What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=cf96d474e209855f2d8c501f9bb9c81286f6b97b;hb=2d6be9a94eb65474a7272d3766881521ed35a760;hp=75afae872444fa133618b222e0fdd898faa8f6ab;hpb=dc6f1dbbd2c3e951c94f969703d595ea22e33f73;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 75afae8..cf96d47 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,36 +1,103 @@ - - -What's new ? - - -

What's new ?

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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

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-

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

+ +