opened files / URL lists

Applet can launch the full application

Applet has transparency for features (Java 1.2 required)

Applet has user defined colours parameter

Issues Resolved

Redundancy Panel reinstalled in the Applet

Monospaced font - EPS / rescaling bug fixed

Annotation files with sequence references bug fixed

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

- - + + + +What's new ? + + +

+ What's new ? +

+ The Jalview 2.7 release features new web services, and important + improvements to the way in which Jalview handles alignments and + associated PDB structures, as well as numerous minor improvements and + bug fixes. Version 2.7 of the JalviewLite applet also features a + significantly enhanced Javascript API enabling it to be more easily + integrated with javascript based web applications.
For full + details see the Jalview 2.7 + release history. +

+ Highlights in Jalview Desktop Version 2.7 +

New structure viewer + options: +
- Colour and superimpose 3D structures of complexes and + multi-domain chains using several different alignments
- Drag and drop to associate PDB files with sequences that + have the same name
- Open and superimpose all associated structures for the + current selection
+
New web services for alignment + analysis
Improved graphical user interface for JABAWSservices. +
Sort associated alignment views option in tree viewer
Default colours for shading alignment + by quantitative annotation. +
Jalview Desktop RSS + reader - following important updates at http://www.jalview.org/feeds/desktop/rss +

+ +

+ Issues Resolved (a select list - see the release history for full details) + +

+ Issues in the Jalview Desktop +

Problems viewing associated structures for sequences + retrieved from UNIPROT
Problems viewing Jalview projects from older versions in + version 2.6
Preservation of hidden annotation rows and tree bootstrap + values in projects
Newly added JABAWS servers not always visible in web services + menu

+ Issues specific to the JalviewLite Applet +

Layout problems when lots of annotation rows are displayed
<= shown as = in annotation row tooltip
export features raises exception when no features exist
relative URLs not handled properly when used in parameters + and annotation files

+ Issues affecting both applet and application +

sequence numbering not preserved in MSF alignment output
sequence associated secondary structure not correctly parsed + in interleaved stockholm
sequences containing lowercase letters are not properly + associated with their pdb files
Jalview PDB file reader does not extract sequence from deoxy + nucleotide chains correctly
Sequence length given in alignment properties window is off + by 1

+ +