X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=448430d6afa3682fefa553af124b0750b0df2a49;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=b40113183b4676c1809f6f1a011ca285c7fbba94;hpb=b25e74cbff1b97e12c1f3b4ea0b1914a13a5c474;p=jalview.git
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-
-
What's new ?
-
-What's new ?
-If you are reading this then you will already have seen some of the recent changes
- made to Jalview.
- Jalview takes advantage of some of the more recent user interface developments
- in the Java programming language. For instance Jalview is now a multi windowed
- application, this keeps all your Jalview windows neatly together in one main
- application window.
-If you were familiar with the original Jalview, here is a list of important
- features you should know about the current development:
-
- - Editing sequences is no longer the default when mouse clicking the alignment.
- Instead, mouse clicking on the alignment creates a "selection region"
- which may be full sequences or groups of residues.
- - To insert or edit the gaps in one sequence in alignment, the "Shift"
- key must be held down when dragging the mouse.
- - To insert or edit gaps for a group of sequences, the "Alt" key
- (or in X windows the "Control" key) must be held down.
- - Selecting colour schemes in the colour menu either sets just the "background"
- colourscheme for the alignment, or - when the tickbox "Apply colour to
- all groups" is ticked, applies the scheme to the background and all groups
- defined on the alignment.
- - Use the right mouse button (apple and click on the Mac) whilst the pointer
- is within the selection area to access the "define" region menu
- to define a new region, give it a name, and change its colourscheme and display
- properties.
- - Conservation is automatically updated whenever the alignment is edited
- - There is no "quick draw" option
- - Edits can be undone, and redone!
-
-
-
- Release |
- New Features |
- Issues Resolved |
-
-
- 2.05b
- 30/8/05 |
-
- - Choose EPS export as lineart or text
- - Jar files are executable
- - Can read in Uracil - maps to unknown residue
- |
-
- - Known OutOfMemory errors give warning message
- - Overview window calculated more efficiently
- - Several GUI bugs resolved
- |
-
-
- 2.05
- 30/8/05 |
-
- - Edit and annotate in "Wrapped" view
- |
-
- - Several GUI bugs resolved
- |
-
-
- 2.04
- 24/8/05 |
-
- - Hold down mouse wheel & scroll to change font size
- |
-
- - Improved JPred client reliability
- - Improved loading of Jalview files
- |
-
-
- 2.03
- 18/8/05 |
-
- - Set Proxy server name and port in preferences
- - Multiple URL links from sequence ids
- - User Defined Colours can have a scheme name and added to Colour Menu
- - Choose to ignore gaps in consensus calculation
- - Unix users can set default web browser
- - Runs without GUI for batch processing
- - Dynamically generated Web Service Menus
- |
-
- - InstallAnywhere download for Sparc Solaris
- |
-
-
- 2.02
- 18/7/05 |
- |
-
- - Copy & Paste order of sequences maintains alignment order.
- |
-
-
- 2.01
- 12/7/05 |
-
- - Use delete key for deleting selection.
- - Use Mouse wheel to scroll sequences.
- - Help file updated to describe how to add alignment annotations.
- - Version and build date written to build properties file.
- - InstallAnywhere installation will check for updates at launch of Jalview.
- |
-
- - Delete gaps bug fixed.
- - FileChooser sorts columns.
- - Can remove groups one by one.
- - Filechooser icons installed.
- - Finder ignores return character when searching. Return key will initiate
- a search.
-
- |
-
-
- 2.0
- 20/6/05 |
- |
- |
-
-
-
-
-
+
+
+
+What's new ?
+
+
+
+ What's new in Jalview 2.10.0b1 ?
+
+
+ Jalview 2.10.0b1 is a patch release for 2.10, the next major release
+ in the Jalview 2 series. Full details are in the Jalview 2.10b1 Release
+ Notes, but the highlights are below.
+
+
+ - Drag and drop reinstated for the Jalview desktop on
+ Windows, Linux and older OSX systems.
+ - Problems loading local PDB files have been fixed
+ - Conservation shading can be disabled for PID and consensus
+ based colour scheme
+
+ Major highlights of the 2.10.0 Release
+
+ - Ensembl sequence fetcher
Annotated
+ Genes, transcripts and proteins can be retrieved via Jalview's new
+ Ensembl REST
+ client. Support for import of Ensembl data allows:
+
+ - Aligned locus view
Transcripts
+ retrieved for a gene identifier via the Ensembl or
+ EnsemblGenomes sequence databases are automatically aligned to
+ their reference genome, and introns hidden from the view.
+ - Sequence variant data
Jalview
+ propagates variant annotation on genomic regions onto
+ transcripts and protein products, complete with associated
+ metadata such as clinical significance.
+
+ - Ensembl and ENA 'show cross-references'
+ support
The Calculations menu's 'Show
+ cross-references' now offers Ensembl as well as EMBLCDS and
+ Uniprot when CDS/Protein mapping data is available for download or
+ display. This allows variant annotation to be added directly to an
+ alignment of UniProt sequences.
+ - Working with structures
+
+ - More accurate structure mappings
+ Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
+ to match structures
+ to UniProt sequences, even for structures containing
+ multiple copies of a sequence.
+ - Import structures as mmCIF
Jalview
+ now downloads data from the EMBL-EBI's PDBe site as mmCIF. This allows very large
+ structures to be imported, such as the HIV virus capsid
+ assembly.
+ - Chimera users will need to upgrade to
+ 1.11.1
If you use Chimera to view structures
+ downloaded by Jalview 2.10, you will need to make sure you are
+ running the latest version of Chimera.
+
+ - UniProt Free Text Search
The new
+ search dialog for UniProt allows you to browse and retrieve
+ sequences with free-text search, or structured queries.
+ - Reference sequence alignment view
+ Jalview 2.9 introduced support for reference sequences. In 2.10,
+ when a reference sequence is defined for the alignment, the
+ alignment column ruler is now numbered according to the reference
+ sequence. The reference sequence for alignment views can also be
+ saved and restored from Jalview projects.
+
+
+
+