X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=cf96d474e209855f2d8c501f9bb9c81286f6b97b;hb=2d6be9a94eb65474a7272d3766881521ed35a760;hp=98f01dcb37f40bf99cffaaa3dcc1c60df63647fa;hpb=244a1460b0d7ae9a7a8c57d3a767b327788e8bd3;p=jalview.git
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+
What's new ?
-What's new ?
-Jalview Version 2.4
-
- VAMSAS Interoperation Client
- DAS Sequence Fetching
- PFAM full alignment retrieval
- DNA/Protein Product traversal (Experimental)
- .. (more to come)
- URL links can be generated using regular
- expressions and created for sequence database cross references
-
-Issues Resolved
-
+
+ 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
+
+
-<--Jalview Version 2.3
-
- Jmol 11.0.2 integration
- PDB views stored in Jalview XML files
- Slide sequences
- Edit sequence in place
- EMBL CDS features
- DAS Feature mapping
- Feature ordering
- Alignment Properties
- Annotation Scores
- Sort by scores
- Feature/annotation editing in applet
-
-Issues Resolved
-
- 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
-
-->
-
-See the Release History page for
-details of all new features and resolved issues.
+
+ 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
+